From d18a199927e5e5639bf23c49893d7b71dbcd9c7f Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Thu, 21 Mar 2013 16:58:09 +0000
Subject: [PATCH] Release 13.04 drop boxes
SVN: 28669
---
.../2/as/initialize-master-data.py | 2919 +++++++++++++++++
.../2/dss/data-sources/.gitignore | 0
.../create-flowcell-hiseq.py | 209 ++
.../create-flowcell-hiseq/plugin.properties | 12 +
.../read-rta-timestamp/plugin.properties | 11 +
.../read-rta-timestamp/read-rta-timestamp.py | 76 +
.../register-basecall-stats/plugin.properties | 11 +
.../register-basecall-stats.py | 62 +
.../register-flowcell/plugin.properties | 11 +
.../register-flowcell-hiseq.py | 138 +
.../register-lane-hiseq/plugin.properties | 12 +
.../register-lane-hiseq.py | 223 ++
.../register-runstatistics/plugin.properties | 11 +
.../register-runstatistics.py | 57 +
.../register-unaligned/plugin.properties | 11 +
.../register-unaligned/register-unaligned.py | 185 ++
.../2/dss/maintenance-tasks/.gitignore | 0
.../2/dss/reporting-plugins/.gitignore | 0
.../illumina-ngs/2/dss/services/.gitignore | 0
19 files changed, 3948 insertions(+)
create mode 100644 deep_sequencing_unit/source/core-plugins/illumina-ngs/2/as/initialize-master-data.py
create mode 100644 deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/data-sources/.gitignore
create mode 100644 deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/create-flowcell-hiseq/create-flowcell-hiseq.py
create mode 100644 deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/create-flowcell-hiseq/plugin.properties
create mode 100644 deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/read-rta-timestamp/plugin.properties
create mode 100644 deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/read-rta-timestamp/read-rta-timestamp.py
create mode 100644 deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-basecall-stats/plugin.properties
create mode 100644 deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-basecall-stats/register-basecall-stats.py
create mode 100644 deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-flowcell/plugin.properties
create mode 100644 deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-flowcell/register-flowcell-hiseq.py
create mode 100644 deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-lane-hiseq/plugin.properties
create mode 100755 deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-lane-hiseq/register-lane-hiseq.py
create mode 100644 deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-runstatistics/plugin.properties
create mode 100644 deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-runstatistics/register-runstatistics.py
create mode 100644 deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-unaligned/plugin.properties
create mode 100755 deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-unaligned/register-unaligned.py
create mode 100644 deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/maintenance-tasks/.gitignore
create mode 100644 deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/reporting-plugins/.gitignore
create mode 100644 deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/services/.gitignore
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/as/initialize-master-data.py b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/as/initialize-master-data.py
new file mode 100644
index 00000000000..1a373785b9f
--- /dev/null
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/as/initialize-master-data.py
@@ -0,0 +1,2919 @@
+# -*- coding: utf-8 -*-
+import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.DataType as DataType
+
+print ("Importing Master Data...")
+
+tr = service.transaction()
+
+
+file_type_FASTQ_PHRED_64 = tr.getOrCreateNewFileFormatType('FASTQ_PHRED_64')
+file_type_FASTQ_PHRED_64.setDescription('FastQ Format with PHRED+64 quality values (as deliverd by Illumina GA Pipeline >= 1.3)')
+
+print "Imported 7 File Formats"
+vocabulary_AGILENT_KIT = tr.getOrCreateNewVocabulary('AGILENT_KIT')
+vocabulary_AGILENT_KIT.setDescription(None)
+vocabulary_AGILENT_KIT.setUrlTemplate(None)
+vocabulary_AGILENT_KIT.setManagedInternally(False)
+vocabulary_AGILENT_KIT.setInternalNamespace(False)
+vocabulary_AGILENT_KIT.setChosenFromList(True)
+
+vocabulary_term_AGILENT_KIT_AGILENT_DNA_KIT_1000 = tr.createNewVocabularyTerm('AGILENT_DNA_KIT_1000')
+vocabulary_term_AGILENT_KIT_AGILENT_DNA_KIT_1000.setDescription(None)
+vocabulary_term_AGILENT_KIT_AGILENT_DNA_KIT_1000.setLabel(None)
+vocabulary_term_AGILENT_KIT_AGILENT_DNA_KIT_1000.setOrdinal(1)
+vocabulary_AGILENT_KIT.addTerm(vocabulary_term_AGILENT_KIT_AGILENT_DNA_KIT_1000)
+
+vocabulary_term_AGILENT_KIT_AGILENT_HIGH_SENSITIVITY_DNA_KIT = tr.createNewVocabularyTerm('AGILENT_HIGH_SENSITIVITY_DNA_KIT')
+vocabulary_term_AGILENT_KIT_AGILENT_HIGH_SENSITIVITY_DNA_KIT.setDescription(None)
+vocabulary_term_AGILENT_KIT_AGILENT_HIGH_SENSITIVITY_DNA_KIT.setLabel(None)
+vocabulary_term_AGILENT_KIT_AGILENT_HIGH_SENSITIVITY_DNA_KIT.setOrdinal(2)
+vocabulary_AGILENT_KIT.addTerm(vocabulary_term_AGILENT_KIT_AGILENT_HIGH_SENSITIVITY_DNA_KIT)
+
+vocabulary_ALIGNMENT_SOFTWARE = tr.getOrCreateNewVocabulary('ALIGNMENT_SOFTWARE')
+vocabulary_ALIGNMENT_SOFTWARE.setDescription('If an alignment is requested, which software package should be use?')
+vocabulary_ALIGNMENT_SOFTWARE.setUrlTemplate(None)
+vocabulary_ALIGNMENT_SOFTWARE.setManagedInternally(False)
+vocabulary_ALIGNMENT_SOFTWARE.setInternalNamespace(False)
+vocabulary_ALIGNMENT_SOFTWARE.setChosenFromList(True)
+
+vocabulary_term_ALIGNMENT_SOFTWARE_NOT_NEEDED = tr.createNewVocabularyTerm('NOT_NEEDED')
+vocabulary_term_ALIGNMENT_SOFTWARE_NOT_NEEDED.setDescription(None)
+vocabulary_term_ALIGNMENT_SOFTWARE_NOT_NEEDED.setLabel(None)
+vocabulary_term_ALIGNMENT_SOFTWARE_NOT_NEEDED.setOrdinal(1)
+vocabulary_ALIGNMENT_SOFTWARE.addTerm(vocabulary_term_ALIGNMENT_SOFTWARE_NOT_NEEDED)
+
+vocabulary_term_ALIGNMENT_SOFTWARE_ELAND = tr.createNewVocabularyTerm('ELAND')
+vocabulary_term_ALIGNMENT_SOFTWARE_ELAND.setDescription(None)
+vocabulary_term_ALIGNMENT_SOFTWARE_ELAND.setLabel(None)
+vocabulary_term_ALIGNMENT_SOFTWARE_ELAND.setOrdinal(2)
+vocabulary_ALIGNMENT_SOFTWARE.addTerm(vocabulary_term_ALIGNMENT_SOFTWARE_ELAND)
+
+vocabulary_term_ALIGNMENT_SOFTWARE_MAQ = tr.createNewVocabularyTerm('MAQ')
+vocabulary_term_ALIGNMENT_SOFTWARE_MAQ.setDescription(None)
+vocabulary_term_ALIGNMENT_SOFTWARE_MAQ.setLabel(None)
+vocabulary_term_ALIGNMENT_SOFTWARE_MAQ.setOrdinal(3)
+vocabulary_ALIGNMENT_SOFTWARE.addTerm(vocabulary_term_ALIGNMENT_SOFTWARE_MAQ)
+
+vocabulary_term_ALIGNMENT_SOFTWARE_BWA = tr.createNewVocabularyTerm('BWA')
+vocabulary_term_ALIGNMENT_SOFTWARE_BWA.setDescription(None)
+vocabulary_term_ALIGNMENT_SOFTWARE_BWA.setLabel(None)
+vocabulary_term_ALIGNMENT_SOFTWARE_BWA.setOrdinal(4)
+vocabulary_ALIGNMENT_SOFTWARE.addTerm(vocabulary_term_ALIGNMENT_SOFTWARE_BWA)
+
+vocabulary_term_ALIGNMENT_SOFTWARE_NOVOALIGN = tr.createNewVocabularyTerm('NOVOALIGN')
+vocabulary_term_ALIGNMENT_SOFTWARE_NOVOALIGN.setDescription(None)
+vocabulary_term_ALIGNMENT_SOFTWARE_NOVOALIGN.setLabel(None)
+vocabulary_term_ALIGNMENT_SOFTWARE_NOVOALIGN.setOrdinal(6)
+vocabulary_ALIGNMENT_SOFTWARE.addTerm(vocabulary_term_ALIGNMENT_SOFTWARE_NOVOALIGN)
+
+vocabulary_term_ALIGNMENT_SOFTWARE_BOWTIE = tr.createNewVocabularyTerm('BOWTIE')
+vocabulary_term_ALIGNMENT_SOFTWARE_BOWTIE.setDescription(None)
+vocabulary_term_ALIGNMENT_SOFTWARE_BOWTIE.setLabel(None)
+vocabulary_term_ALIGNMENT_SOFTWARE_BOWTIE.setOrdinal(7)
+vocabulary_ALIGNMENT_SOFTWARE.addTerm(vocabulary_term_ALIGNMENT_SOFTWARE_BOWTIE)
+
+vocabulary_CASAVA_VERSION = tr.getOrCreateNewVocabulary('CASAVA_VERSION')
+vocabulary_CASAVA_VERSION.setDescription('Post analyzing software')
+vocabulary_CASAVA_VERSION.setUrlTemplate(None)
+vocabulary_CASAVA_VERSION.setManagedInternally(False)
+vocabulary_CASAVA_VERSION.setInternalNamespace(False)
+vocabulary_CASAVA_VERSION.setChosenFromList(True)
+
+vocabulary_term_CASAVA_VERSION_18 = tr.createNewVocabularyTerm('1.8')
+vocabulary_term_CASAVA_VERSION_18.setDescription(None)
+vocabulary_term_CASAVA_VERSION_18.setLabel(None)
+vocabulary_term_CASAVA_VERSION_18.setOrdinal(1)
+vocabulary_CASAVA_VERSION.addTerm(vocabulary_term_CASAVA_VERSION_18)
+
+vocabulary_term_CASAVA_VERSION_17 = tr.createNewVocabularyTerm('1.7')
+vocabulary_term_CASAVA_VERSION_17.setDescription(None)
+vocabulary_term_CASAVA_VERSION_17.setLabel(None)
+vocabulary_term_CASAVA_VERSION_17.setOrdinal(2)
+vocabulary_CASAVA_VERSION.addTerm(vocabulary_term_CASAVA_VERSION_17)
+
+vocabulary_CLUSTER_GENERATION_KIT_VERSION = tr.getOrCreateNewVocabulary('CLUSTER_GENERATION_KIT_VERSION')
+vocabulary_CLUSTER_GENERATION_KIT_VERSION.setDescription('Version of the Cluster Generation Kit')
+vocabulary_CLUSTER_GENERATION_KIT_VERSION.setUrlTemplate(None)
+vocabulary_CLUSTER_GENERATION_KIT_VERSION.setManagedInternally(False)
+vocabulary_CLUSTER_GENERATION_KIT_VERSION.setInternalNamespace(False)
+vocabulary_CLUSTER_GENERATION_KIT_VERSION.setChosenFromList(True)
+
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_TRUSEQ_CBOT_HS_V3 = tr.createNewVocabularyTerm('TRUSEQ_CBOT_HS_V3')
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_TRUSEQ_CBOT_HS_V3.setDescription(None)
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_TRUSEQ_CBOT_HS_V3.setLabel('TruSeq cBot-HS v3')
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_TRUSEQ_CBOT_HS_V3.setOrdinal(1)
+vocabulary_CLUSTER_GENERATION_KIT_VERSION.addTerm(vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_TRUSEQ_CBOT_HS_V3)
+
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_TRUSEQ_CBOT_HS_V25 = tr.createNewVocabularyTerm('TRUSEQ_CBOT_HS_V2.5')
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_TRUSEQ_CBOT_HS_V25.setDescription(None)
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_TRUSEQ_CBOT_HS_V25.setLabel('TruSeq cBot-HS v2.5')
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_TRUSEQ_CBOT_HS_V25.setOrdinal(2)
+vocabulary_CLUSTER_GENERATION_KIT_VERSION.addTerm(vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_TRUSEQ_CBOT_HS_V25)
+
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_TRUSEQ_CBOT_GA_V2 = tr.createNewVocabularyTerm('TRUSEQ_CBOT_GA_V2')
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_TRUSEQ_CBOT_GA_V2.setDescription(None)
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_TRUSEQ_CBOT_GA_V2.setLabel('TrueSeq cBot-GA v2')
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_TRUSEQ_CBOT_GA_V2.setOrdinal(3)
+vocabulary_CLUSTER_GENERATION_KIT_VERSION.addTerm(vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_TRUSEQ_CBOT_GA_V2)
+
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_TRUSEQ_CS_GA_V5 = tr.createNewVocabularyTerm('TRUSEQ_CS_GA_V5')
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_TRUSEQ_CS_GA_V5.setDescription(None)
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_TRUSEQ_CS_GA_V5.setLabel('TrueSeq CS-GA v5')
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_TRUSEQ_CS_GA_V5.setOrdinal(4)
+vocabulary_CLUSTER_GENERATION_KIT_VERSION.addTerm(vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_TRUSEQ_CS_GA_V5)
+
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_V5 = tr.createNewVocabularyTerm('V5')
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_V5.setDescription(None)
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_V5.setLabel(None)
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_V5.setOrdinal(5)
+vocabulary_CLUSTER_GENERATION_KIT_VERSION.addTerm(vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_V5)
+
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_V4 = tr.createNewVocabularyTerm('V4')
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_V4.setDescription(None)
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_V4.setLabel(None)
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_V4.setOrdinal(6)
+vocabulary_CLUSTER_GENERATION_KIT_VERSION.addTerm(vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_V4)
+
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_V2 = tr.createNewVocabularyTerm('V2')
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_V2.setDescription(None)
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_V2.setLabel(None)
+vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_V2.setOrdinal(7)
+vocabulary_CLUSTER_GENERATION_KIT_VERSION.addTerm(vocabulary_term_CLUSTER_GENERATION_KIT_VERSION_V2)
+
+vocabulary_CLUSTER_STATION = tr.getOrCreateNewVocabulary('CLUSTER_STATION')
+vocabulary_CLUSTER_STATION.setDescription('Cluster Station')
+vocabulary_CLUSTER_STATION.setUrlTemplate(None)
+vocabulary_CLUSTER_STATION.setManagedInternally(False)
+vocabulary_CLUSTER_STATION.setInternalNamespace(False)
+vocabulary_CLUSTER_STATION.setChosenFromList(True)
+
+vocabulary_term_CLUSTER_STATION_CBOT = tr.createNewVocabularyTerm('CBOT')
+vocabulary_term_CLUSTER_STATION_CBOT.setDescription(None)
+vocabulary_term_CLUSTER_STATION_CBOT.setLabel('cBot')
+vocabulary_term_CLUSTER_STATION_CBOT.setOrdinal(1)
+vocabulary_CLUSTER_STATION.addTerm(vocabulary_term_CLUSTER_STATION_CBOT)
+
+vocabulary_term_CLUSTER_STATION_CBOT2 = tr.createNewVocabularyTerm('CBOT2')
+vocabulary_term_CLUSTER_STATION_CBOT2.setDescription('Second cBot')
+vocabulary_term_CLUSTER_STATION_CBOT2.setLabel('cBot2')
+vocabulary_term_CLUSTER_STATION_CBOT2.setOrdinal(2)
+vocabulary_CLUSTER_STATION.addTerm(vocabulary_term_CLUSTER_STATION_CBOT2)
+
+vocabulary_CONTROL_LANE = tr.getOrCreateNewVocabulary('CONTROL_LANE')
+vocabulary_CONTROL_LANE.setDescription(None)
+vocabulary_CONTROL_LANE.setUrlTemplate(None)
+vocabulary_CONTROL_LANE.setManagedInternally(False)
+vocabulary_CONTROL_LANE.setInternalNamespace(False)
+vocabulary_CONTROL_LANE.setChosenFromList(True)
+
+vocabulary_term_CONTROL_LANE_1 = tr.createNewVocabularyTerm('1')
+vocabulary_term_CONTROL_LANE_1.setDescription(None)
+vocabulary_term_CONTROL_LANE_1.setLabel(None)
+vocabulary_term_CONTROL_LANE_1.setOrdinal(1)
+vocabulary_CONTROL_LANE.addTerm(vocabulary_term_CONTROL_LANE_1)
+
+vocabulary_term_CONTROL_LANE_2 = tr.createNewVocabularyTerm('2')
+vocabulary_term_CONTROL_LANE_2.setDescription(None)
+vocabulary_term_CONTROL_LANE_2.setLabel(None)
+vocabulary_term_CONTROL_LANE_2.setOrdinal(2)
+vocabulary_CONTROL_LANE.addTerm(vocabulary_term_CONTROL_LANE_2)
+
+vocabulary_term_CONTROL_LANE_3 = tr.createNewVocabularyTerm('3')
+vocabulary_term_CONTROL_LANE_3.setDescription(None)
+vocabulary_term_CONTROL_LANE_3.setLabel(None)
+vocabulary_term_CONTROL_LANE_3.setOrdinal(3)
+vocabulary_CONTROL_LANE.addTerm(vocabulary_term_CONTROL_LANE_3)
+
+vocabulary_term_CONTROL_LANE_4 = tr.createNewVocabularyTerm('4')
+vocabulary_term_CONTROL_LANE_4.setDescription(None)
+vocabulary_term_CONTROL_LANE_4.setLabel(None)
+vocabulary_term_CONTROL_LANE_4.setOrdinal(4)
+vocabulary_CONTROL_LANE.addTerm(vocabulary_term_CONTROL_LANE_4)
+
+vocabulary_term_CONTROL_LANE_5 = tr.createNewVocabularyTerm('5')
+vocabulary_term_CONTROL_LANE_5.setDescription(None)
+vocabulary_term_CONTROL_LANE_5.setLabel(None)
+vocabulary_term_CONTROL_LANE_5.setOrdinal(5)
+vocabulary_CONTROL_LANE.addTerm(vocabulary_term_CONTROL_LANE_5)
+
+vocabulary_term_CONTROL_LANE_6 = tr.createNewVocabularyTerm('6')
+vocabulary_term_CONTROL_LANE_6.setDescription(None)
+vocabulary_term_CONTROL_LANE_6.setLabel(None)
+vocabulary_term_CONTROL_LANE_6.setOrdinal(6)
+vocabulary_CONTROL_LANE.addTerm(vocabulary_term_CONTROL_LANE_6)
+
+vocabulary_term_CONTROL_LANE_7 = tr.createNewVocabularyTerm('7')
+vocabulary_term_CONTROL_LANE_7.setDescription(None)
+vocabulary_term_CONTROL_LANE_7.setLabel(None)
+vocabulary_term_CONTROL_LANE_7.setOrdinal(7)
+vocabulary_CONTROL_LANE.addTerm(vocabulary_term_CONTROL_LANE_7)
+
+vocabulary_term_CONTROL_LANE_8 = tr.createNewVocabularyTerm('8')
+vocabulary_term_CONTROL_LANE_8.setDescription(None)
+vocabulary_term_CONTROL_LANE_8.setLabel(None)
+vocabulary_term_CONTROL_LANE_8.setOrdinal(8)
+vocabulary_CONTROL_LANE.addTerm(vocabulary_term_CONTROL_LANE_8)
+
+vocabulary_term_CONTROL_LANE_NONE = tr.createNewVocabularyTerm('NONE')
+vocabulary_term_CONTROL_LANE_NONE.setDescription(None)
+vocabulary_term_CONTROL_LANE_NONE.setLabel(None)
+vocabulary_term_CONTROL_LANE_NONE.setOrdinal(9)
+vocabulary_CONTROL_LANE.addTerm(vocabulary_term_CONTROL_LANE_NONE)
+
+vocabulary_term_CONTROL_LANE_0 = tr.createNewVocabularyTerm('0')
+vocabulary_term_CONTROL_LANE_0.setDescription(None)
+vocabulary_term_CONTROL_LANE_0.setLabel(None)
+vocabulary_term_CONTROL_LANE_0.setOrdinal(10)
+vocabulary_CONTROL_LANE.addTerm(vocabulary_term_CONTROL_LANE_0)
+
+vocabulary_END_TYPE = tr.getOrCreateNewVocabulary('END_TYPE')
+vocabulary_END_TYPE.setDescription('Sequencing method')
+vocabulary_END_TYPE.setUrlTemplate(None)
+vocabulary_END_TYPE.setManagedInternally(False)
+vocabulary_END_TYPE.setInternalNamespace(False)
+vocabulary_END_TYPE.setChosenFromList(True)
+
+vocabulary_term_END_TYPE_SINGLE_READ = tr.createNewVocabularyTerm('SINGLE_READ')
+vocabulary_term_END_TYPE_SINGLE_READ.setDescription(None)
+vocabulary_term_END_TYPE_SINGLE_READ.setLabel(None)
+vocabulary_term_END_TYPE_SINGLE_READ.setOrdinal(1)
+vocabulary_END_TYPE.addTerm(vocabulary_term_END_TYPE_SINGLE_READ)
+
+vocabulary_term_END_TYPE_PAIRED_END = tr.createNewVocabularyTerm('PAIRED_END')
+vocabulary_term_END_TYPE_PAIRED_END.setDescription(None)
+vocabulary_term_END_TYPE_PAIRED_END.setLabel(None)
+vocabulary_term_END_TYPE_PAIRED_END.setOrdinal(2)
+vocabulary_END_TYPE.addTerm(vocabulary_term_END_TYPE_PAIRED_END)
+
+vocabulary_EXPERIMENT_DESIGN = tr.getOrCreateNewVocabulary('EXPERIMENT_DESIGN')
+vocabulary_EXPERIMENT_DESIGN.setDescription('General Intent')
+vocabulary_EXPERIMENT_DESIGN.setUrlTemplate(None)
+vocabulary_EXPERIMENT_DESIGN.setManagedInternally(False)
+vocabulary_EXPERIMENT_DESIGN.setInternalNamespace(False)
+vocabulary_EXPERIMENT_DESIGN.setChosenFromList(True)
+
+vocabulary_term_EXPERIMENT_DESIGN_BINDING_SITE_IDENTIFICATION = tr.createNewVocabularyTerm('BINDING_SITE_IDENTIFICATION')
+vocabulary_term_EXPERIMENT_DESIGN_BINDING_SITE_IDENTIFICATION.setDescription(None)
+vocabulary_term_EXPERIMENT_DESIGN_BINDING_SITE_IDENTIFICATION.setLabel('Binding Site Identification')
+vocabulary_term_EXPERIMENT_DESIGN_BINDING_SITE_IDENTIFICATION.setOrdinal(1)
+vocabulary_EXPERIMENT_DESIGN.addTerm(vocabulary_term_EXPERIMENT_DESIGN_BINDING_SITE_IDENTIFICATION)
+
+vocabulary_term_EXPERIMENT_DESIGN_CHROMATIN_MARKS = tr.createNewVocabularyTerm('CHROMATIN_MARKS')
+vocabulary_term_EXPERIMENT_DESIGN_CHROMATIN_MARKS.setDescription(None)
+vocabulary_term_EXPERIMENT_DESIGN_CHROMATIN_MARKS.setLabel('Chromatin Marks')
+vocabulary_term_EXPERIMENT_DESIGN_CHROMATIN_MARKS.setOrdinal(2)
+vocabulary_EXPERIMENT_DESIGN.addTerm(vocabulary_term_EXPERIMENT_DESIGN_CHROMATIN_MARKS)
+
+vocabulary_term_EXPERIMENT_DESIGN_COMPARATIVE_GENOMIC_HYBRIDIZATION = tr.createNewVocabularyTerm('COMPARATIVE_GENOMIC_HYBRIDIZATION')
+vocabulary_term_EXPERIMENT_DESIGN_COMPARATIVE_GENOMIC_HYBRIDIZATION.setDescription(None)
+vocabulary_term_EXPERIMENT_DESIGN_COMPARATIVE_GENOMIC_HYBRIDIZATION.setLabel('Comparative Genomic Hybridization')
+vocabulary_term_EXPERIMENT_DESIGN_COMPARATIVE_GENOMIC_HYBRIDIZATION.setOrdinal(3)
+vocabulary_EXPERIMENT_DESIGN.addTerm(vocabulary_term_EXPERIMENT_DESIGN_COMPARATIVE_GENOMIC_HYBRIDIZATION)
+
+vocabulary_term_EXPERIMENT_DESIGN_DIFFERENTIAL_EXPRESSION = tr.createNewVocabularyTerm('DIFFERENTIAL_EXPRESSION')
+vocabulary_term_EXPERIMENT_DESIGN_DIFFERENTIAL_EXPRESSION.setDescription(None)
+vocabulary_term_EXPERIMENT_DESIGN_DIFFERENTIAL_EXPRESSION.setLabel('Differential Expression')
+vocabulary_term_EXPERIMENT_DESIGN_DIFFERENTIAL_EXPRESSION.setOrdinal(4)
+vocabulary_EXPERIMENT_DESIGN.addTerm(vocabulary_term_EXPERIMENT_DESIGN_DIFFERENTIAL_EXPRESSION)
+
+vocabulary_term_EXPERIMENT_DESIGN_DIFFERENTIAL_SPLICING = tr.createNewVocabularyTerm('DIFFERENTIAL_SPLICING')
+vocabulary_term_EXPERIMENT_DESIGN_DIFFERENTIAL_SPLICING.setDescription(None)
+vocabulary_term_EXPERIMENT_DESIGN_DIFFERENTIAL_SPLICING.setLabel('Differential Splicing')
+vocabulary_term_EXPERIMENT_DESIGN_DIFFERENTIAL_SPLICING.setOrdinal(5)
+vocabulary_EXPERIMENT_DESIGN.addTerm(vocabulary_term_EXPERIMENT_DESIGN_DIFFERENTIAL_SPLICING)
+
+vocabulary_term_EXPERIMENT_DESIGN_EXPRESSION = tr.createNewVocabularyTerm('EXPRESSION')
+vocabulary_term_EXPERIMENT_DESIGN_EXPRESSION.setDescription(None)
+vocabulary_term_EXPERIMENT_DESIGN_EXPRESSION.setLabel('Expression')
+vocabulary_term_EXPERIMENT_DESIGN_EXPRESSION.setOrdinal(6)
+vocabulary_EXPERIMENT_DESIGN.addTerm(vocabulary_term_EXPERIMENT_DESIGN_EXPRESSION)
+
+vocabulary_term_EXPERIMENT_DESIGN_SEQUENCE_ENRICHMENT = tr.createNewVocabularyTerm('SEQUENCE_ENRICHMENT')
+vocabulary_term_EXPERIMENT_DESIGN_SEQUENCE_ENRICHMENT.setDescription(None)
+vocabulary_term_EXPERIMENT_DESIGN_SEQUENCE_ENRICHMENT.setLabel('Sequence Enrichment')
+vocabulary_term_EXPERIMENT_DESIGN_SEQUENCE_ENRICHMENT.setOrdinal(7)
+vocabulary_EXPERIMENT_DESIGN.addTerm(vocabulary_term_EXPERIMENT_DESIGN_SEQUENCE_ENRICHMENT)
+
+vocabulary_term_EXPERIMENT_DESIGN_TRANSCRIPT_IDENTIFICATION = tr.createNewVocabularyTerm('TRANSCRIPT_IDENTIFICATION')
+vocabulary_term_EXPERIMENT_DESIGN_TRANSCRIPT_IDENTIFICATION.setDescription(None)
+vocabulary_term_EXPERIMENT_DESIGN_TRANSCRIPT_IDENTIFICATION.setLabel('Transcript Identification')
+vocabulary_term_EXPERIMENT_DESIGN_TRANSCRIPT_IDENTIFICATION.setOrdinal(8)
+vocabulary_EXPERIMENT_DESIGN.addTerm(vocabulary_term_EXPERIMENT_DESIGN_TRANSCRIPT_IDENTIFICATION)
+
+vocabulary_term_EXPERIMENT_DESIGN_OTHER = tr.createNewVocabularyTerm('OTHER')
+vocabulary_term_EXPERIMENT_DESIGN_OTHER.setDescription(None)
+vocabulary_term_EXPERIMENT_DESIGN_OTHER.setLabel('Other')
+vocabulary_term_EXPERIMENT_DESIGN_OTHER.setOrdinal(9)
+vocabulary_EXPERIMENT_DESIGN.addTerm(vocabulary_term_EXPERIMENT_DESIGN_OTHER)
+
+vocabulary_INDEX1 = tr.getOrCreateNewVocabulary('INDEX1')
+vocabulary_INDEX1.setDescription('Index 1 for Illumina Indexing')
+vocabulary_INDEX1.setUrlTemplate(None)
+vocabulary_INDEX1.setManagedInternally(False)
+vocabulary_INDEX1.setInternalNamespace(False)
+vocabulary_INDEX1.setChosenFromList(True)
+
+vocabulary_term_INDEX1_NONE = tr.createNewVocabularyTerm('NONE')
+vocabulary_term_INDEX1_NONE.setDescription('No Index')
+vocabulary_term_INDEX1_NONE.setLabel(' None')
+vocabulary_term_INDEX1_NONE.setOrdinal(1)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_NONE)
+
+vocabulary_term_INDEX1_ATCACGA = tr.createNewVocabularyTerm('ATCACGA')
+vocabulary_term_INDEX1_ATCACGA.setDescription('Illumina, Nextera or Scriptseq')
+vocabulary_term_INDEX1_ATCACGA.setLabel('Index1 ATCACGA')
+vocabulary_term_INDEX1_ATCACGA.setOrdinal(2)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_ATCACGA)
+
+vocabulary_term_INDEX1_CGATGTA = tr.createNewVocabularyTerm('CGATGTA')
+vocabulary_term_INDEX1_CGATGTA.setDescription('Illumina, Nextera or Scriptseq')
+vocabulary_term_INDEX1_CGATGTA.setLabel('Index2 CGATGTA')
+vocabulary_term_INDEX1_CGATGTA.setOrdinal(3)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CGATGTA)
+
+vocabulary_term_INDEX1_TTAGGCA = tr.createNewVocabularyTerm('TTAGGCA')
+vocabulary_term_INDEX1_TTAGGCA.setDescription('Illumina, Nextera or Scriptseq')
+vocabulary_term_INDEX1_TTAGGCA.setLabel('Index3 TTAGGCA')
+vocabulary_term_INDEX1_TTAGGCA.setOrdinal(4)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_TTAGGCA)
+
+vocabulary_term_INDEX1_TGACCAA = tr.createNewVocabularyTerm('TGACCAA')
+vocabulary_term_INDEX1_TGACCAA.setDescription('Illumina, Nextera or Scriptseq')
+vocabulary_term_INDEX1_TGACCAA.setLabel('Index4 TGACCAA')
+vocabulary_term_INDEX1_TGACCAA.setOrdinal(5)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_TGACCAA)
+
+vocabulary_term_INDEX1_ACAGTGA = tr.createNewVocabularyTerm('ACAGTGA')
+vocabulary_term_INDEX1_ACAGTGA.setDescription('Illumina, Nextera or Scriptseq')
+vocabulary_term_INDEX1_ACAGTGA.setLabel('Index5 ACAGTGA')
+vocabulary_term_INDEX1_ACAGTGA.setOrdinal(6)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_ACAGTGA)
+
+vocabulary_term_INDEX1_GCCAATA = tr.createNewVocabularyTerm('GCCAATA')
+vocabulary_term_INDEX1_GCCAATA.setDescription('Illumina, Nextera or Scriptseq')
+vocabulary_term_INDEX1_GCCAATA.setLabel('Index6 GCCAATA')
+vocabulary_term_INDEX1_GCCAATA.setOrdinal(7)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_GCCAATA)
+
+vocabulary_term_INDEX1_CAGATCA = tr.createNewVocabularyTerm('CAGATCA')
+vocabulary_term_INDEX1_CAGATCA.setDescription('Illumina, Nextera or Scriptseq')
+vocabulary_term_INDEX1_CAGATCA.setLabel('Index7 CAGATCA')
+vocabulary_term_INDEX1_CAGATCA.setOrdinal(8)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CAGATCA)
+
+vocabulary_term_INDEX1_ACTTGAA = tr.createNewVocabularyTerm('ACTTGAA')
+vocabulary_term_INDEX1_ACTTGAA.setDescription('Illumina, Nextera or Scriptseq')
+vocabulary_term_INDEX1_ACTTGAA.setLabel('Index8 ACTTGAA')
+vocabulary_term_INDEX1_ACTTGAA.setOrdinal(9)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_ACTTGAA)
+
+vocabulary_term_INDEX1_GATCAGA = tr.createNewVocabularyTerm('GATCAGA')
+vocabulary_term_INDEX1_GATCAGA.setDescription('Illumina, Nextera or Scriptseq')
+vocabulary_term_INDEX1_GATCAGA.setLabel('Index9 GATCAGA')
+vocabulary_term_INDEX1_GATCAGA.setOrdinal(10)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_GATCAGA)
+
+vocabulary_term_INDEX1_TAGCTTA = tr.createNewVocabularyTerm('TAGCTTA')
+vocabulary_term_INDEX1_TAGCTTA.setDescription('Illumina, Nextera or Scriptseq')
+vocabulary_term_INDEX1_TAGCTTA.setLabel('Index10 TAGCTTA')
+vocabulary_term_INDEX1_TAGCTTA.setOrdinal(11)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_TAGCTTA)
+
+vocabulary_term_INDEX1_GGCTACA = tr.createNewVocabularyTerm('GGCTACA')
+vocabulary_term_INDEX1_GGCTACA.setDescription('Illumina, Nextera or Scriptseq')
+vocabulary_term_INDEX1_GGCTACA.setLabel('Index11 GGCTACA')
+vocabulary_term_INDEX1_GGCTACA.setOrdinal(12)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_GGCTACA)
+
+vocabulary_term_INDEX1_CTTGTAA = tr.createNewVocabularyTerm('CTTGTAA')
+vocabulary_term_INDEX1_CTTGTAA.setDescription('Illumina, Nextera or Scriptseq')
+vocabulary_term_INDEX1_CTTGTAA.setLabel('Index12 CTTGTAA')
+vocabulary_term_INDEX1_CTTGTAA.setOrdinal(13)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CTTGTAA)
+
+vocabulary_term_INDEX1_AGATACA = tr.createNewVocabularyTerm('AGATACA')
+vocabulary_term_INDEX1_AGATACA.setDescription('Illumina, Nextera or Scriptseq')
+vocabulary_term_INDEX1_AGATACA.setLabel('Index13 AGATAC')
+vocabulary_term_INDEX1_AGATACA.setOrdinal(14)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_AGATACA)
+
+vocabulary_term_INDEX1_AGTTCCG = tr.createNewVocabularyTerm('AGTTCCG')
+vocabulary_term_INDEX1_AGTTCCG.setDescription('Illumina, Nextera or Scriptseq')
+vocabulary_term_INDEX1_AGTTCCG.setLabel('Index14 AGTTCCG')
+vocabulary_term_INDEX1_AGTTCCG.setOrdinal(15)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_AGTTCCG)
+
+vocabulary_term_INDEX1_ATGTCAG = tr.createNewVocabularyTerm('ATGTCAG')
+vocabulary_term_INDEX1_ATGTCAG.setDescription('Illumina, Nextera or Scriptseq')
+vocabulary_term_INDEX1_ATGTCAG.setLabel('Index15 ATGTCAG')
+vocabulary_term_INDEX1_ATGTCAG.setOrdinal(16)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_ATGTCAG)
+
+vocabulary_term_INDEX1_CCGTCCC = tr.createNewVocabularyTerm('CCGTCCC')
+vocabulary_term_INDEX1_CCGTCCC.setDescription('Illumina, Nextera or Scriptseq')
+vocabulary_term_INDEX1_CCGTCCC.setLabel('Index16 CCGTCCC')
+vocabulary_term_INDEX1_CCGTCCC.setOrdinal(17)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CCGTCCC)
+
+vocabulary_term_INDEX1_GTCCGCA = tr.createNewVocabularyTerm('GTCCGCA')
+vocabulary_term_INDEX1_GTCCGCA.setDescription('Illumina, Nextera or Scriptseq')
+vocabulary_term_INDEX1_GTCCGCA.setLabel('Index18 GTCCGCA')
+vocabulary_term_INDEX1_GTCCGCA.setOrdinal(18)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_GTCCGCA)
+
+vocabulary_term_INDEX1_GTGAAAC = tr.createNewVocabularyTerm('GTGAAAC')
+vocabulary_term_INDEX1_GTGAAAC.setDescription('Illumina, Nextera or Scriptseq')
+vocabulary_term_INDEX1_GTGAAAC.setLabel('Index19 GTGAAAC')
+vocabulary_term_INDEX1_GTGAAAC.setOrdinal(19)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_GTGAAAC)
+
+vocabulary_term_INDEX1_GTGGCCT = tr.createNewVocabularyTerm('GTGGCCT')
+vocabulary_term_INDEX1_GTGGCCT.setDescription('Illumina, Nextera or Scriptseq')
+vocabulary_term_INDEX1_GTGGCCT.setLabel('Index20 GTGGCCT')
+vocabulary_term_INDEX1_GTGGCCT.setOrdinal(20)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_GTGGCCT)
+
+vocabulary_term_INDEX1_GTTTCGG = tr.createNewVocabularyTerm('GTTTCGG')
+vocabulary_term_INDEX1_GTTTCGG.setDescription('Illumina, Nextera or Scriptseq')
+vocabulary_term_INDEX1_GTTTCGG.setLabel('Index21 GTTTCGG')
+vocabulary_term_INDEX1_GTTTCGG.setOrdinal(21)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_GTTTCGG)
+
+vocabulary_term_INDEX1_CGTACGT = tr.createNewVocabularyTerm('CGTACGT')
+vocabulary_term_INDEX1_CGTACGT.setDescription('Illumina, Nextera or Scriptseq')
+vocabulary_term_INDEX1_CGTACGT.setLabel('Index22 CGTACGT')
+vocabulary_term_INDEX1_CGTACGT.setOrdinal(22)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CGTACGT)
+
+vocabulary_term_INDEX1_GAGTGGA = tr.createNewVocabularyTerm('GAGTGGA')
+vocabulary_term_INDEX1_GAGTGGA.setDescription('Illumina, Nextera or Scriptseq')
+vocabulary_term_INDEX1_GAGTGGA.setLabel('Index23 GAGTGGA')
+vocabulary_term_INDEX1_GAGTGGA.setOrdinal(23)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_GAGTGGA)
+
+vocabulary_term_INDEX1_ACTGATA = tr.createNewVocabularyTerm('ACTGATA')
+vocabulary_term_INDEX1_ACTGATA.setDescription('Illumina, Nextera or Scriptseq')
+vocabulary_term_INDEX1_ACTGATA.setLabel('Index25 ACTGATA')
+vocabulary_term_INDEX1_ACTGATA.setOrdinal(24)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_ACTGATA)
+
+vocabulary_term_INDEX1_ATTCCTT = tr.createNewVocabularyTerm('ATTCCTT')
+vocabulary_term_INDEX1_ATTCCTT.setDescription('Illumina, Nextera or Scriptseq')
+vocabulary_term_INDEX1_ATTCCTT.setLabel('Index27 ATTCCTT')
+vocabulary_term_INDEX1_ATTCCTT.setOrdinal(25)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_ATTCCTT)
+
+vocabulary_term_INDEX1_TAAGGCGA = tr.createNewVocabularyTerm('TAAGGCGA')
+vocabulary_term_INDEX1_TAAGGCGA.setDescription('Nextera DNA')
+vocabulary_term_INDEX1_TAAGGCGA.setLabel('Index1 (i7) N701 TAAGGCGA')
+vocabulary_term_INDEX1_TAAGGCGA.setOrdinal(26)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_TAAGGCGA)
+
+vocabulary_term_INDEX1_CGTACTAG = tr.createNewVocabularyTerm('CGTACTAG')
+vocabulary_term_INDEX1_CGTACTAG.setDescription('Nextera DNA')
+vocabulary_term_INDEX1_CGTACTAG.setLabel('Index1 (i7) N702 CGTACTAG')
+vocabulary_term_INDEX1_CGTACTAG.setOrdinal(27)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CGTACTAG)
+
+vocabulary_term_INDEX1_AGGCAGAA = tr.createNewVocabularyTerm('AGGCAGAA')
+vocabulary_term_INDEX1_AGGCAGAA.setDescription('Nextera DNA')
+vocabulary_term_INDEX1_AGGCAGAA.setLabel('Index1 (i7) N703 AGGCAGAA')
+vocabulary_term_INDEX1_AGGCAGAA.setOrdinal(28)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_AGGCAGAA)
+
+vocabulary_term_INDEX1_TCCTGAGC = tr.createNewVocabularyTerm('TCCTGAGC')
+vocabulary_term_INDEX1_TCCTGAGC.setDescription('Nextera DNA')
+vocabulary_term_INDEX1_TCCTGAGC.setLabel('Index1 (i7) N704 TCCTGAGC')
+vocabulary_term_INDEX1_TCCTGAGC.setOrdinal(29)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_TCCTGAGC)
+
+vocabulary_term_INDEX1_GGACTCCT = tr.createNewVocabularyTerm('GGACTCCT')
+vocabulary_term_INDEX1_GGACTCCT.setDescription('Nextera DNA')
+vocabulary_term_INDEX1_GGACTCCT.setLabel('Index1 (i7) N705 GGACTCCT')
+vocabulary_term_INDEX1_GGACTCCT.setOrdinal(30)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_GGACTCCT)
+
+vocabulary_term_INDEX1_TAGGCATG = tr.createNewVocabularyTerm('TAGGCATG')
+vocabulary_term_INDEX1_TAGGCATG.setDescription('Nextera DNA')
+vocabulary_term_INDEX1_TAGGCATG.setLabel('Index1 (i7) N706 TAGGCATG')
+vocabulary_term_INDEX1_TAGGCATG.setOrdinal(31)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_TAGGCATG)
+
+vocabulary_term_INDEX1_CTCTCTAC = tr.createNewVocabularyTerm('CTCTCTAC')
+vocabulary_term_INDEX1_CTCTCTAC.setDescription('Nextera DNA')
+vocabulary_term_INDEX1_CTCTCTAC.setLabel('Index1 (i7) N707 CTCTCTAC')
+vocabulary_term_INDEX1_CTCTCTAC.setOrdinal(32)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CTCTCTAC)
+
+vocabulary_term_INDEX1_CAGAGAGG = tr.createNewVocabularyTerm('CAGAGAGG')
+vocabulary_term_INDEX1_CAGAGAGG.setDescription('Nextera DNA')
+vocabulary_term_INDEX1_CAGAGAGG.setLabel('Index1 (i7) N708 CAGAGAGG')
+vocabulary_term_INDEX1_CAGAGAGG.setOrdinal(33)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CAGAGAGG)
+
+vocabulary_term_INDEX1_GCTACGCT = tr.createNewVocabularyTerm('GCTACGCT')
+vocabulary_term_INDEX1_GCTACGCT.setDescription('Nextera DNA')
+vocabulary_term_INDEX1_GCTACGCT.setLabel('Index1 (i7) N709 GCTACGCT')
+vocabulary_term_INDEX1_GCTACGCT.setOrdinal(34)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_GCTACGCT)
+
+vocabulary_term_INDEX1_CGAGGCTG = tr.createNewVocabularyTerm('CGAGGCTG')
+vocabulary_term_INDEX1_CGAGGCTG.setDescription('Nextera DNA')
+vocabulary_term_INDEX1_CGAGGCTG.setLabel('Index1 (i7) N710 CGAGGCTG')
+vocabulary_term_INDEX1_CGAGGCTG.setOrdinal(35)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CGAGGCTG)
+
+vocabulary_term_INDEX1_AAGAGGCA = tr.createNewVocabularyTerm('AAGAGGCA')
+vocabulary_term_INDEX1_AAGAGGCA.setDescription('Nextera DNA')
+vocabulary_term_INDEX1_AAGAGGCA.setLabel('Index1 (i7) N711 AAGAGGCA')
+vocabulary_term_INDEX1_AAGAGGCA.setOrdinal(36)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_AAGAGGCA)
+
+vocabulary_term_INDEX1_GTAGAGGA = tr.createNewVocabularyTerm('GTAGAGGA')
+vocabulary_term_INDEX1_GTAGAGGA.setDescription('Nextera DNA')
+vocabulary_term_INDEX1_GTAGAGGA.setLabel('Index1 (i7) N712 GTAGAGGA')
+vocabulary_term_INDEX1_GTAGAGGA.setOrdinal(37)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_GTAGAGGA)
+
+vocabulary_term_INDEX1_AAGACTA = tr.createNewVocabularyTerm('AAGACTA')
+vocabulary_term_INDEX1_AAGACTA.setDescription(None)
+vocabulary_term_INDEX1_AAGACTA.setLabel('02 AAGACT')
+vocabulary_term_INDEX1_AAGACTA.setOrdinal(38)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_AAGACTA)
+
+vocabulary_term_INDEX1_ACTTCAA = tr.createNewVocabularyTerm('ACTTCAA')
+vocabulary_term_INDEX1_ACTTCAA.setDescription(None)
+vocabulary_term_INDEX1_ACTTCAA.setLabel('10 ACTTCA')
+vocabulary_term_INDEX1_ACTTCAA.setOrdinal(39)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_ACTTCAA)
+
+vocabulary_term_INDEX1_AGGTTGA = tr.createNewVocabularyTerm('AGGTTGA')
+vocabulary_term_INDEX1_AGGTTGA.setDescription(None)
+vocabulary_term_INDEX1_AGGTTGA.setLabel('17 AGGTTG')
+vocabulary_term_INDEX1_AGGTTGA.setOrdinal(40)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_AGGTTGA)
+
+vocabulary_term_INDEX1_TTCGTCA = tr.createNewVocabularyTerm('TTCGTCA')
+vocabulary_term_INDEX1_TTCGTCA.setDescription(None)
+vocabulary_term_INDEX1_TTCGTCA.setLabel('17 TTCGTCA')
+vocabulary_term_INDEX1_TTCGTCA.setOrdinal(41)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_TTCGTCA)
+
+vocabulary_term_INDEX1_AGCATAA = tr.createNewVocabularyTerm('AGCATAA')
+vocabulary_term_INDEX1_AGCATAA.setDescription(None)
+vocabulary_term_INDEX1_AGCATAA.setLabel('20 AGCATAA')
+vocabulary_term_INDEX1_AGCATAA.setOrdinal(42)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_AGCATAA)
+
+vocabulary_term_INDEX1_ATACGCA = tr.createNewVocabularyTerm('ATACGCA')
+vocabulary_term_INDEX1_ATACGCA.setDescription(None)
+vocabulary_term_INDEX1_ATACGCA.setLabel('20 ATACGC')
+vocabulary_term_INDEX1_ATACGCA.setOrdinal(43)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_ATACGCA)
+
+vocabulary_term_INDEX1_CAGATGA = tr.createNewVocabularyTerm('CAGATGA')
+vocabulary_term_INDEX1_CAGATGA.setDescription(None)
+vocabulary_term_INDEX1_CAGATGA.setLabel('28 CAGATG')
+vocabulary_term_INDEX1_CAGATGA.setOrdinal(44)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CAGATGA)
+
+vocabulary_term_INDEX1_CCGAATA = tr.createNewVocabularyTerm('CCGAATA')
+vocabulary_term_INDEX1_CCGAATA.setDescription(None)
+vocabulary_term_INDEX1_CCGAATA.setLabel('34 CCGAAT')
+vocabulary_term_INDEX1_CCGAATA.setOrdinal(45)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CCGAATA)
+
+vocabulary_term_INDEX1_CGCTCGA = tr.createNewVocabularyTerm('CGCTCGA')
+vocabulary_term_INDEX1_CGCTCGA.setDescription(None)
+vocabulary_term_INDEX1_CGCTCGA.setLabel('43 CGCTCG')
+vocabulary_term_INDEX1_CGCTCGA.setOrdinal(46)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CGCTCGA)
+
+vocabulary_term_INDEX1_CGTATTA = tr.createNewVocabularyTerm('CGTATTA')
+vocabulary_term_INDEX1_CGTATTA.setDescription(None)
+vocabulary_term_INDEX1_CGTATTA.setLabel('45 CGTATT')
+vocabulary_term_INDEX1_CGTATTA.setOrdinal(47)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CGTATTA)
+
+vocabulary_term_INDEX1_CCATGAA = tr.createNewVocabularyTerm('CCATGAA')
+vocabulary_term_INDEX1_CCATGAA.setDescription(None)
+vocabulary_term_INDEX1_CCATGAA.setLabel('50 CCATGAA')
+vocabulary_term_INDEX1_CCATGAA.setOrdinal(48)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CCATGAA)
+
+vocabulary_term_INDEX1_CTGACCA = tr.createNewVocabularyTerm('CTGACCA')
+vocabulary_term_INDEX1_CTGACCA.setDescription(None)
+vocabulary_term_INDEX1_CTGACCA.setLabel('50 CTGACC')
+vocabulary_term_INDEX1_CTGACCA.setOrdinal(49)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CTGACCA)
+
+vocabulary_term_INDEX1_GAAGCCA = tr.createNewVocabularyTerm('GAAGCCA')
+vocabulary_term_INDEX1_GAAGCCA.setDescription(None)
+vocabulary_term_INDEX1_GAAGCCA.setLabel('52 GAAGCC')
+vocabulary_term_INDEX1_GAAGCCA.setOrdinal(50)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_GAAGCCA)
+
+vocabulary_term_INDEX1_NOINDEX = tr.createNewVocabularyTerm('NOINDEX')
+vocabulary_term_INDEX1_NOINDEX.setDescription(None)
+vocabulary_term_INDEX1_NOINDEX.setLabel(None)
+vocabulary_term_INDEX1_NOINDEX.setOrdinal(51)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_NOINDEX)
+
+vocabulary_term_INDEX1_GCTGAAA = tr.createNewVocabularyTerm('GCTGAAA')
+vocabulary_term_INDEX1_GCTGAAA.setDescription(None)
+vocabulary_term_INDEX1_GCTGAAA.setLabel('59 GCTGAA')
+vocabulary_term_INDEX1_GCTGAAA.setOrdinal(52)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_GCTGAAA)
+
+vocabulary_term_INDEX1_GTCGCGA = tr.createNewVocabularyTerm('GTCGCGA')
+vocabulary_term_INDEX1_GTCGCGA.setDescription(None)
+vocabulary_term_INDEX1_GTCGCGA.setLabel('64 GTCGCG')
+vocabulary_term_INDEX1_GTCGCGA.setOrdinal(53)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_GTCGCGA)
+
+vocabulary_term_INDEX1_TAAGATA = tr.createNewVocabularyTerm('TAAGATA')
+vocabulary_term_INDEX1_TAAGATA.setDescription(None)
+vocabulary_term_INDEX1_TAAGATA.setLabel('65 TAAGAT')
+vocabulary_term_INDEX1_TAAGATA.setOrdinal(54)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_TAAGATA)
+
+vocabulary_term_INDEX1_GCGCTGA = tr.createNewVocabularyTerm('GCGCTGA')
+vocabulary_term_INDEX1_GCGCTGA.setDescription(None)
+vocabulary_term_INDEX1_GCGCTGA.setLabel('66 GCGCTGA')
+vocabulary_term_INDEX1_GCGCTGA.setOrdinal(55)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_GCGCTGA)
+
+vocabulary_term_INDEX1_TATCGTA = tr.createNewVocabularyTerm('TATCGTA')
+vocabulary_term_INDEX1_TATCGTA.setDescription(None)
+vocabulary_term_INDEX1_TATCGTA.setLabel('66 TATCGT')
+vocabulary_term_INDEX1_TATCGTA.setOrdinal(56)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_TATCGTA)
+
+vocabulary_term_INDEX1_TCCTACA = tr.createNewVocabularyTerm('TCCTACA')
+vocabulary_term_INDEX1_TCCTACA.setDescription(None)
+vocabulary_term_INDEX1_TCCTACA.setLabel('68 TCCTAC')
+vocabulary_term_INDEX1_TCCTACA.setOrdinal(57)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_TCCTACA)
+
+vocabulary_term_INDEX1_TCTATAA = tr.createNewVocabularyTerm('TCTATAA')
+vocabulary_term_INDEX1_TCTATAA.setDescription(None)
+vocabulary_term_INDEX1_TCTATAA.setLabel('70 TCTATA')
+vocabulary_term_INDEX1_TCTATAA.setOrdinal(58)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_TCTATAA)
+
+vocabulary_term_INDEX1_TTACTTA = tr.createNewVocabularyTerm('TTACTTA')
+vocabulary_term_INDEX1_TTACTTA.setDescription(None)
+vocabulary_term_INDEX1_TTACTTA.setLabel('74 TTACTT')
+vocabulary_term_INDEX1_TTACTTA.setOrdinal(59)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_TTACTTA)
+
+vocabulary_term_INDEX1_TTCCGAA = tr.createNewVocabularyTerm('TTCCGAA')
+vocabulary_term_INDEX1_TTCCGAA.setDescription(None)
+vocabulary_term_INDEX1_TTCCGAA.setLabel('75 TTCCGA')
+vocabulary_term_INDEX1_TTCCGAA.setOrdinal(60)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_TTCCGAA)
+
+vocabulary_term_INDEX1_ATGTCAA = tr.createNewVocabularyTerm('ATGTCAA')
+vocabulary_term_INDEX1_ATGTCAA.setDescription(None)
+vocabulary_term_INDEX1_ATGTCAA.setLabel('DNA Adapter 15')
+vocabulary_term_INDEX1_ATGTCAA.setOrdinal(61)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_ATGTCAA)
+
+vocabulary_term_INDEX1_CCGTCCA = tr.createNewVocabularyTerm('CCGTCCA')
+vocabulary_term_INDEX1_CCGTCCA.setDescription(None)
+vocabulary_term_INDEX1_CCGTCCA.setLabel('DNA Adapter 16')
+vocabulary_term_INDEX1_CCGTCCA.setOrdinal(62)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CCGTCCA)
+
+vocabulary_term_INDEX1_GTAGAGA = tr.createNewVocabularyTerm('GTAGAGA')
+vocabulary_term_INDEX1_GTAGAGA.setDescription(None)
+vocabulary_term_INDEX1_GTAGAGA.setLabel('DNA Adapter 17')
+vocabulary_term_INDEX1_GTAGAGA.setOrdinal(63)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_GTAGAGA)
+
+vocabulary_term_INDEX1_GTGAAAA = tr.createNewVocabularyTerm('GTGAAAA')
+vocabulary_term_INDEX1_GTGAAAA.setDescription(None)
+vocabulary_term_INDEX1_GTGAAAA.setLabel('DNA Adapter 19')
+vocabulary_term_INDEX1_GTGAAAA.setOrdinal(64)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_GTGAAAA)
+
+vocabulary_term_INDEX1_GTGGCCA = tr.createNewVocabularyTerm('GTGGCCA')
+vocabulary_term_INDEX1_GTGGCCA.setDescription(None)
+vocabulary_term_INDEX1_GTGGCCA.setLabel('DNA Adapter 20')
+vocabulary_term_INDEX1_GTGGCCA.setOrdinal(65)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_GTGGCCA)
+
+vocabulary_term_INDEX1_GTTTCGA = tr.createNewVocabularyTerm('GTTTCGA')
+vocabulary_term_INDEX1_GTTTCGA.setDescription(None)
+vocabulary_term_INDEX1_GTTTCGA.setLabel('DNA Adapter 21')
+vocabulary_term_INDEX1_GTTTCGA.setOrdinal(66)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_GTTTCGA)
+
+vocabulary_term_INDEX1_CGTACGA = tr.createNewVocabularyTerm('CGTACGA')
+vocabulary_term_INDEX1_CGTACGA.setDescription(None)
+vocabulary_term_INDEX1_CGTACGA.setLabel('DNA Adapter 22')
+vocabulary_term_INDEX1_CGTACGA.setOrdinal(67)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CGTACGA)
+
+vocabulary_term_INDEX1_GGTAGCA = tr.createNewVocabularyTerm('GGTAGCA')
+vocabulary_term_INDEX1_GGTAGCA.setDescription(None)
+vocabulary_term_INDEX1_GGTAGCA.setLabel('DNA Adapter 24')
+vocabulary_term_INDEX1_GGTAGCA.setOrdinal(68)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_GGTAGCA)
+
+vocabulary_term_INDEX1_ATGAGCA = tr.createNewVocabularyTerm('ATGAGCA')
+vocabulary_term_INDEX1_ATGAGCA.setDescription(None)
+vocabulary_term_INDEX1_ATGAGCA.setLabel('DNA Adapter 26')
+vocabulary_term_INDEX1_ATGAGCA.setOrdinal(69)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_ATGAGCA)
+
+vocabulary_term_INDEX1_ATTCCTA = tr.createNewVocabularyTerm('ATTCCTA')
+vocabulary_term_INDEX1_ATTCCTA.setDescription(None)
+vocabulary_term_INDEX1_ATTCCTA.setLabel('DNA Adapter 27')
+vocabulary_term_INDEX1_ATTCCTA.setOrdinal(70)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_ATTCCTA)
+
+vocabulary_term_INDEX1_CAAAAGA = tr.createNewVocabularyTerm('CAAAAGA')
+vocabulary_term_INDEX1_CAAAAGA.setDescription(None)
+vocabulary_term_INDEX1_CAAAAGA.setLabel('DNA Adapter 28')
+vocabulary_term_INDEX1_CAAAAGA.setOrdinal(71)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CAAAAGA)
+
+vocabulary_term_INDEX1_CAACTAA = tr.createNewVocabularyTerm('CAACTAA')
+vocabulary_term_INDEX1_CAACTAA.setDescription(None)
+vocabulary_term_INDEX1_CAACTAA.setLabel('DNA Adapter 29')
+vocabulary_term_INDEX1_CAACTAA.setOrdinal(72)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CAACTAA)
+
+vocabulary_term_INDEX1_CACCGGA = tr.createNewVocabularyTerm('CACCGGA')
+vocabulary_term_INDEX1_CACCGGA.setDescription(None)
+vocabulary_term_INDEX1_CACCGGA.setLabel('DNA Adapter 30')
+vocabulary_term_INDEX1_CACCGGA.setOrdinal(73)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CACCGGA)
+
+vocabulary_term_INDEX1_CACGATA = tr.createNewVocabularyTerm('CACGATA')
+vocabulary_term_INDEX1_CACGATA.setDescription(None)
+vocabulary_term_INDEX1_CACGATA.setLabel('DNA Adapter 31')
+vocabulary_term_INDEX1_CACGATA.setOrdinal(74)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CACGATA)
+
+vocabulary_term_INDEX1_CACTCAA = tr.createNewVocabularyTerm('CACTCAA')
+vocabulary_term_INDEX1_CACTCAA.setDescription(None)
+vocabulary_term_INDEX1_CACTCAA.setLabel('DNA Adapter 32')
+vocabulary_term_INDEX1_CACTCAA.setOrdinal(75)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CACTCAA)
+
+vocabulary_term_INDEX1_CAGGCGA = tr.createNewVocabularyTerm('CAGGCGA')
+vocabulary_term_INDEX1_CAGGCGA.setDescription(None)
+vocabulary_term_INDEX1_CAGGCGA.setLabel('DNA Adapter 33')
+vocabulary_term_INDEX1_CAGGCGA.setOrdinal(76)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CAGGCGA)
+
+vocabulary_term_INDEX1_CATGGCA = tr.createNewVocabularyTerm('CATGGCA')
+vocabulary_term_INDEX1_CATGGCA.setDescription(None)
+vocabulary_term_INDEX1_CATGGCA.setLabel('DNA Adapter 34')
+vocabulary_term_INDEX1_CATGGCA.setOrdinal(77)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CATGGCA)
+
+vocabulary_term_INDEX1_CATTTTA = tr.createNewVocabularyTerm('CATTTTA')
+vocabulary_term_INDEX1_CATTTTA.setDescription(None)
+vocabulary_term_INDEX1_CATTTTA.setLabel('DNA Adapter 35')
+vocabulary_term_INDEX1_CATTTTA.setOrdinal(78)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CATTTTA)
+
+vocabulary_term_INDEX1_CCAACAA = tr.createNewVocabularyTerm('CCAACAA')
+vocabulary_term_INDEX1_CCAACAA.setDescription(None)
+vocabulary_term_INDEX1_CCAACAA.setLabel('DNA Adapter 36')
+vocabulary_term_INDEX1_CCAACAA.setOrdinal(79)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CCAACAA)
+
+vocabulary_term_INDEX1_CGGAATA = tr.createNewVocabularyTerm('CGGAATA')
+vocabulary_term_INDEX1_CGGAATA.setDescription(None)
+vocabulary_term_INDEX1_CGGAATA.setLabel('DNA Adapter 37')
+vocabulary_term_INDEX1_CGGAATA.setOrdinal(80)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CGGAATA)
+
+vocabulary_term_INDEX1_CTAGCTA = tr.createNewVocabularyTerm('CTAGCTA')
+vocabulary_term_INDEX1_CTAGCTA.setDescription(None)
+vocabulary_term_INDEX1_CTAGCTA.setLabel('DNA Adapter 38')
+vocabulary_term_INDEX1_CTAGCTA.setOrdinal(81)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CTAGCTA)
+
+vocabulary_term_INDEX1_CTATACA = tr.createNewVocabularyTerm('CTATACA')
+vocabulary_term_INDEX1_CTATACA.setDescription(None)
+vocabulary_term_INDEX1_CTATACA.setLabel('DNA Adapter 39')
+vocabulary_term_INDEX1_CTATACA.setOrdinal(82)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CTATACA)
+
+vocabulary_term_INDEX1_CTCAGAA = tr.createNewVocabularyTerm('CTCAGAA')
+vocabulary_term_INDEX1_CTCAGAA.setDescription(None)
+vocabulary_term_INDEX1_CTCAGAA.setLabel('DNA Adapter 40')
+vocabulary_term_INDEX1_CTCAGAA.setOrdinal(83)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_CTCAGAA)
+
+vocabulary_term_INDEX1_GACGACA = tr.createNewVocabularyTerm('GACGACA')
+vocabulary_term_INDEX1_GACGACA.setDescription(None)
+vocabulary_term_INDEX1_GACGACA.setLabel('DNA Adapter 41')
+vocabulary_term_INDEX1_GACGACA.setOrdinal(84)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_GACGACA)
+
+vocabulary_term_INDEX1_TAATCGA = tr.createNewVocabularyTerm('TAATCGA')
+vocabulary_term_INDEX1_TAATCGA.setDescription(None)
+vocabulary_term_INDEX1_TAATCGA.setLabel('DNA Adapter 42')
+vocabulary_term_INDEX1_TAATCGA.setOrdinal(85)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_TAATCGA)
+
+vocabulary_term_INDEX1_TACAGCA = tr.createNewVocabularyTerm('TACAGCA')
+vocabulary_term_INDEX1_TACAGCA.setDescription(None)
+vocabulary_term_INDEX1_TACAGCA.setLabel('DNA Adapter 43')
+vocabulary_term_INDEX1_TACAGCA.setOrdinal(86)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_TACAGCA)
+
+vocabulary_term_INDEX1_TATAATA = tr.createNewVocabularyTerm('TATAATA')
+vocabulary_term_INDEX1_TATAATA.setDescription(None)
+vocabulary_term_INDEX1_TATAATA.setLabel('DNA Adapter 44')
+vocabulary_term_INDEX1_TATAATA.setOrdinal(87)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_TATAATA)
+
+vocabulary_term_INDEX1_TCATTCA = tr.createNewVocabularyTerm('TCATTCA')
+vocabulary_term_INDEX1_TCATTCA.setDescription(None)
+vocabulary_term_INDEX1_TCATTCA.setLabel('DNA Adapter 45')
+vocabulary_term_INDEX1_TCATTCA.setOrdinal(88)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_TCATTCA)
+
+vocabulary_term_INDEX1_TCCCGAA = tr.createNewVocabularyTerm('TCCCGAA')
+vocabulary_term_INDEX1_TCCCGAA.setDescription(None)
+vocabulary_term_INDEX1_TCCCGAA.setLabel('DNA Adapter 46')
+vocabulary_term_INDEX1_TCCCGAA.setOrdinal(89)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_TCCCGAA)
+
+vocabulary_term_INDEX1_TCGAAGA = tr.createNewVocabularyTerm('TCGAAGA')
+vocabulary_term_INDEX1_TCGAAGA.setDescription(None)
+vocabulary_term_INDEX1_TCGAAGA.setLabel('DNA Adapter 47')
+vocabulary_term_INDEX1_TCGAAGA.setOrdinal(90)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_TCGAAGA)
+
+vocabulary_term_INDEX1_TCGGCAA = tr.createNewVocabularyTerm('TCGGCAA')
+vocabulary_term_INDEX1_TCGGCAA.setDescription(None)
+vocabulary_term_INDEX1_TCGGCAA.setLabel('DNA Adapter 48')
+vocabulary_term_INDEX1_TCGGCAA.setOrdinal(91)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_TCGGCAA)
+
+vocabulary_term_INDEX1_AGTCAAC = tr.createNewVocabularyTerm('AGTCAAC')
+vocabulary_term_INDEX1_AGTCAAC.setDescription(None)
+vocabulary_term_INDEX1_AGTCAAC.setLabel('Index13 AGTCAAC')
+vocabulary_term_INDEX1_AGTCAAC.setOrdinal(92)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_AGTCAAC)
+
+vocabulary_term_INDEX1_AATGCGA = tr.createNewVocabularyTerm('AATGCGA')
+vocabulary_term_INDEX1_AATGCGA.setDescription(None)
+vocabulary_term_INDEX1_AATGCGA.setLabel('Lib AATGCGA')
+vocabulary_term_INDEX1_AATGCGA.setOrdinal(93)
+vocabulary_INDEX1.addTerm(vocabulary_term_INDEX1_AATGCGA)
+
+vocabulary_INDEX2 = tr.getOrCreateNewVocabulary('INDEX2')
+vocabulary_INDEX2.setDescription('Index 2 for Illumina Dual Indexing')
+vocabulary_INDEX2.setUrlTemplate(None)
+vocabulary_INDEX2.setManagedInternally(False)
+vocabulary_INDEX2.setInternalNamespace(False)
+vocabulary_INDEX2.setChosenFromList(True)
+
+vocabulary_term_INDEX2_NONE = tr.createNewVocabularyTerm('NONE')
+vocabulary_term_INDEX2_NONE.setDescription('No Index')
+vocabulary_term_INDEX2_NONE.setLabel('None')
+vocabulary_term_INDEX2_NONE.setOrdinal(1)
+vocabulary_INDEX2.addTerm(vocabulary_term_INDEX2_NONE)
+
+vocabulary_term_INDEX2_TAGATCGC = tr.createNewVocabularyTerm('TAGATCGC')
+vocabulary_term_INDEX2_TAGATCGC.setDescription('Nextera DNA')
+vocabulary_term_INDEX2_TAGATCGC.setLabel('Index2 (i5) N501 TAGATCGC')
+vocabulary_term_INDEX2_TAGATCGC.setOrdinal(2)
+vocabulary_INDEX2.addTerm(vocabulary_term_INDEX2_TAGATCGC)
+
+vocabulary_term_INDEX2_CTCTCTAT = tr.createNewVocabularyTerm('CTCTCTAT')
+vocabulary_term_INDEX2_CTCTCTAT.setDescription('Nextera DNA')
+vocabulary_term_INDEX2_CTCTCTAT.setLabel('Index2 (i5) N502 CTCTCTAT')
+vocabulary_term_INDEX2_CTCTCTAT.setOrdinal(3)
+vocabulary_INDEX2.addTerm(vocabulary_term_INDEX2_CTCTCTAT)
+
+vocabulary_term_INDEX2_TATCCTCT = tr.createNewVocabularyTerm('TATCCTCT')
+vocabulary_term_INDEX2_TATCCTCT.setDescription('Nextera DNA')
+vocabulary_term_INDEX2_TATCCTCT.setLabel('Index2 (i5) N503 TATCCTCT')
+vocabulary_term_INDEX2_TATCCTCT.setOrdinal(4)
+vocabulary_INDEX2.addTerm(vocabulary_term_INDEX2_TATCCTCT)
+
+vocabulary_term_INDEX2_AGAGTAGA = tr.createNewVocabularyTerm('AGAGTAGA')
+vocabulary_term_INDEX2_AGAGTAGA.setDescription('Nextera DNA')
+vocabulary_term_INDEX2_AGAGTAGA.setLabel('Index2 (i5) N504 AGAGTAGA')
+vocabulary_term_INDEX2_AGAGTAGA.setOrdinal(5)
+vocabulary_INDEX2.addTerm(vocabulary_term_INDEX2_AGAGTAGA)
+
+vocabulary_term_INDEX2_GTAAGGAG = tr.createNewVocabularyTerm('GTAAGGAG')
+vocabulary_term_INDEX2_GTAAGGAG.setDescription('Nextera DNA')
+vocabulary_term_INDEX2_GTAAGGAG.setLabel('Index2 (i5) N505 GTAAGGAG')
+vocabulary_term_INDEX2_GTAAGGAG.setOrdinal(6)
+vocabulary_INDEX2.addTerm(vocabulary_term_INDEX2_GTAAGGAG)
+
+vocabulary_term_INDEX2_ACTGCATA = tr.createNewVocabularyTerm('ACTGCATA')
+vocabulary_term_INDEX2_ACTGCATA.setDescription('Nextera DNA')
+vocabulary_term_INDEX2_ACTGCATA.setLabel('Index2 (i5) N506 ACTGCATA')
+vocabulary_term_INDEX2_ACTGCATA.setOrdinal(7)
+vocabulary_INDEX2.addTerm(vocabulary_term_INDEX2_ACTGCATA)
+
+vocabulary_term_INDEX2_AAGGAGTA = tr.createNewVocabularyTerm('AAGGAGTA')
+vocabulary_term_INDEX2_AAGGAGTA.setDescription('Nextera DNA')
+vocabulary_term_INDEX2_AAGGAGTA.setLabel('Index2 (i5) N507 AAGGAGTA')
+vocabulary_term_INDEX2_AAGGAGTA.setOrdinal(8)
+vocabulary_INDEX2.addTerm(vocabulary_term_INDEX2_AAGGAGTA)
+
+vocabulary_term_INDEX2_CTAAGCCT = tr.createNewVocabularyTerm('CTAAGCCT')
+vocabulary_term_INDEX2_CTAAGCCT.setDescription('Nextera DNA')
+vocabulary_term_INDEX2_CTAAGCCT.setLabel('Index2 (i5) N508 CTAAGCCT')
+vocabulary_term_INDEX2_CTAAGCCT.setOrdinal(9)
+vocabulary_INDEX2.addTerm(vocabulary_term_INDEX2_CTAAGCCT)
+
+vocabulary_term_INDEX2_NOINDEX = tr.createNewVocabularyTerm('NOINDEX')
+vocabulary_term_INDEX2_NOINDEX.setDescription(None)
+vocabulary_term_INDEX2_NOINDEX.setLabel(None)
+vocabulary_term_INDEX2_NOINDEX.setOrdinal(10)
+vocabulary_INDEX2.addTerm(vocabulary_term_INDEX2_NOINDEX)
+
+vocabulary_KIT = tr.getOrCreateNewVocabulary('KIT')
+vocabulary_KIT.setDescription('Illumina Kit used for preparation')
+vocabulary_KIT.setUrlTemplate(None)
+vocabulary_KIT.setManagedInternally(False)
+vocabulary_KIT.setInternalNamespace(False)
+vocabulary_KIT.setChosenFromList(True)
+
+vocabulary_term_KIT_CHIP_SEQ_SAMPLE_PREP = tr.createNewVocabularyTerm('CHIP_SEQ_SAMPLE_PREP')
+vocabulary_term_KIT_CHIP_SEQ_SAMPLE_PREP.setDescription(None)
+vocabulary_term_KIT_CHIP_SEQ_SAMPLE_PREP.setLabel('ChIP-Seq Sample Preparation Kit')
+vocabulary_term_KIT_CHIP_SEQ_SAMPLE_PREP.setOrdinal(1)
+vocabulary_KIT.addTerm(vocabulary_term_KIT_CHIP_SEQ_SAMPLE_PREP)
+
+vocabulary_term_KIT_NEBNEXT_DNA_SAMPLE_PREP_MASTER_MIX_SET1 = tr.createNewVocabularyTerm('NEBNEXT_DNA_SAMPLE_PREP_MASTER_MIX_SET1')
+vocabulary_term_KIT_NEBNEXT_DNA_SAMPLE_PREP_MASTER_MIX_SET1.setDescription(None)
+vocabulary_term_KIT_NEBNEXT_DNA_SAMPLE_PREP_MASTER_MIX_SET1.setLabel('NEB Genomic DNA Sample Preparation Kit')
+vocabulary_term_KIT_NEBNEXT_DNA_SAMPLE_PREP_MASTER_MIX_SET1.setOrdinal(2)
+vocabulary_KIT.addTerm(vocabulary_term_KIT_NEBNEXT_DNA_SAMPLE_PREP_MASTER_MIX_SET1)
+
+vocabulary_term_KIT_NEB_CHIP_SEQ_SAMPLE_PREPARATION_KIT = tr.createNewVocabularyTerm('NEB_CHIP_SEQ_SAMPLE_PREPARATION_KIT')
+vocabulary_term_KIT_NEB_CHIP_SEQ_SAMPLE_PREPARATION_KIT.setDescription(None)
+vocabulary_term_KIT_NEB_CHIP_SEQ_SAMPLE_PREPARATION_KIT.setLabel('NEB_ChIP_Seq_Sample_Preparation_Kit')
+vocabulary_term_KIT_NEB_CHIP_SEQ_SAMPLE_PREPARATION_KIT.setOrdinal(3)
+vocabulary_KIT.addTerm(vocabulary_term_KIT_NEB_CHIP_SEQ_SAMPLE_PREPARATION_KIT)
+
+vocabulary_term_KIT_GENOMICDNA_SAMPLE_PREP = tr.createNewVocabularyTerm('GENOMICDNA_SAMPLE_PREP')
+vocabulary_term_KIT_GENOMICDNA_SAMPLE_PREP.setDescription(None)
+vocabulary_term_KIT_GENOMICDNA_SAMPLE_PREP.setLabel('Illumina Genomic DNA Sample Preparation Kit')
+vocabulary_term_KIT_GENOMICDNA_SAMPLE_PREP.setOrdinal(4)
+vocabulary_KIT.addTerm(vocabulary_term_KIT_GENOMICDNA_SAMPLE_PREP)
+
+vocabulary_term_KIT_PAIRED_END_DNA_SAMPLE_PREP = tr.createNewVocabularyTerm('PAIRED_END_DNA_SAMPLE_PREP')
+vocabulary_term_KIT_PAIRED_END_DNA_SAMPLE_PREP.setDescription(None)
+vocabulary_term_KIT_PAIRED_END_DNA_SAMPLE_PREP.setLabel('Paired End DNA Sample Prep Oligo Kit')
+vocabulary_term_KIT_PAIRED_END_DNA_SAMPLE_PREP.setOrdinal(5)
+vocabulary_KIT.addTerm(vocabulary_term_KIT_PAIRED_END_DNA_SAMPLE_PREP)
+
+vocabulary_term_KIT_MRNA_SEQ_SAMPLE_PREP = tr.createNewVocabularyTerm('MRNA_SEQ_SAMPLE_PREP')
+vocabulary_term_KIT_MRNA_SEQ_SAMPLE_PREP.setDescription(None)
+vocabulary_term_KIT_MRNA_SEQ_SAMPLE_PREP.setLabel('mRNA-Seq Sample Preparation Kit')
+vocabulary_term_KIT_MRNA_SEQ_SAMPLE_PREP.setOrdinal(6)
+vocabulary_KIT.addTerm(vocabulary_term_KIT_MRNA_SEQ_SAMPLE_PREP)
+
+vocabulary_term_KIT_RIBOZERO_SCRIPTSEQ_MRNASEQ_KIT = tr.createNewVocabularyTerm('RIBOZERO_SCRIPTSEQ_MRNA-SEQ_KIT')
+vocabulary_term_KIT_RIBOZERO_SCRIPTSEQ_MRNASEQ_KIT.setDescription(None)
+vocabulary_term_KIT_RIBOZERO_SCRIPTSEQ_MRNASEQ_KIT.setLabel('RiboZero ScriptSeq mRNA-Seq_Epicentre-kit')
+vocabulary_term_KIT_RIBOZERO_SCRIPTSEQ_MRNASEQ_KIT.setOrdinal(7)
+vocabulary_KIT.addTerm(vocabulary_term_KIT_RIBOZERO_SCRIPTSEQ_MRNASEQ_KIT)
+
+vocabulary_term_KIT_POLYA_SCRIPTSEQ_MRNASEQ_KIT = tr.createNewVocabularyTerm('POLYA_SCRIPTSEQ_MRNA-SEQ_KIT')
+vocabulary_term_KIT_POLYA_SCRIPTSEQ_MRNASEQ_KIT.setDescription(None)
+vocabulary_term_KIT_POLYA_SCRIPTSEQ_MRNASEQ_KIT.setLabel('PolyA(Beads) ScriptSeq mRNA-Seq_Epicentre-kit')
+vocabulary_term_KIT_POLYA_SCRIPTSEQ_MRNASEQ_KIT.setOrdinal(8)
+vocabulary_KIT.addTerm(vocabulary_term_KIT_POLYA_SCRIPTSEQ_MRNASEQ_KIT)
+
+vocabulary_term_KIT_NEXTERA_DNA_SAMPLE_PREP_KITS = tr.createNewVocabularyTerm('NEXTERA_DNA_SAMPLE_PREP_KITS')
+vocabulary_term_KIT_NEXTERA_DNA_SAMPLE_PREP_KITS.setDescription(None)
+vocabulary_term_KIT_NEXTERA_DNA_SAMPLE_PREP_KITS.setLabel('Nextera Genomic DNA Sample Preparation Kit BufferLMW(Epicentre)')
+vocabulary_term_KIT_NEXTERA_DNA_SAMPLE_PREP_KITS.setOrdinal(9)
+vocabulary_KIT.addTerm(vocabulary_term_KIT_NEXTERA_DNA_SAMPLE_PREP_KITS)
+
+vocabulary_term_KIT_NEXTERA_DNA_SAMPLE_PREP_KIT_BUFFER_HMW = tr.createNewVocabularyTerm('NEXTERA_DNA_SAMPLE_PREP_KIT_BUFFER_HMW')
+vocabulary_term_KIT_NEXTERA_DNA_SAMPLE_PREP_KIT_BUFFER_HMW.setDescription(None)
+vocabulary_term_KIT_NEXTERA_DNA_SAMPLE_PREP_KIT_BUFFER_HMW.setLabel('Nextera Genomic DNA Sample Preparation Kit BufferHMW(Epicentre)')
+vocabulary_term_KIT_NEXTERA_DNA_SAMPLE_PREP_KIT_BUFFER_HMW.setOrdinal(10)
+vocabulary_KIT.addTerm(vocabulary_term_KIT_NEXTERA_DNA_SAMPLE_PREP_KIT_BUFFER_HMW)
+
+vocabulary_term_KIT_AGILENT_SURESELECT_ENRICHMENTSYSTEM = tr.createNewVocabularyTerm('AGILENT_SURESELECT_ENRICHMENTSYSTEM')
+vocabulary_term_KIT_AGILENT_SURESELECT_ENRICHMENTSYSTEM.setDescription(None)
+vocabulary_term_KIT_AGILENT_SURESELECT_ENRICHMENTSYSTEM.setLabel('Agilent_SureSelect_EnrichmentSystem')
+vocabulary_term_KIT_AGILENT_SURESELECT_ENRICHMENTSYSTEM.setOrdinal(11)
+vocabulary_KIT.addTerm(vocabulary_term_KIT_AGILENT_SURESELECT_ENRICHMENTSYSTEM)
+
+vocabulary_term_KIT_TRUSEQRNA_SAMPLE_PREP_KIT = tr.createNewVocabularyTerm('TRUSEQRNA_SAMPLE_PREP_KIT')
+vocabulary_term_KIT_TRUSEQRNA_SAMPLE_PREP_KIT.setDescription(None)
+vocabulary_term_KIT_TRUSEQRNA_SAMPLE_PREP_KIT.setLabel('TruSeq_RNA_SamplePrepKit_Illumina')
+vocabulary_term_KIT_TRUSEQRNA_SAMPLE_PREP_KIT.setOrdinal(12)
+vocabulary_KIT.addTerm(vocabulary_term_KIT_TRUSEQRNA_SAMPLE_PREP_KIT)
+
+vocabulary_term_KIT_TRUESEQ_CHIP_SAMPLE_PREP_KIT = tr.createNewVocabularyTerm('TRUESEQ_CHIP_SAMPLE_PREP_KIT')
+vocabulary_term_KIT_TRUESEQ_CHIP_SAMPLE_PREP_KIT.setDescription(None)
+vocabulary_term_KIT_TRUESEQ_CHIP_SAMPLE_PREP_KIT.setLabel(None)
+vocabulary_term_KIT_TRUESEQ_CHIP_SAMPLE_PREP_KIT.setOrdinal(13)
+vocabulary_KIT.addTerm(vocabulary_term_KIT_TRUESEQ_CHIP_SAMPLE_PREP_KIT)
+
+vocabulary_term_KIT_TRUSEQ_DNA_SAMPLE_PREP_KIT = tr.createNewVocabularyTerm('TRUSEQ_DNA_SAMPLE_PREP_KIT')
+vocabulary_term_KIT_TRUSEQ_DNA_SAMPLE_PREP_KIT.setDescription(None)
+vocabulary_term_KIT_TRUSEQ_DNA_SAMPLE_PREP_KIT.setLabel('TruSeq_DNA_SamplePrepKit_Illumina')
+vocabulary_term_KIT_TRUSEQ_DNA_SAMPLE_PREP_KIT.setOrdinal(14)
+vocabulary_KIT.addTerm(vocabulary_term_KIT_TRUSEQ_DNA_SAMPLE_PREP_KIT)
+
+vocabulary_term_KIT_NONE = tr.createNewVocabularyTerm('NONE')
+vocabulary_term_KIT_NONE.setDescription(None)
+vocabulary_term_KIT_NONE.setLabel('None (Already prepared)')
+vocabulary_term_KIT_NONE.setOrdinal(15)
+vocabulary_KIT.addTerm(vocabulary_term_KIT_NONE)
+
+vocabulary_MACS_VERSION = tr.getOrCreateNewVocabulary('MACS_VERSION')
+vocabulary_MACS_VERSION.setDescription('Used MACS version for Peak Calling')
+vocabulary_MACS_VERSION.setUrlTemplate(None)
+vocabulary_MACS_VERSION.setManagedInternally(False)
+vocabulary_MACS_VERSION.setInternalNamespace(False)
+vocabulary_MACS_VERSION.setChosenFromList(True)
+
+vocabulary_term_MACS_VERSION_140RC2 = tr.createNewVocabularyTerm('1.4.0RC2')
+vocabulary_term_MACS_VERSION_140RC2.setDescription(None)
+vocabulary_term_MACS_VERSION_140RC2.setLabel('macs14 1.4.0rc2 20110214 (Valentine)')
+vocabulary_term_MACS_VERSION_140RC2.setOrdinal(1)
+vocabulary_MACS_VERSION.addTerm(vocabulary_term_MACS_VERSION_140RC2)
+
+vocabulary_term_MACS_VERSION_1371 = tr.createNewVocabularyTerm('1.3.7.1')
+vocabulary_term_MACS_VERSION_1371.setDescription(None)
+vocabulary_term_MACS_VERSION_1371.setLabel('macs 1.3.7.1 (Oktoberfest, bug fixed #1)')
+vocabulary_term_MACS_VERSION_1371.setOrdinal(2)
+vocabulary_MACS_VERSION.addTerm(vocabulary_term_MACS_VERSION_1371)
+
+vocabulary_MISMATCH_IN_INDEX = tr.getOrCreateNewVocabulary('MISMATCH_IN_INDEX')
+vocabulary_MISMATCH_IN_INDEX.setDescription('Mismatch in Index allowed')
+vocabulary_MISMATCH_IN_INDEX.setUrlTemplate(None)
+vocabulary_MISMATCH_IN_INDEX.setManagedInternally(False)
+vocabulary_MISMATCH_IN_INDEX.setInternalNamespace(False)
+vocabulary_MISMATCH_IN_INDEX.setChosenFromList(True)
+
+vocabulary_term_MISMATCH_IN_INDEX_NONE = tr.createNewVocabularyTerm('NONE')
+vocabulary_term_MISMATCH_IN_INDEX_NONE.setDescription(None)
+vocabulary_term_MISMATCH_IN_INDEX_NONE.setLabel(None)
+vocabulary_term_MISMATCH_IN_INDEX_NONE.setOrdinal(1)
+vocabulary_MISMATCH_IN_INDEX.addTerm(vocabulary_term_MISMATCH_IN_INDEX_NONE)
+
+vocabulary_term_MISMATCH_IN_INDEX_ONE = tr.createNewVocabularyTerm('ONE')
+vocabulary_term_MISMATCH_IN_INDEX_ONE.setDescription(None)
+vocabulary_term_MISMATCH_IN_INDEX_ONE.setLabel(None)
+vocabulary_term_MISMATCH_IN_INDEX_ONE.setOrdinal(2)
+vocabulary_MISMATCH_IN_INDEX.addTerm(vocabulary_term_MISMATCH_IN_INDEX_ONE)
+
+vocabulary_NANO_DROP = tr.getOrCreateNewVocabulary('NANO_DROP')
+vocabulary_NANO_DROP.setDescription('Device for measuring the total amount of genetic material contained in the probe')
+vocabulary_NANO_DROP.setUrlTemplate(None)
+vocabulary_NANO_DROP.setManagedInternally(False)
+vocabulary_NANO_DROP.setInternalNamespace(False)
+vocabulary_NANO_DROP.setChosenFromList(True)
+
+vocabulary_term_NANO_DROP_CONCND3300 = tr.createNewVocabularyTerm('CONCND3300')
+vocabulary_term_NANO_DROP_CONCND3300.setDescription(None)
+vocabulary_term_NANO_DROP_CONCND3300.setLabel('Conc Nano Drop 3300')
+vocabulary_term_NANO_DROP_CONCND3300.setOrdinal(1)
+vocabulary_NANO_DROP.addTerm(vocabulary_term_NANO_DROP_CONCND3300)
+
+vocabulary_term_NANO_DROP_CONCND1000 = tr.createNewVocabularyTerm('CONCND1000')
+vocabulary_term_NANO_DROP_CONCND1000.setDescription(None)
+vocabulary_term_NANO_DROP_CONCND1000.setLabel('Conc Nano Drop 1000')
+vocabulary_term_NANO_DROP_CONCND1000.setOrdinal(2)
+vocabulary_NANO_DROP.addTerm(vocabulary_term_NANO_DROP_CONCND1000)
+
+vocabulary_term_NANO_DROP_CONCND2000 = tr.createNewVocabularyTerm('CONCND2000')
+vocabulary_term_NANO_DROP_CONCND2000.setDescription(None)
+vocabulary_term_NANO_DROP_CONCND2000.setLabel('Conc Nano Drop 2000')
+vocabulary_term_NANO_DROP_CONCND2000.setOrdinal(3)
+vocabulary_NANO_DROP.addTerm(vocabulary_term_NANO_DROP_CONCND2000)
+
+vocabulary_NCBI_TAXONOMY = tr.getOrCreateNewVocabulary('NCBI_TAXONOMY')
+vocabulary_NCBI_TAXONOMY.setDescription(None)
+vocabulary_NCBI_TAXONOMY.setUrlTemplate('http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=$term$')
+vocabulary_NCBI_TAXONOMY.setManagedInternally(False)
+vocabulary_NCBI_TAXONOMY.setInternalNamespace(False)
+vocabulary_NCBI_TAXONOMY.setChosenFromList(True)
+
+vocabulary_term_NCBI_TAXONOMY_10090 = tr.createNewVocabularyTerm('10090')
+vocabulary_term_NCBI_TAXONOMY_10090.setDescription('Genbank common name: house mouse\ Inherited blast name: rodents')
+vocabulary_term_NCBI_TAXONOMY_10090.setLabel('Mus musculus')
+vocabulary_term_NCBI_TAXONOMY_10090.setOrdinal(1)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_10090)
+
+vocabulary_term_NCBI_TAXONOMY_9606 = tr.createNewVocabularyTerm('9606')
+vocabulary_term_NCBI_TAXONOMY_9606.setDescription('Genbank common name: human\ Inherited blast name: primates')
+vocabulary_term_NCBI_TAXONOMY_9606.setLabel('Homo sapiens')
+vocabulary_term_NCBI_TAXONOMY_9606.setOrdinal(2)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_9606)
+
+vocabulary_term_NCBI_TAXONOMY_7227 = tr.createNewVocabularyTerm('7227')
+vocabulary_term_NCBI_TAXONOMY_7227.setDescription('Genbank common name: fruit fly\ Inherited blast name: flies')
+vocabulary_term_NCBI_TAXONOMY_7227.setLabel('Drosophila melanogaster')
+vocabulary_term_NCBI_TAXONOMY_7227.setOrdinal(3)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_7227)
+
+vocabulary_term_NCBI_TAXONOMY_6239 = tr.createNewVocabularyTerm('6239')
+vocabulary_term_NCBI_TAXONOMY_6239.setDescription('Inherited blast name: nematodes')
+vocabulary_term_NCBI_TAXONOMY_6239.setLabel('Caenorhabditis elegans')
+vocabulary_term_NCBI_TAXONOMY_6239.setOrdinal(4)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_6239)
+
+vocabulary_term_NCBI_TAXONOMY_4932 = tr.createNewVocabularyTerm('4932')
+vocabulary_term_NCBI_TAXONOMY_4932.setDescription('Genbank common name: baker\'s yeast\ Inherited blast name: ascomycetes')
+vocabulary_term_NCBI_TAXONOMY_4932.setLabel('Saccharomyces cerevisiae')
+vocabulary_term_NCBI_TAXONOMY_4932.setOrdinal(5)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_4932)
+
+vocabulary_term_NCBI_TAXONOMY_10116 = tr.createNewVocabularyTerm('10116')
+vocabulary_term_NCBI_TAXONOMY_10116.setDescription('Genbank common name: Norway rat\ Inherited blast name: rodents')
+vocabulary_term_NCBI_TAXONOMY_10116.setLabel('Rattus norvegicus')
+vocabulary_term_NCBI_TAXONOMY_10116.setOrdinal(6)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_10116)
+
+vocabulary_term_NCBI_TAXONOMY_6669 = tr.createNewVocabularyTerm('6669')
+vocabulary_term_NCBI_TAXONOMY_6669.setDescription('Genbank common name: common water flea\ Inherited blast name: crustaceans')
+vocabulary_term_NCBI_TAXONOMY_6669.setLabel('Daphnia pulex')
+vocabulary_term_NCBI_TAXONOMY_6669.setOrdinal(7)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_6669)
+
+vocabulary_term_NCBI_TAXONOMY_562 = tr.createNewVocabularyTerm('562')
+vocabulary_term_NCBI_TAXONOMY_562.setDescription('Inherited blast name: enterobacteria')
+vocabulary_term_NCBI_TAXONOMY_562.setLabel('Escherichia coli')
+vocabulary_term_NCBI_TAXONOMY_562.setOrdinal(8)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_562)
+
+vocabulary_term_NCBI_TAXONOMY_623 = tr.createNewVocabularyTerm('623')
+vocabulary_term_NCBI_TAXONOMY_623.setDescription('Inherited blast name: enterobacteria')
+vocabulary_term_NCBI_TAXONOMY_623.setLabel('Shigella flexneri')
+vocabulary_term_NCBI_TAXONOMY_623.setOrdinal(9)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_623)
+
+vocabulary_term_NCBI_TAXONOMY_10847 = tr.createNewVocabularyTerm('10847')
+vocabulary_term_NCBI_TAXONOMY_10847.setDescription('Inherited blast name: viruses')
+vocabulary_term_NCBI_TAXONOMY_10847.setLabel('Enterobacteria phage phiX174')
+vocabulary_term_NCBI_TAXONOMY_10847.setOrdinal(10)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_10847)
+
+vocabulary_term_NCBI_TAXONOMY_190650 = tr.createNewVocabularyTerm('190650')
+vocabulary_term_NCBI_TAXONOMY_190650.setDescription('Inherited blast name: a-proteobacteria')
+vocabulary_term_NCBI_TAXONOMY_190650.setLabel('Caulobacter crescentus CB15')
+vocabulary_term_NCBI_TAXONOMY_190650.setOrdinal(11)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_190650)
+
+vocabulary_term_NCBI_TAXONOMY_8113 = tr.createNewVocabularyTerm('8113')
+vocabulary_term_NCBI_TAXONOMY_8113.setDescription('Genbank common name: cichlids\ Inherited blast name: bony fishes')
+vocabulary_term_NCBI_TAXONOMY_8113.setLabel('Cichlidae')
+vocabulary_term_NCBI_TAXONOMY_8113.setOrdinal(12)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_8113)
+
+vocabulary_term_NCBI_TAXONOMY_481459 = tr.createNewVocabularyTerm('481459')
+vocabulary_term_NCBI_TAXONOMY_481459.setDescription('Genbank common name: three-spined stickleback\ Inherited blast name: bony fishes')
+vocabulary_term_NCBI_TAXONOMY_481459.setLabel('Gasterosteus aculeatus aculeatus')
+vocabulary_term_NCBI_TAXONOMY_481459.setOrdinal(13)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_481459)
+
+vocabulary_term_NCBI_TAXONOMY_282301 = tr.createNewVocabularyTerm('282301')
+vocabulary_term_NCBI_TAXONOMY_282301.setDescription('Inherited blast name: flatworms')
+vocabulary_term_NCBI_TAXONOMY_282301.setLabel('Macrostomum lignano')
+vocabulary_term_NCBI_TAXONOMY_282301.setOrdinal(14)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_282301)
+
+vocabulary_term_NCBI_TAXONOMY_99287 = tr.createNewVocabularyTerm('99287')
+vocabulary_term_NCBI_TAXONOMY_99287.setDescription('Inherited blast name: enterobacteria')
+vocabulary_term_NCBI_TAXONOMY_99287.setLabel('Salmonella enterica subsp. enterica serovar Typhimurium str. LT2')
+vocabulary_term_NCBI_TAXONOMY_99287.setOrdinal(15)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_99287)
+
+vocabulary_term_NCBI_TAXONOMY_4896 = tr.createNewVocabularyTerm('4896')
+vocabulary_term_NCBI_TAXONOMY_4896.setDescription('Genbank common name: fission yeast\ Inherited blast name: ascomycetes')
+vocabulary_term_NCBI_TAXONOMY_4896.setLabel('Schizosaccharomyces pombe')
+vocabulary_term_NCBI_TAXONOMY_4896.setOrdinal(16)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_4896)
+
+vocabulary_term_NCBI_TAXONOMY_4897 = tr.createNewVocabularyTerm('4897')
+vocabulary_term_NCBI_TAXONOMY_4897.setDescription('Inherited blast name: ascomycetes')
+vocabulary_term_NCBI_TAXONOMY_4897.setLabel('Schizosaccharomyces japonicus')
+vocabulary_term_NCBI_TAXONOMY_4897.setOrdinal(17)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_4897)
+
+vocabulary_term_NCBI_TAXONOMY_7955 = tr.createNewVocabularyTerm('7955')
+vocabulary_term_NCBI_TAXONOMY_7955.setDescription('Genbank common name: zebrafish\ Inherited blast name: bony fishes')
+vocabulary_term_NCBI_TAXONOMY_7955.setLabel('Danio rerio')
+vocabulary_term_NCBI_TAXONOMY_7955.setOrdinal(18)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_7955)
+
+vocabulary_term_NCBI_TAXONOMY_3702 = tr.createNewVocabularyTerm('3702')
+vocabulary_term_NCBI_TAXONOMY_3702.setDescription('Genbank common name: thale cress\ Inherited blast name: eudicots')
+vocabulary_term_NCBI_TAXONOMY_3702.setLabel('Arabidopsis thaliana')
+vocabulary_term_NCBI_TAXONOMY_3702.setOrdinal(19)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_3702)
+
+vocabulary_term_NCBI_TAXONOMY_225322 = tr.createNewVocabularyTerm('225322')
+vocabulary_term_NCBI_TAXONOMY_225322.setDescription('Bacterium which infects Daphnia\ Pasteuria ramosa Metchnikoff 1888 (Approved Lists 1980) emend. Starr et al. 1986\ Ebert D, Rainey P, Embley TM, Scholz D. Development, life\ cycle, ultrastructure and phylogenetic position of Pasteuria ramosa Metchnikoff 1888: rediscovery of an obligate \ endoparasite of Daphnia magna Straus. Philos Trans R Soc \ Lond Ser B. 1996;351:1689.')
+vocabulary_term_NCBI_TAXONOMY_225322.setLabel('Pasteuria ramosa')
+vocabulary_term_NCBI_TAXONOMY_225322.setOrdinal(20)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_225322)
+
+vocabulary_term_NCBI_TAXONOMY_9913 = tr.createNewVocabularyTerm('9913')
+vocabulary_term_NCBI_TAXONOMY_9913.setDescription('Genbank common name: cattle\ Inherited blast name: even-toed ungulates')
+vocabulary_term_NCBI_TAXONOMY_9913.setLabel('Bos taurus')
+vocabulary_term_NCBI_TAXONOMY_9913.setOrdinal(21)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_9913)
+
+vocabulary_term_NCBI_TAXONOMY_9823 = tr.createNewVocabularyTerm('9823')
+vocabulary_term_NCBI_TAXONOMY_9823.setDescription('Genbank common name: pig\ Inherited blast name: even-toed ungulates')
+vocabulary_term_NCBI_TAXONOMY_9823.setLabel('Sus scrofa')
+vocabulary_term_NCBI_TAXONOMY_9823.setOrdinal(22)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_9823)
+
+vocabulary_term_NCBI_TAXONOMY_9940 = tr.createNewVocabularyTerm('9940')
+vocabulary_term_NCBI_TAXONOMY_9940.setDescription('Genbank common name: sheep\ Inherited blast name: even-toed ungulates')
+vocabulary_term_NCBI_TAXONOMY_9940.setLabel('Ovis aries')
+vocabulary_term_NCBI_TAXONOMY_9940.setOrdinal(23)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_9940)
+
+vocabulary_term_NCBI_TAXONOMY_9925 = tr.createNewVocabularyTerm('9925')
+vocabulary_term_NCBI_TAXONOMY_9925.setDescription('Genbank common name: goat\ Inherited blast name: even-toed ungulates')
+vocabulary_term_NCBI_TAXONOMY_9925.setLabel('Capra hircus')
+vocabulary_term_NCBI_TAXONOMY_9925.setOrdinal(24)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_9925)
+
+vocabulary_term_NCBI_TAXONOMY_8153 = tr.createNewVocabularyTerm('8153')
+vocabulary_term_NCBI_TAXONOMY_8153.setDescription('Common name: cichlid fish')
+vocabulary_term_NCBI_TAXONOMY_8153.setLabel('Haplochromis burtoni')
+vocabulary_term_NCBI_TAXONOMY_8153.setOrdinal(25)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_8153)
+
+vocabulary_term_NCBI_TAXONOMY_61818 = tr.createNewVocabularyTerm('61818')
+vocabulary_term_NCBI_TAXONOMY_61818.setDescription('Common name: bony fish')
+vocabulary_term_NCBI_TAXONOMY_61818.setLabel('Amphilophus (nicaraguan)')
+vocabulary_term_NCBI_TAXONOMY_61818.setOrdinal(26)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_61818)
+
+vocabulary_term_NCBI_TAXONOMY_35525 = tr.createNewVocabularyTerm('35525')
+vocabulary_term_NCBI_TAXONOMY_35525.setDescription('Common name: water flea')
+vocabulary_term_NCBI_TAXONOMY_35525.setLabel('Daphnia Magna')
+vocabulary_term_NCBI_TAXONOMY_35525.setOrdinal(27)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_35525)
+
+vocabulary_term_NCBI_TAXONOMY_4081 = tr.createNewVocabularyTerm('4081')
+vocabulary_term_NCBI_TAXONOMY_4081.setDescription('Common Name: tomato')
+vocabulary_term_NCBI_TAXONOMY_4081.setLabel('Solanum lycopersicum (tomato)')
+vocabulary_term_NCBI_TAXONOMY_4081.setOrdinal(28)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_4081)
+
+vocabulary_term_NCBI_TAXONOMY_13068 = tr.createNewVocabularyTerm('13068')
+vocabulary_term_NCBI_TAXONOMY_13068.setDescription('Common name: earwig')
+vocabulary_term_NCBI_TAXONOMY_13068.setLabel('Forficula auricularia (earwig)')
+vocabulary_term_NCBI_TAXONOMY_13068.setOrdinal(29)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_13068)
+
+vocabulary_term_NCBI_TAXONOMY_3569 = tr.createNewVocabularyTerm('3569')
+vocabulary_term_NCBI_TAXONOMY_3569.setDescription('Genbank common name: clove pink')
+vocabulary_term_NCBI_TAXONOMY_3569.setLabel('Dianthus')
+vocabulary_term_NCBI_TAXONOMY_3569.setOrdinal(30)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_3569)
+
+vocabulary_term_NCBI_TAXONOMY_3573 = tr.createNewVocabularyTerm('3573')
+vocabulary_term_NCBI_TAXONOMY_3573.setDescription('Genbank common name: campions\ Inherited blast name: eudicots')
+vocabulary_term_NCBI_TAXONOMY_3573.setLabel('Silene')
+vocabulary_term_NCBI_TAXONOMY_3573.setOrdinal(31)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_3573)
+
+vocabulary_term_NCBI_TAXONOMY_32644 = tr.createNewVocabularyTerm('32644')
+vocabulary_term_NCBI_TAXONOMY_32644.setDescription('Inherited blast name: unclassified')
+vocabulary_term_NCBI_TAXONOMY_32644.setLabel('unidentified')
+vocabulary_term_NCBI_TAXONOMY_32644.setOrdinal(32)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_32644)
+
+vocabulary_term_NCBI_TAXONOMY_0000 = tr.createNewVocabularyTerm('0000')
+vocabulary_term_NCBI_TAXONOMY_0000.setDescription(None)
+vocabulary_term_NCBI_TAXONOMY_0000.setLabel('OTHER')
+vocabulary_term_NCBI_TAXONOMY_0000.setOrdinal(33)
+vocabulary_NCBI_TAXONOMY.addTerm(vocabulary_term_NCBI_TAXONOMY_0000)
+
+vocabulary_PIPELINE_VERSION = tr.getOrCreateNewVocabulary('PIPELINE_VERSION')
+vocabulary_PIPELINE_VERSION.setDescription('With which pipeline version has the data been analyzed?')
+vocabulary_PIPELINE_VERSION.setUrlTemplate(None)
+vocabulary_PIPELINE_VERSION.setManagedInternally(False)
+vocabulary_PIPELINE_VERSION.setInternalNamespace(False)
+vocabulary_PIPELINE_VERSION.setChosenFromList(True)
+
+vocabulary_term_PIPELINE_VERSION_11348 = tr.createNewVocabularyTerm('1.13.48')
+vocabulary_term_PIPELINE_VERSION_11348.setDescription(None)
+vocabulary_term_PIPELINE_VERSION_11348.setLabel('RTA 1.13.48')
+vocabulary_term_PIPELINE_VERSION_11348.setOrdinal(1)
+vocabulary_PIPELINE_VERSION.addTerm(vocabulary_term_PIPELINE_VERSION_11348)
+
+vocabulary_term_PIPELINE_VERSION_11242 = tr.createNewVocabularyTerm('1.12.4.2')
+vocabulary_term_PIPELINE_VERSION_11242.setDescription('Real Time Analysis in combination with HCS 1.4.8')
+vocabulary_term_PIPELINE_VERSION_11242.setLabel('RTA 1.12.4.2 (HiSeq 2000)')
+vocabulary_term_PIPELINE_VERSION_11242.setOrdinal(2)
+vocabulary_PIPELINE_VERSION.addTerm(vocabulary_term_PIPELINE_VERSION_11242)
+
+vocabulary_term_PIPELINE_VERSION_112 = tr.createNewVocabularyTerm('1.12')
+vocabulary_term_PIPELINE_VERSION_112.setDescription('Real Time Analysis 1.12 HiSeq 2000')
+vocabulary_term_PIPELINE_VERSION_112.setLabel('RTA 1.12')
+vocabulary_term_PIPELINE_VERSION_112.setOrdinal(3)
+vocabulary_PIPELINE_VERSION.addTerm(vocabulary_term_PIPELINE_VERSION_112)
+
+vocabulary_term_PIPELINE_VERSION_19 = tr.createNewVocabularyTerm('1.9')
+vocabulary_term_PIPELINE_VERSION_19.setDescription('Real Time Analysis 1.9')
+vocabulary_term_PIPELINE_VERSION_19.setLabel('RTA 1.9 (GA IIx)')
+vocabulary_term_PIPELINE_VERSION_19.setOrdinal(4)
+vocabulary_PIPELINE_VERSION.addTerm(vocabulary_term_PIPELINE_VERSION_19)
+
+vocabulary_term_PIPELINE_VERSION_RTA_18 = tr.createNewVocabularyTerm('RTA_1.8')
+vocabulary_term_PIPELINE_VERSION_RTA_18.setDescription('Real Time Analysis 1.8')
+vocabulary_term_PIPELINE_VERSION_RTA_18.setLabel('RTA 1.8')
+vocabulary_term_PIPELINE_VERSION_RTA_18.setOrdinal(5)
+vocabulary_PIPELINE_VERSION.addTerm(vocabulary_term_PIPELINE_VERSION_RTA_18)
+
+vocabulary_term_PIPELINE_VERSION_RTA_16 = tr.createNewVocabularyTerm('RTA_1.6')
+vocabulary_term_PIPELINE_VERSION_RTA_16.setDescription('Real Time Analysis 1.6')
+vocabulary_term_PIPELINE_VERSION_RTA_16.setLabel('RTA 1.6')
+vocabulary_term_PIPELINE_VERSION_RTA_16.setOrdinal(6)
+vocabulary_PIPELINE_VERSION.addTerm(vocabulary_term_PIPELINE_VERSION_RTA_16)
+
+vocabulary_term_PIPELINE_VERSION_RTA_15 = tr.createNewVocabularyTerm('RTA_1.5')
+vocabulary_term_PIPELINE_VERSION_RTA_15.setDescription(None)
+vocabulary_term_PIPELINE_VERSION_RTA_15.setLabel('RTA 1.5')
+vocabulary_term_PIPELINE_VERSION_RTA_15.setOrdinal(7)
+vocabulary_PIPELINE_VERSION.addTerm(vocabulary_term_PIPELINE_VERSION_RTA_15)
+
+vocabulary_term_PIPELINE_VERSION_RTA_14150 = tr.createNewVocabularyTerm('RTA_1.4.15.0')
+vocabulary_term_PIPELINE_VERSION_RTA_14150.setDescription(None)
+vocabulary_term_PIPELINE_VERSION_RTA_14150.setLabel('RTA 1.4.15.0')
+vocabulary_term_PIPELINE_VERSION_RTA_14150.setOrdinal(8)
+vocabulary_PIPELINE_VERSION.addTerm(vocabulary_term_PIPELINE_VERSION_RTA_14150)
+
+vocabulary_term_PIPELINE_VERSION_15 = tr.createNewVocabularyTerm('1.5')
+vocabulary_term_PIPELINE_VERSION_15.setDescription(None)
+vocabulary_term_PIPELINE_VERSION_15.setLabel(None)
+vocabulary_term_PIPELINE_VERSION_15.setOrdinal(9)
+vocabulary_PIPELINE_VERSION.addTerm(vocabulary_term_PIPELINE_VERSION_15)
+
+vocabulary_term_PIPELINE_VERSION_14 = tr.createNewVocabularyTerm('1.4')
+vocabulary_term_PIPELINE_VERSION_14.setDescription(None)
+vocabulary_term_PIPELINE_VERSION_14.setLabel(None)
+vocabulary_term_PIPELINE_VERSION_14.setOrdinal(10)
+vocabulary_PIPELINE_VERSION.addTerm(vocabulary_term_PIPELINE_VERSION_14)
+
+vocabulary_term_PIPELINE_VERSION_132 = tr.createNewVocabularyTerm('1.3.2')
+vocabulary_term_PIPELINE_VERSION_132.setDescription(None)
+vocabulary_term_PIPELINE_VERSION_132.setLabel(None)
+vocabulary_term_PIPELINE_VERSION_132.setOrdinal(11)
+vocabulary_PIPELINE_VERSION.addTerm(vocabulary_term_PIPELINE_VERSION_132)
+
+vocabulary_term_PIPELINE_VERSION_10 = tr.createNewVocabularyTerm('1.0')
+vocabulary_term_PIPELINE_VERSION_10.setDescription(None)
+vocabulary_term_PIPELINE_VERSION_10.setLabel(None)
+vocabulary_term_PIPELINE_VERSION_10.setOrdinal(12)
+vocabulary_PIPELINE_VERSION.addTerm(vocabulary_term_PIPELINE_VERSION_10)
+
+vocabulary_term_PIPELINE_VERSION_PRE_10 = tr.createNewVocabularyTerm('PRE_1.0')
+vocabulary_term_PIPELINE_VERSION_PRE_10.setDescription('Before Pipeline Version 1.0')
+vocabulary_term_PIPELINE_VERSION_PRE_10.setLabel(None)
+vocabulary_term_PIPELINE_VERSION_PRE_10.setOrdinal(13)
+vocabulary_PIPELINE_VERSION.addTerm(vocabulary_term_PIPELINE_VERSION_PRE_10)
+
+vocabulary_term_PIPELINE_VERSION_NONE = tr.createNewVocabularyTerm('NONE')
+vocabulary_term_PIPELINE_VERSION_NONE.setDescription(None)
+vocabulary_term_PIPELINE_VERSION_NONE.setLabel(None)
+vocabulary_term_PIPELINE_VERSION_NONE.setOrdinal(14)
+vocabulary_PIPELINE_VERSION.addTerm(vocabulary_term_PIPELINE_VERSION_NONE)
+
+vocabulary_SAMPLE_TYPE = tr.getOrCreateNewVocabulary('SAMPLE_TYPE')
+vocabulary_SAMPLE_TYPE.setDescription('Type of sample delivered by the customer')
+vocabulary_SAMPLE_TYPE.setUrlTemplate(None)
+vocabulary_SAMPLE_TYPE.setManagedInternally(False)
+vocabulary_SAMPLE_TYPE.setInternalNamespace(False)
+vocabulary_SAMPLE_TYPE.setChosenFromList(True)
+
+vocabulary_term_SAMPLE_TYPE_PROCESSED_DNA_LIBRARY = tr.createNewVocabularyTerm('PROCESSED_DNA_LIBRARY')
+vocabulary_term_SAMPLE_TYPE_PROCESSED_DNA_LIBRARY.setDescription(None)
+vocabulary_term_SAMPLE_TYPE_PROCESSED_DNA_LIBRARY.setLabel(None)
+vocabulary_term_SAMPLE_TYPE_PROCESSED_DNA_LIBRARY.setOrdinal(1)
+vocabulary_SAMPLE_TYPE.addTerm(vocabulary_term_SAMPLE_TYPE_PROCESSED_DNA_LIBRARY)
+
+vocabulary_term_SAMPLE_TYPE_POOLED_SAMPLE = tr.createNewVocabularyTerm('POOLED_SAMPLE')
+vocabulary_term_SAMPLE_TYPE_POOLED_SAMPLE.setDescription(None)
+vocabulary_term_SAMPLE_TYPE_POOLED_SAMPLE.setLabel(None)
+vocabulary_term_SAMPLE_TYPE_POOLED_SAMPLE.setOrdinal(2)
+vocabulary_SAMPLE_TYPE.addTerm(vocabulary_term_SAMPLE_TYPE_POOLED_SAMPLE)
+
+vocabulary_term_SAMPLE_TYPE_GENOMIC_DNA = tr.createNewVocabularyTerm('GENOMIC_DNA')
+vocabulary_term_SAMPLE_TYPE_GENOMIC_DNA.setDescription(None)
+vocabulary_term_SAMPLE_TYPE_GENOMIC_DNA.setLabel(None)
+vocabulary_term_SAMPLE_TYPE_GENOMIC_DNA.setOrdinal(3)
+vocabulary_SAMPLE_TYPE.addTerm(vocabulary_term_SAMPLE_TYPE_GENOMIC_DNA)
+
+vocabulary_term_SAMPLE_TYPE_SMALL_RNA = tr.createNewVocabularyTerm('SMALL_RNA')
+vocabulary_term_SAMPLE_TYPE_SMALL_RNA.setDescription(None)
+vocabulary_term_SAMPLE_TYPE_SMALL_RNA.setLabel(None)
+vocabulary_term_SAMPLE_TYPE_SMALL_RNA.setOrdinal(4)
+vocabulary_SAMPLE_TYPE.addTerm(vocabulary_term_SAMPLE_TYPE_SMALL_RNA)
+
+vocabulary_term_SAMPLE_TYPE_TOTAL_RNA = tr.createNewVocabularyTerm('TOTAL_RNA')
+vocabulary_term_SAMPLE_TYPE_TOTAL_RNA.setDescription(None)
+vocabulary_term_SAMPLE_TYPE_TOTAL_RNA.setLabel(None)
+vocabulary_term_SAMPLE_TYPE_TOTAL_RNA.setOrdinal(5)
+vocabulary_SAMPLE_TYPE.addTerm(vocabulary_term_SAMPLE_TYPE_TOTAL_RNA)
+
+vocabulary_term_SAMPLE_TYPE_CHIP = tr.createNewVocabularyTerm('CHIP')
+vocabulary_term_SAMPLE_TYPE_CHIP.setDescription(None)
+vocabulary_term_SAMPLE_TYPE_CHIP.setLabel(None)
+vocabulary_term_SAMPLE_TYPE_CHIP.setOrdinal(6)
+vocabulary_SAMPLE_TYPE.addTerm(vocabulary_term_SAMPLE_TYPE_CHIP)
+
+vocabulary_term_SAMPLE_TYPE_VIRAL = tr.createNewVocabularyTerm('VIRAL')
+vocabulary_term_SAMPLE_TYPE_VIRAL.setDescription(None)
+vocabulary_term_SAMPLE_TYPE_VIRAL.setLabel(None)
+vocabulary_term_SAMPLE_TYPE_VIRAL.setOrdinal(7)
+vocabulary_SAMPLE_TYPE.addTerm(vocabulary_term_SAMPLE_TYPE_VIRAL)
+
+vocabulary_term_SAMPLE_TYPE_SYNTHETIC = tr.createNewVocabularyTerm('SYNTHETIC')
+vocabulary_term_SAMPLE_TYPE_SYNTHETIC.setDescription(None)
+vocabulary_term_SAMPLE_TYPE_SYNTHETIC.setLabel(None)
+vocabulary_term_SAMPLE_TYPE_SYNTHETIC.setOrdinal(8)
+vocabulary_SAMPLE_TYPE.addTerm(vocabulary_term_SAMPLE_TYPE_SYNTHETIC)
+
+vocabulary_term_SAMPLE_TYPE_FRAGMENTED_GENOMIC_DNA = tr.createNewVocabularyTerm('FRAGMENTED_GENOMIC_DNA')
+vocabulary_term_SAMPLE_TYPE_FRAGMENTED_GENOMIC_DNA.setDescription(None)
+vocabulary_term_SAMPLE_TYPE_FRAGMENTED_GENOMIC_DNA.setLabel(None)
+vocabulary_term_SAMPLE_TYPE_FRAGMENTED_GENOMIC_DNA.setOrdinal(9)
+vocabulary_SAMPLE_TYPE.addTerm(vocabulary_term_SAMPLE_TYPE_FRAGMENTED_GENOMIC_DNA)
+
+vocabulary_term_SAMPLE_TYPE_MRNA = tr.createNewVocabularyTerm('MRNA')
+vocabulary_term_SAMPLE_TYPE_MRNA.setDescription(None)
+vocabulary_term_SAMPLE_TYPE_MRNA.setLabel(None)
+vocabulary_term_SAMPLE_TYPE_MRNA.setOrdinal(10)
+vocabulary_SAMPLE_TYPE.addTerm(vocabulary_term_SAMPLE_TYPE_MRNA)
+
+vocabulary_term_SAMPLE_TYPE_OTHER = tr.createNewVocabularyTerm('OTHER')
+vocabulary_term_SAMPLE_TYPE_OTHER.setDescription(None)
+vocabulary_term_SAMPLE_TYPE_OTHER.setLabel(None)
+vocabulary_term_SAMPLE_TYPE_OTHER.setOrdinal(11)
+vocabulary_SAMPLE_TYPE.addTerm(vocabulary_term_SAMPLE_TYPE_OTHER)
+
+vocabulary_term_SAMPLE_TYPE_BISULFITE_CHIP = tr.createNewVocabularyTerm('BISULFITE_CHIP')
+vocabulary_term_SAMPLE_TYPE_BISULFITE_CHIP.setDescription(None)
+vocabulary_term_SAMPLE_TYPE_BISULFITE_CHIP.setLabel(None)
+vocabulary_term_SAMPLE_TYPE_BISULFITE_CHIP.setOrdinal(13)
+vocabulary_SAMPLE_TYPE.addTerm(vocabulary_term_SAMPLE_TYPE_BISULFITE_CHIP)
+
+vocabulary_term_SAMPLE_TYPE_NONGENOMIC = tr.createNewVocabularyTerm('NON-GENOMIC')
+vocabulary_term_SAMPLE_TYPE_NONGENOMIC.setDescription(None)
+vocabulary_term_SAMPLE_TYPE_NONGENOMIC.setLabel(None)
+vocabulary_term_SAMPLE_TYPE_NONGENOMIC.setOrdinal(14)
+vocabulary_SAMPLE_TYPE.addTerm(vocabulary_term_SAMPLE_TYPE_NONGENOMIC)
+
+vocabulary_term_SAMPLE_TYPE_BISULFITE_TREATED = tr.createNewVocabularyTerm('BISULFITE_TREATED')
+vocabulary_term_SAMPLE_TYPE_BISULFITE_TREATED.setDescription(None)
+vocabulary_term_SAMPLE_TYPE_BISULFITE_TREATED.setLabel(None)
+vocabulary_term_SAMPLE_TYPE_BISULFITE_TREATED.setOrdinal(15)
+vocabulary_SAMPLE_TYPE.addTerm(vocabulary_term_SAMPLE_TYPE_BISULFITE_TREATED)
+
+vocabulary_SBS_SEQUENCING_KIT_VERSION = tr.getOrCreateNewVocabulary('SBS_SEQUENCING_KIT_VERSION')
+vocabulary_SBS_SEQUENCING_KIT_VERSION.setDescription('Version of the Sequencing by Synthesis (SBS) Kit')
+vocabulary_SBS_SEQUENCING_KIT_VERSION.setUrlTemplate(None)
+vocabulary_SBS_SEQUENCING_KIT_VERSION.setManagedInternally(False)
+vocabulary_SBS_SEQUENCING_KIT_VERSION.setInternalNamespace(False)
+vocabulary_SBS_SEQUENCING_KIT_VERSION.setChosenFromList(True)
+
+vocabulary_term_SBS_SEQUENCING_KIT_VERSION_TRUSEQ_V5 = tr.createNewVocabularyTerm('TRUSEQ_V5')
+vocabulary_term_SBS_SEQUENCING_KIT_VERSION_TRUSEQ_V5.setDescription(None)
+vocabulary_term_SBS_SEQUENCING_KIT_VERSION_TRUSEQ_V5.setLabel('TruSeq v5')
+vocabulary_term_SBS_SEQUENCING_KIT_VERSION_TRUSEQ_V5.setOrdinal(1)
+vocabulary_SBS_SEQUENCING_KIT_VERSION.addTerm(vocabulary_term_SBS_SEQUENCING_KIT_VERSION_TRUSEQ_V5)
+
+vocabulary_term_SBS_SEQUENCING_KIT_VERSION_V5 = tr.createNewVocabularyTerm('V5')
+vocabulary_term_SBS_SEQUENCING_KIT_VERSION_V5.setDescription(None)
+vocabulary_term_SBS_SEQUENCING_KIT_VERSION_V5.setLabel(None)
+vocabulary_term_SBS_SEQUENCING_KIT_VERSION_V5.setOrdinal(2)
+vocabulary_SBS_SEQUENCING_KIT_VERSION.addTerm(vocabulary_term_SBS_SEQUENCING_KIT_VERSION_V5)
+
+vocabulary_term_SBS_SEQUENCING_KIT_VERSION_V4 = tr.createNewVocabularyTerm('V4')
+vocabulary_term_SBS_SEQUENCING_KIT_VERSION_V4.setDescription(None)
+vocabulary_term_SBS_SEQUENCING_KIT_VERSION_V4.setLabel(None)
+vocabulary_term_SBS_SEQUENCING_KIT_VERSION_V4.setOrdinal(3)
+vocabulary_SBS_SEQUENCING_KIT_VERSION.addTerm(vocabulary_term_SBS_SEQUENCING_KIT_VERSION_V4)
+
+vocabulary_term_SBS_SEQUENCING_KIT_VERSION_V3 = tr.createNewVocabularyTerm('V3')
+vocabulary_term_SBS_SEQUENCING_KIT_VERSION_V3.setDescription(None)
+vocabulary_term_SBS_SEQUENCING_KIT_VERSION_V3.setLabel(None)
+vocabulary_term_SBS_SEQUENCING_KIT_VERSION_V3.setOrdinal(4)
+vocabulary_SBS_SEQUENCING_KIT_VERSION.addTerm(vocabulary_term_SBS_SEQUENCING_KIT_VERSION_V3)
+
+vocabulary_term_SBS_SEQUENCING_KIT_VERSION_SBS_HS_V3 = tr.createNewVocabularyTerm('SBS_HS_V3')
+vocabulary_term_SBS_SEQUENCING_KIT_VERSION_SBS_HS_V3.setDescription(None)
+vocabulary_term_SBS_SEQUENCING_KIT_VERSION_SBS_HS_V3.setLabel('TruSeq SBS HS v3')
+vocabulary_term_SBS_SEQUENCING_KIT_VERSION_SBS_HS_V3.setOrdinal(5)
+vocabulary_SBS_SEQUENCING_KIT_VERSION.addTerm(vocabulary_term_SBS_SEQUENCING_KIT_VERSION_SBS_HS_V3)
+
+vocabulary_SEQUENCER = tr.getOrCreateNewVocabulary('SEQUENCER')
+vocabulary_SEQUENCER.setDescription('Which Sequencer was used?')
+vocabulary_SEQUENCER.setUrlTemplate(None)
+vocabulary_SEQUENCER.setManagedInternally(False)
+vocabulary_SEQUENCER.setInternalNamespace(False)
+vocabulary_SEQUENCER.setChosenFromList(True)
+
+vocabulary_term_SEQUENCER_M00721 = tr.createNewVocabularyTerm('M00721')
+vocabulary_term_SEQUENCER_M00721.setDescription(None)
+vocabulary_term_SEQUENCER_M00721.setLabel('MiSeq')
+vocabulary_term_SEQUENCER_M00721.setOrdinal(6)
+vocabulary_SEQUENCER.addTerm(vocabulary_term_SEQUENCER_M00721)
+
+vocabulary_term_SEQUENCER_SN792 = tr.createNewVocabularyTerm('SN792')
+vocabulary_term_SEQUENCER_SN792.setDescription(None)
+vocabulary_term_SEQUENCER_SN792.setLabel('HiSeq 2000')
+vocabulary_term_SEQUENCER_SN792.setOrdinal(7)
+vocabulary_SEQUENCER.addTerm(vocabulary_term_SEQUENCER_SN792)
+
+vocabulary_SEQUENCING_APPLICATION = tr.getOrCreateNewVocabulary('SEQUENCING_APPLICATION')
+vocabulary_SEQUENCING_APPLICATION.setDescription('Type of experiment of the High Throughput Sequencing applications')
+vocabulary_SEQUENCING_APPLICATION.setUrlTemplate(None)
+vocabulary_SEQUENCING_APPLICATION.setManagedInternally(False)
+vocabulary_SEQUENCING_APPLICATION.setInternalNamespace(False)
+vocabulary_SEQUENCING_APPLICATION.setChosenFromList(True)
+
+vocabulary_term_SEQUENCING_APPLICATION_SMALL_RNA_SEQ = tr.createNewVocabularyTerm('SMALL_RNA_SEQ')
+vocabulary_term_SEQUENCING_APPLICATION_SMALL_RNA_SEQ.setDescription(None)
+vocabulary_term_SEQUENCING_APPLICATION_SMALL_RNA_SEQ.setLabel(None)
+vocabulary_term_SEQUENCING_APPLICATION_SMALL_RNA_SEQ.setOrdinal(1)
+vocabulary_SEQUENCING_APPLICATION.addTerm(vocabulary_term_SEQUENCING_APPLICATION_SMALL_RNA_SEQ)
+
+vocabulary_term_SEQUENCING_APPLICATION_RNA_SEQ = tr.createNewVocabularyTerm('RNA_SEQ')
+vocabulary_term_SEQUENCING_APPLICATION_RNA_SEQ.setDescription(None)
+vocabulary_term_SEQUENCING_APPLICATION_RNA_SEQ.setLabel(None)
+vocabulary_term_SEQUENCING_APPLICATION_RNA_SEQ.setOrdinal(2)
+vocabulary_SEQUENCING_APPLICATION.addTerm(vocabulary_term_SEQUENCING_APPLICATION_RNA_SEQ)
+
+vocabulary_term_SEQUENCING_APPLICATION_GENOMIC_DNA_SEQ = tr.createNewVocabularyTerm('GENOMIC_DNA_SEQ')
+vocabulary_term_SEQUENCING_APPLICATION_GENOMIC_DNA_SEQ.setDescription(None)
+vocabulary_term_SEQUENCING_APPLICATION_GENOMIC_DNA_SEQ.setLabel(None)
+vocabulary_term_SEQUENCING_APPLICATION_GENOMIC_DNA_SEQ.setOrdinal(3)
+vocabulary_SEQUENCING_APPLICATION.addTerm(vocabulary_term_SEQUENCING_APPLICATION_GENOMIC_DNA_SEQ)
+
+vocabulary_term_SEQUENCING_APPLICATION_CHIP_SEQ = tr.createNewVocabularyTerm('CHIP_SEQ')
+vocabulary_term_SEQUENCING_APPLICATION_CHIP_SEQ.setDescription(None)
+vocabulary_term_SEQUENCING_APPLICATION_CHIP_SEQ.setLabel(None)
+vocabulary_term_SEQUENCING_APPLICATION_CHIP_SEQ.setOrdinal(4)
+vocabulary_SEQUENCING_APPLICATION.addTerm(vocabulary_term_SEQUENCING_APPLICATION_CHIP_SEQ)
+
+vocabulary_YES_NO = tr.getOrCreateNewVocabulary('YES_NO')
+vocabulary_YES_NO.setDescription('Just offers YES or NO')
+vocabulary_YES_NO.setUrlTemplate(None)
+vocabulary_YES_NO.setManagedInternally(False)
+vocabulary_YES_NO.setInternalNamespace(False)
+vocabulary_YES_NO.setChosenFromList(True)
+
+vocabulary_term_YES_NO_YES = tr.createNewVocabularyTerm('YES')
+vocabulary_term_YES_NO_YES.setDescription(None)
+vocabulary_term_YES_NO_YES.setLabel(None)
+vocabulary_term_YES_NO_YES.setOrdinal(1)
+vocabulary_YES_NO.addTerm(vocabulary_term_YES_NO_YES)
+
+vocabulary_term_YES_NO_NO = tr.createNewVocabularyTerm('NO')
+vocabulary_term_YES_NO_NO.setDescription(None)
+vocabulary_term_YES_NO_NO.setLabel(None)
+vocabulary_term_YES_NO_NO.setOrdinal(2)
+vocabulary_YES_NO.addTerm(vocabulary_term_YES_NO_NO)
+
+print "Imported 22 Vocabularies"
+script_Diff_time = tr.getOrCreateNewScript('Diff_time')
+script_Diff_time.setName('Diff_time')
+script_Diff_time.setDescription('Calculates the difference of two given dates')
+script_Diff_time.setScript('''from datetime import datetime
+
+def dateTimeSplitter(openbisDate):
+ dateAndTime, tz = openbisDate.rsplit(" ", 1)
+ pythonDateTime = datetime.strptime(dateAndTime, "%Y-%m-%d %H:%M:%S")
+ return pythonDateTime
+
+def calculate():
+
+ try:
+ start = dateTimeSplitter(entity.propertyValue('FLOW_CELL_SEQUENCED_ON'))
+ end = dateTimeSplitter(entity.propertyValue('SEQUENCER_FINISHED'))
+ diffTime = end-start
+ return str(diffTime)
+ except:
+ return "N/A"
+''')
+script_Diff_time.setEntityForScript('SAMPLE')
+script_Diff_time.setScriptType('DYNAMIC_PROPERTY')
+
+script_Has_Parents = tr.getOrCreateNewScript('Has_Parents')
+script_Has_Parents.setName('Has_Parents')
+script_Has_Parents.setDescription('Check if the Entity has a parent')
+script_Has_Parents.setScript('''def validate(entity, isNew):
+ parents = entity.entityPE().parents
+ if parents:
+ return None
+ else:
+ return "No Parents have been selected!"
+''')
+script_Has_Parents.setEntityForScript('SAMPLE')
+script_Has_Parents.setScriptType('ENTITY_VALIDATION')
+
+print "Imported 2 Scripts"
+exp_type_HT_SEQUENCING = tr.getOrCreateNewExperimentType('HT_SEQUENCING')
+exp_type_HT_SEQUENCING.setDescription('High Throughput Sequencing (e.g. Illumina HiSeq, Illumina GA)')
+
+
+print "Imported 1 Experiment Types"
+samp_type_ILLUMINA_FLOW_CELL = tr.getOrCreateNewSampleType('ILLUMINA_FLOW_CELL')
+samp_type_ILLUMINA_FLOW_CELL.setDescription('Container of ILLUMINA_FLOW_LANES\ Can be created automatically by a drop box and the properties can be filled from the RunInfo.xml and runParameters.xml files')
+samp_type_ILLUMINA_FLOW_CELL.setListable(True)
+samp_type_ILLUMINA_FLOW_CELL.setShowContainer(False)
+samp_type_ILLUMINA_FLOW_CELL.setShowParents(False)
+samp_type_ILLUMINA_FLOW_CELL.setSubcodeUnique(False)
+samp_type_ILLUMINA_FLOW_CELL.setAutoGeneratedCode(False)
+samp_type_ILLUMINA_FLOW_CELL.setShowParentMetadata(False)
+samp_type_ILLUMINA_FLOW_CELL.setGeneratedCodePrefix('FLOWCELL-')
+
+
+samp_type_ILLUMINA_FLOW_LANE = tr.getOrCreateNewSampleType('ILLUMINA_FLOW_LANE')
+samp_type_ILLUMINA_FLOW_LANE.setDescription('Child of LIBRARY or POOL')
+samp_type_ILLUMINA_FLOW_LANE.setListable(True)
+samp_type_ILLUMINA_FLOW_LANE.setShowContainer(True)
+samp_type_ILLUMINA_FLOW_LANE.setShowParents(True)
+samp_type_ILLUMINA_FLOW_LANE.setSubcodeUnique(False)
+samp_type_ILLUMINA_FLOW_LANE.setAutoGeneratedCode(False)
+samp_type_ILLUMINA_FLOW_LANE.setShowParentMetadata(True)
+samp_type_ILLUMINA_FLOW_LANE.setGeneratedCodePrefix('FLOWLANE-')
+
+
+samp_type_LIBRARY = tr.getOrCreateNewSampleType('LIBRARY')
+samp_type_LIBRARY.setDescription('Child of RAW and potential parent of POOL')
+samp_type_LIBRARY.setListable(True)
+samp_type_LIBRARY.setShowContainer(False)
+samp_type_LIBRARY.setShowParents(True)
+samp_type_LIBRARY.setSubcodeUnique(False)
+samp_type_LIBRARY.setAutoGeneratedCode(True)
+samp_type_LIBRARY.setShowParentMetadata(True)
+samp_type_LIBRARY.setGeneratedCodePrefix('BSSE-QGF-LIBRARY-')
+samp_type_LIBRARY.setValidationScript(script_Has_Parents)
+
+samp_type_LIBRARY_POOL = tr.getOrCreateNewSampleType('LIBRARY_POOL')
+samp_type_LIBRARY_POOL.setDescription('Child of several LIBRARY samples, used for multiplexing')
+samp_type_LIBRARY_POOL.setListable(True)
+samp_type_LIBRARY_POOL.setShowContainer(False)
+samp_type_LIBRARY_POOL.setShowParents(True)
+samp_type_LIBRARY_POOL.setSubcodeUnique(False)
+samp_type_LIBRARY_POOL.setAutoGeneratedCode(True)
+samp_type_LIBRARY_POOL.setShowParentMetadata(True)
+samp_type_LIBRARY_POOL.setGeneratedCodePrefix('BSSE-QGF-POOL-')
+samp_type_LIBRARY_POOL.setValidationScript(script_Has_Parents)
+
+samp_type_MASTER_SAMPLE = tr.getOrCreateNewSampleType('MASTER_SAMPLE')
+samp_type_MASTER_SAMPLE.setDescription('Sample Type holding Master Data and a parent to RAW')
+samp_type_MASTER_SAMPLE.setListable(True)
+samp_type_MASTER_SAMPLE.setShowContainer(False)
+samp_type_MASTER_SAMPLE.setShowParents(False)
+samp_type_MASTER_SAMPLE.setSubcodeUnique(False)
+samp_type_MASTER_SAMPLE.setAutoGeneratedCode(True)
+samp_type_MASTER_SAMPLE.setShowParentMetadata(False)
+samp_type_MASTER_SAMPLE.setGeneratedCodePrefix('BSSE-QGF-MASTER-')
+
+
+samp_type_RAW_SAMPLE = tr.getOrCreateNewSampleType('RAW_SAMPLE')
+samp_type_RAW_SAMPLE.setDescription('Child of MASTER')
+samp_type_RAW_SAMPLE.setListable(True)
+samp_type_RAW_SAMPLE.setShowContainer(False)
+samp_type_RAW_SAMPLE.setShowParents(True)
+samp_type_RAW_SAMPLE.setSubcodeUnique(False)
+samp_type_RAW_SAMPLE.setAutoGeneratedCode(True)
+samp_type_RAW_SAMPLE.setShowParentMetadata(True)
+samp_type_RAW_SAMPLE.setGeneratedCodePrefix('BSSE-QGF-RAW-')
+samp_type_RAW_SAMPLE.setValidationScript(script_Has_Parents)
+
+print "Imported 6 Sample Types"
+data_set_type_ALIGNMENT = tr.getOrCreateNewDataSetType('ALIGNMENT')
+data_set_type_ALIGNMENT.setDescription('Aligner ouput, ideally bam/sam')
+data_set_type_ALIGNMENT.setDataSetKind('PHYSICAL')
+data_set_type_ALIGNMENT.setMainDataSetPattern(None)
+data_set_type_ALIGNMENT.setMainDataSetPath(None)
+data_set_type_ALIGNMENT.setDeletionDisallowed(False)
+
+
+data_set_type_BASECALL_STATS = tr.getOrCreateNewDataSetType('BASECALL_STATS')
+data_set_type_BASECALL_STATS.setDescription('Base Call Statistics from the Illumina Pipeline (configureBclToFastq.pl)')
+data_set_type_BASECALL_STATS.setDataSetKind('PHYSICAL')
+data_set_type_BASECALL_STATS.setMainDataSetPattern(original/.*/.*/Demultiplex_Stats.htm)
+data_set_type_BASECALL_STATS.setMainDataSetPath(None)
+data_set_type_BASECALL_STATS.setDeletionDisallowed(False)
+
+
+data_set_type_BIGWIGGLE = tr.getOrCreateNewDataSetType('BIGWIGGLE')
+data_set_type_BIGWIGGLE.setDescription('Visualization')
+data_set_type_BIGWIGGLE.setDataSetKind('PHYSICAL')
+data_set_type_BIGWIGGLE.setMainDataSetPattern(None)
+data_set_type_BIGWIGGLE.setMainDataSetPath(None)
+data_set_type_BIGWIGGLE.setDeletionDisallowed(False)
+
+
+data_set_type_ELAND_ALIGNMENT = tr.getOrCreateNewDataSetType('ELAND_ALIGNMENT')
+data_set_type_ELAND_ALIGNMENT.setDescription('Illumina Eland Alignment Output')
+data_set_type_ELAND_ALIGNMENT.setDataSetKind('PHYSICAL')
+data_set_type_ELAND_ALIGNMENT.setMainDataSetPattern(None)
+data_set_type_ELAND_ALIGNMENT.setMainDataSetPath(None)
+data_set_type_ELAND_ALIGNMENT.setDeletionDisallowed(False)
+
+
+data_set_type_FASTQ_GZ = tr.getOrCreateNewDataSetType('FASTQ_GZ')
+data_set_type_FASTQ_GZ.setDescription('Gzipped Fastq file produced by Casava 1.8+')
+data_set_type_FASTQ_GZ.setDataSetKind('PHYSICAL')
+data_set_type_FASTQ_GZ.setMainDataSetPattern(None)
+data_set_type_FASTQ_GZ.setMainDataSetPath(None)
+data_set_type_FASTQ_GZ.setDeletionDisallowed(False)
+
+
+data_set_type_ILLUMINA_HISEQ_OUTPUT = tr.getOrCreateNewDataSetType('ILLUMINA_HISEQ_OUTPUT')
+data_set_type_ILLUMINA_HISEQ_OUTPUT.setDescription('HiSeq2000 Output')
+data_set_type_ILLUMINA_HISEQ_OUTPUT.setDataSetKind('PHYSICAL')
+data_set_type_ILLUMINA_HISEQ_OUTPUT.setMainDataSetPattern(None)
+data_set_type_ILLUMINA_HISEQ_OUTPUT.setMainDataSetPath(None)
+data_set_type_ILLUMINA_HISEQ_OUTPUT.setDeletionDisallowed(False)
+
+
+data_set_type_ILLUMINA_MISEQ_OUTPUT = tr.getOrCreateNewDataSetType('ILLUMINA_MISEQ_OUTPUT')
+data_set_type_ILLUMINA_MISEQ_OUTPUT.setDescription('MiSeq Output')
+data_set_type_ILLUMINA_MISEQ_OUTPUT.setDataSetKind('PHYSICAL')
+data_set_type_ILLUMINA_MISEQ_OUTPUT.setMainDataSetPattern(None)
+data_set_type_ILLUMINA_MISEQ_OUTPUT.setMainDataSetPath(None)
+data_set_type_ILLUMINA_MISEQ_OUTPUT.setDeletionDisallowed(False)
+
+
+data_set_type_MACS_OUTPUT = tr.getOrCreateNewDataSetType('MACS_OUTPUT')
+data_set_type_MACS_OUTPUT.setDescription('MACS Peak Caller output')
+data_set_type_MACS_OUTPUT.setDataSetKind('PHYSICAL')
+data_set_type_MACS_OUTPUT.setMainDataSetPattern(None)
+data_set_type_MACS_OUTPUT.setMainDataSetPath(None)
+data_set_type_MACS_OUTPUT.setDeletionDisallowed(False)
+
+
+data_set_type_QUALITY_JPGS = tr.getOrCreateNewDataSetType('QUALITY_JPGS')
+data_set_type_QUALITY_JPGS.setDescription('R generated Quality plots')
+data_set_type_QUALITY_JPGS.setDataSetKind('PHYSICAL')
+data_set_type_QUALITY_JPGS.setMainDataSetPattern(None)
+data_set_type_QUALITY_JPGS.setMainDataSetPath(None)
+data_set_type_QUALITY_JPGS.setDeletionDisallowed(False)
+
+
+data_set_type_QUALITY_PDFS = tr.getOrCreateNewDataSetType('QUALITY_PDFS')
+data_set_type_QUALITY_PDFS.setDescription('R generated pdfs showing quality data')
+data_set_type_QUALITY_PDFS.setDataSetKind('PHYSICAL')
+data_set_type_QUALITY_PDFS.setMainDataSetPattern(None)
+data_set_type_QUALITY_PDFS.setMainDataSetPath(None)
+data_set_type_QUALITY_PDFS.setDeletionDisallowed(False)
+
+
+data_set_type_QUALITY_SVG = tr.getOrCreateNewDataSetType('QUALITY_SVG')
+data_set_type_QUALITY_SVG.setDescription('R generated Quality plots')
+data_set_type_QUALITY_SVG.setDataSetKind('PHYSICAL')
+data_set_type_QUALITY_SVG.setMainDataSetPattern(None)
+data_set_type_QUALITY_SVG.setMainDataSetPath(None)
+data_set_type_QUALITY_SVG.setDeletionDisallowed(False)
+
+
+data_set_type_RUNINFO = tr.getOrCreateNewDataSetType('RUNINFO')
+data_set_type_RUNINFO.setDescription('Run statstics: Status.html and Status_Files folder')
+data_set_type_RUNINFO.setDataSetKind('PHYSICAL')
+data_set_type_RUNINFO.setMainDataSetPattern(original/.*/Data/Status.htm)
+data_set_type_RUNINFO.setMainDataSetPath(None)
+data_set_type_RUNINFO.setDeletionDisallowed(False)
+
+
+data_set_type_THUMBNAILS = tr.getOrCreateNewDataSetType('THUMBNAILS')
+data_set_type_THUMBNAILS.setDescription('Thumbnails provided by the Illumina software')
+data_set_type_THUMBNAILS.setDataSetKind('PHYSICAL')
+data_set_type_THUMBNAILS.setMainDataSetPattern(None)
+data_set_type_THUMBNAILS.setMainDataSetPath(None)
+data_set_type_THUMBNAILS.setDeletionDisallowed(False)
+
+
+data_set_type_TSV = tr.getOrCreateNewDataSetType('TSV')
+data_set_type_TSV.setDescription('Tab separated files')
+data_set_type_TSV.setDataSetKind('PHYSICAL')
+data_set_type_TSV.setMainDataSetPattern(None)
+data_set_type_TSV.setMainDataSetPath(None)
+data_set_type_TSV.setDeletionDisallowed(False)
+
+
+print "Imported 15 Data Set Types"
+print "Imported 0 Material Types"
+prop_type_AGILENT_KIT = tr.getOrCreateNewPropertyType('AGILENT_KIT', DataType.CONTROLLEDVOCABULARY)
+prop_type_AGILENT_KIT.setLabel('Agilent Kit')
+prop_type_AGILENT_KIT.setManagedInternally(False)
+prop_type_AGILENT_KIT.setInternalNamespace(False)
+
+prop_type_AGILENT_KIT.setVocabulary(vocabulary_AGILENT_KIT)
+
+prop_type_ALIGNMENT_SOFTWARE = tr.getOrCreateNewPropertyType('ALIGNMENT_SOFTWARE', DataType.CONTROLLEDVOCABULARY)
+prop_type_ALIGNMENT_SOFTWARE.setLabel('Alignment software')
+prop_type_ALIGNMENT_SOFTWARE.setManagedInternally(False)
+prop_type_ALIGNMENT_SOFTWARE.setInternalNamespace(False)
+
+prop_type_ALIGNMENT_SOFTWARE.setVocabulary(vocabulary_ALIGNMENT_SOFTWARE)
+
+prop_type_ANALYSIS_FINISHED = tr.getOrCreateNewPropertyType('ANALYSIS_FINISHED', DataType.TIMESTAMP)
+prop_type_ANALYSIS_FINISHED.setLabel('Analysis finished')
+prop_type_ANALYSIS_FINISHED.setManagedInternally(False)
+prop_type_ANALYSIS_FINISHED.setInternalNamespace(False)
+
+
+prop_type_BARCODE_COMPLEXITY_CHECKER = tr.getOrCreateNewPropertyType('BARCODE_COMPLEXITY_CHECKER', DataType.MULTILINE_VARCHAR)
+prop_type_BARCODE_COMPLEXITY_CHECKER.setLabel('Barcode_Complexity_Checker')
+prop_type_BARCODE_COMPLEXITY_CHECKER.setManagedInternally(False)
+prop_type_BARCODE_COMPLEXITY_CHECKER.setInternalNamespace(False)
+
+
+prop_type_BASESCOVERED = tr.getOrCreateNewPropertyType('BASESCOVERED', DataType.INTEGER)
+prop_type_BASESCOVERED.setLabel('bases Covered')
+prop_type_BASESCOVERED.setManagedInternally(False)
+prop_type_BASESCOVERED.setInternalNamespace(False)
+
+
+prop_type_BIOLOGICAL_SAMPLE_ARRIVED = tr.getOrCreateNewPropertyType('BIOLOGICAL_SAMPLE_ARRIVED', DataType.TIMESTAMP)
+prop_type_BIOLOGICAL_SAMPLE_ARRIVED.setLabel('Arrival Date of Biological Sample')
+prop_type_BIOLOGICAL_SAMPLE_ARRIVED.setManagedInternally(False)
+prop_type_BIOLOGICAL_SAMPLE_ARRIVED.setInternalNamespace(False)
+
+
+prop_type_CASAVA_VERSION = tr.getOrCreateNewPropertyType('CASAVA_VERSION', DataType.CONTROLLEDVOCABULARY)
+prop_type_CASAVA_VERSION.setLabel('Casava Version')
+prop_type_CASAVA_VERSION.setManagedInternally(False)
+prop_type_CASAVA_VERSION.setInternalNamespace(False)
+
+prop_type_CASAVA_VERSION.setVocabulary(vocabulary_CASAVA_VERSION)
+
+prop_type_CELL_PLASTICITY_SYSTEMSX = tr.getOrCreateNewPropertyType('CELL_PLASTICITY_SYSTEMSX', DataType.BOOLEAN)
+prop_type_CELL_PLASTICITY_SYSTEMSX.setLabel('Cell Plasticity (SystemsX)')
+prop_type_CELL_PLASTICITY_SYSTEMSX.setManagedInternally(False)
+prop_type_CELL_PLASTICITY_SYSTEMSX.setInternalNamespace(False)
+
+
+prop_type_CHROMCOUNT = tr.getOrCreateNewPropertyType('CHROMCOUNT', DataType.INTEGER)
+prop_type_CHROMCOUNT.setLabel('chrom Count')
+prop_type_CHROMCOUNT.setManagedInternally(False)
+prop_type_CHROMCOUNT.setInternalNamespace(False)
+
+
+prop_type_CLUSTER_GENERATION_KIT_VERSION = tr.getOrCreateNewPropertyType('CLUSTER_GENERATION_KIT_VERSION', DataType.CONTROLLEDVOCABULARY)
+prop_type_CLUSTER_GENERATION_KIT_VERSION.setLabel('CS Generation Kit Version')
+prop_type_CLUSTER_GENERATION_KIT_VERSION.setManagedInternally(False)
+prop_type_CLUSTER_GENERATION_KIT_VERSION.setInternalNamespace(False)
+
+prop_type_CLUSTER_GENERATION_KIT_VERSION.setVocabulary(vocabulary_CLUSTER_GENERATION_KIT_VERSION)
+
+prop_type_CLUSTER_STATION = tr.getOrCreateNewPropertyType('CLUSTER_STATION', DataType.CONTROLLEDVOCABULARY)
+prop_type_CLUSTER_STATION.setLabel('Cluster Station')
+prop_type_CLUSTER_STATION.setManagedInternally(False)
+prop_type_CLUSTER_STATION.setInternalNamespace(False)
+
+prop_type_CLUSTER_STATION.setVocabulary(vocabulary_CLUSTER_STATION)
+
+prop_type_CONCENTRATION = tr.getOrCreateNewPropertyType('CONCENTRATION', DataType.REAL)
+prop_type_CONCENTRATION.setLabel(u'Conc. [ng/µl]')
+prop_type_CONCENTRATION.setManagedInternally(False)
+prop_type_CONCENTRATION.setInternalNamespace(False)
+
+
+prop_type_CONCENTRATION_FLOWLANE = tr.getOrCreateNewPropertyType('CONCENTRATION_FLOWLANE', DataType.REAL)
+prop_type_CONCENTRATION_FLOWLANE.setLabel('Concentration in flow lane [pM]')
+prop_type_CONCENTRATION_FLOWLANE.setManagedInternally(False)
+prop_type_CONCENTRATION_FLOWLANE.setInternalNamespace(False)
+
+
+prop_type_CONCENTRATION_ORIGINAL_ILLUMINA = tr.getOrCreateNewPropertyType('CONCENTRATION_ORIGINAL_ILLUMINA', DataType.REAL)
+prop_type_CONCENTRATION_ORIGINAL_ILLUMINA.setLabel(u'Concentration (original) [ng/μl]')
+prop_type_CONCENTRATION_ORIGINAL_ILLUMINA.setManagedInternally(False)
+prop_type_CONCENTRATION_ORIGINAL_ILLUMINA.setInternalNamespace(False)
+
+
+prop_type_CONCENTRATION_PREPARED_ILLUMINA = tr.getOrCreateNewPropertyType('CONCENTRATION_PREPARED_ILLUMINA', DataType.REAL)
+prop_type_CONCENTRATION_PREPARED_ILLUMINA.setLabel(u'Concentration (prepared) [ng/μl]')
+prop_type_CONCENTRATION_PREPARED_ILLUMINA.setManagedInternally(False)
+prop_type_CONCENTRATION_PREPARED_ILLUMINA.setInternalNamespace(False)
+
+
+prop_type_CONTACT_PERSON_EMAIL = tr.getOrCreateNewPropertyType('CONTACT_PERSON_EMAIL', DataType.VARCHAR)
+prop_type_CONTACT_PERSON_EMAIL.setLabel('Email of Contact Person')
+prop_type_CONTACT_PERSON_EMAIL.setManagedInternally(False)
+prop_type_CONTACT_PERSON_EMAIL.setInternalNamespace(False)
+
+
+prop_type_CONTACT_PERSON_NAME = tr.getOrCreateNewPropertyType('CONTACT_PERSON_NAME', DataType.VARCHAR)
+prop_type_CONTACT_PERSON_NAME.setLabel('Name of Contact Person')
+prop_type_CONTACT_PERSON_NAME.setManagedInternally(False)
+prop_type_CONTACT_PERSON_NAME.setInternalNamespace(False)
+
+
+prop_type_CONTROL_LANE = tr.getOrCreateNewPropertyType('CONTROL_LANE', DataType.CONTROLLEDVOCABULARY)
+prop_type_CONTROL_LANE.setLabel('Control Lane')
+prop_type_CONTROL_LANE.setManagedInternally(False)
+prop_type_CONTROL_LANE.setInternalNamespace(False)
+
+prop_type_CONTROL_LANE.setVocabulary(vocabulary_CONTROL_LANE)
+
+prop_type_CREATED_ON_CS = tr.getOrCreateNewPropertyType('CREATED_ON_CS', DataType.TIMESTAMP)
+prop_type_CREATED_ON_CS.setLabel('Clustering date')
+prop_type_CREATED_ON_CS.setManagedInternally(False)
+prop_type_CREATED_ON_CS.setInternalNamespace(False)
+
+
+prop_type_CS_PROTOCOL_VERSION = tr.getOrCreateNewPropertyType('CS_PROTOCOL_VERSION', DataType.VARCHAR)
+prop_type_CS_PROTOCOL_VERSION.setLabel('CS Protocol Version')
+prop_type_CS_PROTOCOL_VERSION.setManagedInternally(False)
+prop_type_CS_PROTOCOL_VERSION.setInternalNamespace(False)
+
+
+prop_type_CYCLES = tr.getOrCreateNewPropertyType('CYCLES', DataType.INTEGER)
+prop_type_CYCLES.setLabel('Cycles')
+prop_type_CYCLES.setManagedInternally(False)
+prop_type_CYCLES.setInternalNamespace(False)
+
+
+prop_type_DATA_TRANSFERRED = tr.getOrCreateNewPropertyType('DATA_TRANSFERRED', DataType.TIMESTAMP)
+prop_type_DATA_TRANSFERRED.setLabel('Data transferred')
+prop_type_DATA_TRANSFERRED.setManagedInternally(False)
+prop_type_DATA_TRANSFERRED.setInternalNamespace(False)
+
+
+prop_type_DNA_CONCENTRATION_OF_LIBRARY = tr.getOrCreateNewPropertyType('DNA_CONCENTRATION_OF_LIBRARY', DataType.INTEGER)
+prop_type_DNA_CONCENTRATION_OF_LIBRARY.setLabel('DNA concentration of library (nM)')
+prop_type_DNA_CONCENTRATION_OF_LIBRARY.setManagedInternally(False)
+prop_type_DNA_CONCENTRATION_OF_LIBRARY.setInternalNamespace(False)
+
+
+prop_type_DNA_CONCENTRATION_POOL = tr.getOrCreateNewPropertyType('DNA_CONCENTRATION_POOL', DataType.REAL)
+prop_type_DNA_CONCENTRATION_POOL.setLabel('DNA conc. [nM] - customer value')
+prop_type_DNA_CONCENTRATION_POOL.setManagedInternally(False)
+prop_type_DNA_CONCENTRATION_POOL.setInternalNamespace(False)
+
+
+prop_type_DNA_CONCENTRATION_QGF = tr.getOrCreateNewPropertyType('DNA_CONCENTRATION_QGF', DataType.REAL)
+prop_type_DNA_CONCENTRATION_QGF.setLabel('DNA concentration of Pool [nM]')
+prop_type_DNA_CONCENTRATION_QGF.setManagedInternally(False)
+prop_type_DNA_CONCENTRATION_QGF.setInternalNamespace(False)
+
+
+prop_type_END_TYPE = tr.getOrCreateNewPropertyType('END_TYPE', DataType.CONTROLLEDVOCABULARY)
+prop_type_END_TYPE.setLabel('Paired End / Single Read')
+prop_type_END_TYPE.setManagedInternally(False)
+prop_type_END_TYPE.setInternalNamespace(False)
+
+prop_type_END_TYPE.setVocabulary(vocabulary_END_TYPE)
+
+prop_type_EXPERIMENT_DESIGN = tr.getOrCreateNewPropertyType('EXPERIMENT_DESIGN', DataType.CONTROLLEDVOCABULARY)
+prop_type_EXPERIMENT_DESIGN.setLabel('Experiment Design')
+prop_type_EXPERIMENT_DESIGN.setManagedInternally(False)
+prop_type_EXPERIMENT_DESIGN.setInternalNamespace(False)
+
+prop_type_EXPERIMENT_DESIGN.setVocabulary(vocabulary_EXPERIMENT_DESIGN)
+
+prop_type_EXTERNAL_SAMPLE_NAME = tr.getOrCreateNewPropertyType('EXTERNAL_SAMPLE_NAME', DataType.VARCHAR)
+prop_type_EXTERNAL_SAMPLE_NAME.setLabel('External Sample Name')
+prop_type_EXTERNAL_SAMPLE_NAME.setManagedInternally(False)
+prop_type_EXTERNAL_SAMPLE_NAME.setInternalNamespace(False)
+
+
+prop_type_FLOWCELLTYPE = tr.getOrCreateNewPropertyType('FLOWCELLTYPE', DataType.VARCHAR)
+prop_type_FLOWCELLTYPE.setLabel('Flow Cell Type')
+prop_type_FLOWCELLTYPE.setManagedInternally(False)
+prop_type_FLOWCELLTYPE.setInternalNamespace(False)
+
+
+prop_type_FLOW_CELL_SEQUENCED_ON = tr.getOrCreateNewPropertyType('FLOW_CELL_SEQUENCED_ON', DataType.TIMESTAMP)
+prop_type_FLOW_CELL_SEQUENCED_ON.setLabel('Sequencing started')
+prop_type_FLOW_CELL_SEQUENCED_ON.setManagedInternally(False)
+prop_type_FLOW_CELL_SEQUENCED_ON.setInternalNamespace(False)
+
+
+prop_type_FRAGMENT_SIZE_BASE_PAIRS = tr.getOrCreateNewPropertyType('FRAGMENT_SIZE_BASE_PAIRS', DataType.INTEGER)
+prop_type_FRAGMENT_SIZE_BASE_PAIRS.setLabel('Fragment Size [base pairs]')
+prop_type_FRAGMENT_SIZE_BASE_PAIRS.setManagedInternally(False)
+prop_type_FRAGMENT_SIZE_BASE_PAIRS.setInternalNamespace(False)
+
+
+prop_type_FRAGMENT_SIZE_PREPARED_ILLUMINA = tr.getOrCreateNewPropertyType('FRAGMENT_SIZE_PREPARED_ILLUMINA', DataType.INTEGER)
+prop_type_FRAGMENT_SIZE_PREPARED_ILLUMINA.setLabel('Fragment Size (prepared) [base (pairs)]')
+prop_type_FRAGMENT_SIZE_PREPARED_ILLUMINA.setManagedInternally(False)
+prop_type_FRAGMENT_SIZE_PREPARED_ILLUMINA.setInternalNamespace(False)
+
+
+prop_type_ILLUMINA_PIPELINE_VERSION = tr.getOrCreateNewPropertyType('ILLUMINA_PIPELINE_VERSION', DataType.CONTROLLEDVOCABULARY)
+prop_type_ILLUMINA_PIPELINE_VERSION.setLabel('Pipeline Version')
+prop_type_ILLUMINA_PIPELINE_VERSION.setManagedInternally(False)
+prop_type_ILLUMINA_PIPELINE_VERSION.setInternalNamespace(False)
+
+prop_type_ILLUMINA_PIPELINE_VERSION.setVocabulary(vocabulary_PIPELINE_VERSION)
+
+prop_type_INDEX1 = tr.getOrCreateNewPropertyType('INDEX1', DataType.CONTROLLEDVOCABULARY)
+prop_type_INDEX1.setLabel('Index 1')
+prop_type_INDEX1.setManagedInternally(False)
+prop_type_INDEX1.setInternalNamespace(False)
+
+prop_type_INDEX1.setVocabulary(vocabulary_INDEX1)
+
+prop_type_INDEX2 = tr.getOrCreateNewPropertyType('INDEX2', DataType.CONTROLLEDVOCABULARY)
+prop_type_INDEX2.setLabel('Index 2')
+prop_type_INDEX2.setManagedInternally(False)
+prop_type_INDEX2.setInternalNamespace(False)
+
+prop_type_INDEX2.setVocabulary(vocabulary_INDEX2)
+
+prop_type_INDEXREAD = tr.getOrCreateNewPropertyType('INDEXREAD', DataType.INTEGER)
+prop_type_INDEXREAD.setLabel('Length of Index Read1')
+prop_type_INDEXREAD.setManagedInternally(False)
+prop_type_INDEXREAD.setInternalNamespace(False)
+
+
+prop_type_INDEXREAD2 = tr.getOrCreateNewPropertyType('INDEXREAD2', DataType.INTEGER)
+prop_type_INDEXREAD2.setLabel('Length of Index Read2')
+prop_type_INDEXREAD2.setManagedInternally(False)
+prop_type_INDEXREAD2.setInternalNamespace(False)
+
+
+prop_type_INVOICE = tr.getOrCreateNewPropertyType('INVOICE', DataType.BOOLEAN)
+prop_type_INVOICE.setLabel('Invoice sent?')
+prop_type_INVOICE.setManagedInternally(False)
+prop_type_INVOICE.setInternalNamespace(False)
+
+
+prop_type_ISCOMPRESSED = tr.getOrCreateNewPropertyType('ISCOMPRESSED', DataType.BOOLEAN)
+prop_type_ISCOMPRESSED.setLabel('Is Compressed')
+prop_type_ISCOMPRESSED.setManagedInternally(False)
+prop_type_ISCOMPRESSED.setInternalNamespace(False)
+
+
+prop_type_ISSUED_COMMAND = tr.getOrCreateNewPropertyType('ISSUED_COMMAND', DataType.MULTILINE_VARCHAR)
+prop_type_ISSUED_COMMAND.setLabel('Issued Command')
+prop_type_ISSUED_COMMAND.setManagedInternally(False)
+prop_type_ISSUED_COMMAND.setInternalNamespace(False)
+
+
+prop_type_ISSWAPPED = tr.getOrCreateNewPropertyType('ISSWAPPED', DataType.INTEGER)
+prop_type_ISSWAPPED.setLabel('Is byte swapped')
+prop_type_ISSWAPPED.setManagedInternally(False)
+prop_type_ISSWAPPED.setInternalNamespace(False)
+
+
+prop_type_KIT = tr.getOrCreateNewPropertyType('KIT', DataType.CONTROLLEDVOCABULARY)
+prop_type_KIT.setLabel('Library preparation kit')
+prop_type_KIT.setManagedInternally(False)
+prop_type_KIT.setInternalNamespace(False)
+
+prop_type_KIT.setVocabulary(vocabulary_KIT)
+
+prop_type_KIT_PREPARED = tr.getOrCreateNewPropertyType('KIT_PREPARED', DataType.TIMESTAMP)
+prop_type_KIT_PREPARED.setLabel('Sample processed')
+prop_type_KIT_PREPARED.setManagedInternally(False)
+prop_type_KIT_PREPARED.setInternalNamespace(False)
+
+
+prop_type_LANECOUNT = tr.getOrCreateNewPropertyType('LANECOUNT', DataType.INTEGER)
+prop_type_LANECOUNT.setLabel('Lane Count')
+prop_type_LANECOUNT.setManagedInternally(False)
+prop_type_LANECOUNT.setInternalNamespace(False)
+
+
+prop_type_LIBRARY_PROCESSING_FAILED = tr.getOrCreateNewPropertyType('LIBRARY_PROCESSING_FAILED', DataType.BOOLEAN)
+prop_type_LIBRARY_PROCESSING_FAILED.setLabel('Library processing failed')
+prop_type_LIBRARY_PROCESSING_FAILED.setManagedInternally(False)
+prop_type_LIBRARY_PROCESSING_FAILED.setInternalNamespace(False)
+
+
+prop_type_LIBRARY_PROCESSING_POSSIBLE_YES_NO = tr.getOrCreateNewPropertyType('LIBRARY_PROCESSING_POSSIBLE_YES_NO', DataType.CONTROLLEDVOCABULARY)
+prop_type_LIBRARY_PROCESSING_POSSIBLE_YES_NO.setLabel('Library processing possible')
+prop_type_LIBRARY_PROCESSING_POSSIBLE_YES_NO.setManagedInternally(False)
+prop_type_LIBRARY_PROCESSING_POSSIBLE_YES_NO.setInternalNamespace(False)
+
+prop_type_LIBRARY_PROCESSING_POSSIBLE_YES_NO.setVocabulary(vocabulary_YES_NO)
+
+prop_type_LIBRARY_PROCESSING_SUCCESSFUL = tr.getOrCreateNewPropertyType('LIBRARY_PROCESSING_SUCCESSFUL', DataType.BOOLEAN)
+prop_type_LIBRARY_PROCESSING_SUCCESSFUL.setLabel('Library processing successful')
+prop_type_LIBRARY_PROCESSING_SUCCESSFUL.setManagedInternally(False)
+prop_type_LIBRARY_PROCESSING_SUCCESSFUL.setInternalNamespace(False)
+
+
+prop_type_LOT = tr.getOrCreateNewPropertyType('LOT', DataType.INTEGER)
+prop_type_LOT.setLabel('Kit Lot #')
+prop_type_LOT.setManagedInternally(False)
+prop_type_LOT.setInternalNamespace(False)
+
+
+prop_type_MACS_VERSION = tr.getOrCreateNewPropertyType('MACS_VERSION', DataType.CONTROLLEDVOCABULARY)
+prop_type_MACS_VERSION.setLabel('MACS VERSION')
+prop_type_MACS_VERSION.setManagedInternally(False)
+prop_type_MACS_VERSION.setInternalNamespace(False)
+
+prop_type_MACS_VERSION.setVocabulary(vocabulary_MACS_VERSION)
+
+prop_type_MAPPED_READS = tr.getOrCreateNewPropertyType('MAPPED_READS', DataType.INTEGER)
+prop_type_MAPPED_READS.setLabel('Mapped reads')
+prop_type_MAPPED_READS.setManagedInternally(False)
+prop_type_MAPPED_READS.setInternalNamespace(False)
+
+
+prop_type_MAX = tr.getOrCreateNewPropertyType('MAX', DataType.REAL)
+prop_type_MAX.setLabel('Maximum')
+prop_type_MAX.setManagedInternally(False)
+prop_type_MAX.setInternalNamespace(False)
+
+
+prop_type_MEAN = tr.getOrCreateNewPropertyType('MEAN', DataType.REAL)
+prop_type_MEAN.setLabel('Mean')
+prop_type_MEAN.setManagedInternally(False)
+prop_type_MEAN.setInternalNamespace(False)
+
+
+prop_type_MIN = tr.getOrCreateNewPropertyType('MIN', DataType.REAL)
+prop_type_MIN.setLabel('Minimum')
+prop_type_MIN.setManagedInternally(False)
+prop_type_MIN.setInternalNamespace(False)
+
+
+prop_type_MISMATCH_IN_INDEX = tr.getOrCreateNewPropertyType('MISMATCH_IN_INDEX', DataType.CONTROLLEDVOCABULARY)
+prop_type_MISMATCH_IN_INDEX.setLabel('Mismatch in Index')
+prop_type_MISMATCH_IN_INDEX.setManagedInternally(False)
+prop_type_MISMATCH_IN_INDEX.setInternalNamespace(False)
+
+prop_type_MISMATCH_IN_INDEX.setVocabulary(vocabulary_MISMATCH_IN_INDEX)
+
+prop_type_NANO_DROP = tr.getOrCreateNewPropertyType('NANO_DROP', DataType.CONTROLLEDVOCABULARY)
+prop_type_NANO_DROP.setLabel('Nano Drop')
+prop_type_NANO_DROP.setManagedInternally(False)
+prop_type_NANO_DROP.setInternalNamespace(False)
+
+prop_type_NANO_DROP.setVocabulary(vocabulary_NANO_DROP)
+
+prop_type_NCBI_ORGANISM_TAXONOMY = tr.getOrCreateNewPropertyType('NCBI_ORGANISM_TAXONOMY', DataType.CONTROLLEDVOCABULARY)
+prop_type_NCBI_ORGANISM_TAXONOMY.setLabel('Organism (NCBI Taxonomy)')
+prop_type_NCBI_ORGANISM_TAXONOMY.setManagedInternally(False)
+prop_type_NCBI_ORGANISM_TAXONOMY.setInternalNamespace(False)
+
+prop_type_NCBI_ORGANISM_TAXONOMY.setVocabulary(vocabulary_NCBI_TAXONOMY)
+
+prop_type_NM_DNA = tr.getOrCreateNewPropertyType('NM_DNA', DataType.REAL)
+prop_type_NM_DNA.setLabel('Calculated DNA concentration of library (nM)')
+prop_type_NM_DNA.setManagedInternally(False)
+prop_type_NM_DNA.setInternalNamespace(False)
+
+
+prop_type_NOTES = tr.getOrCreateNewPropertyType('NOTES', DataType.MULTILINE_VARCHAR)
+prop_type_NOTES.setLabel('Notes')
+prop_type_NOTES.setManagedInternally(False)
+prop_type_NOTES.setInternalNamespace(False)
+
+
+prop_type_NUMBER_OF_ATTACHMENTS = tr.getOrCreateNewPropertyType('NUMBER_OF_ATTACHMENTS', DataType.INTEGER)
+prop_type_NUMBER_OF_ATTACHMENTS.setLabel('Number of Attachments')
+prop_type_NUMBER_OF_ATTACHMENTS.setManagedInternally(False)
+prop_type_NUMBER_OF_ATTACHMENTS.setInternalNamespace(False)
+
+
+prop_type_PAIRED_END_KIT = tr.getOrCreateNewPropertyType('PAIRED_END_KIT', DataType.VARCHAR)
+prop_type_PAIRED_END_KIT.setLabel('Paired End Kit')
+prop_type_PAIRED_END_KIT.setManagedInternally(False)
+prop_type_PAIRED_END_KIT.setInternalNamespace(False)
+
+
+prop_type_PERCENTAGE_ONE_MISMATCH_READS_INDEX = tr.getOrCreateNewPropertyType('PERCENTAGE_ONE_MISMATCH_READS_INDEX', DataType.REAL)
+prop_type_PERCENTAGE_ONE_MISMATCH_READS_INDEX.setLabel('% One Mismatch Reads (Index)')
+prop_type_PERCENTAGE_ONE_MISMATCH_READS_INDEX.setManagedInternally(False)
+prop_type_PERCENTAGE_ONE_MISMATCH_READS_INDEX.setInternalNamespace(False)
+
+
+prop_type_PERCENTAGE_PASSED_FILTERING = tr.getOrCreateNewPropertyType('PERCENTAGE_PASSED_FILTERING', DataType.REAL)
+prop_type_PERCENTAGE_PASSED_FILTERING.setLabel('% Passes Illumina Filtering (PF)')
+prop_type_PERCENTAGE_PASSED_FILTERING.setManagedInternally(False)
+prop_type_PERCENTAGE_PASSED_FILTERING.setInternalNamespace(False)
+
+
+prop_type_PERCENTAGE_PERFECT_INDEX_READS = tr.getOrCreateNewPropertyType('PERCENTAGE_PERFECT_INDEX_READS', DataType.REAL)
+prop_type_PERCENTAGE_PERFECT_INDEX_READS.setLabel('% Perfect Index Reads')
+prop_type_PERCENTAGE_PERFECT_INDEX_READS.setManagedInternally(False)
+prop_type_PERCENTAGE_PERFECT_INDEX_READS.setInternalNamespace(False)
+
+
+prop_type_PERCENTAGE_RAW_CLUSTERS_PER_LANE = tr.getOrCreateNewPropertyType('PERCENTAGE_RAW_CLUSTERS_PER_LANE', DataType.REAL)
+prop_type_PERCENTAGE_RAW_CLUSTERS_PER_LANE.setLabel('% of raw clusters per lane')
+prop_type_PERCENTAGE_RAW_CLUSTERS_PER_LANE.setManagedInternally(False)
+prop_type_PERCENTAGE_RAW_CLUSTERS_PER_LANE.setInternalNamespace(False)
+
+
+prop_type_PREPARED_BY = tr.getOrCreateNewPropertyType('PREPARED_BY', DataType.VARCHAR)
+prop_type_PREPARED_BY.setLabel('Prepared by')
+prop_type_PREPARED_BY.setManagedInternally(False)
+prop_type_PREPARED_BY.setInternalNamespace(False)
+
+
+prop_type_PRIMARYDATASIZE = tr.getOrCreateNewPropertyType('PRIMARYDATASIZE', DataType.INTEGER)
+prop_type_PRIMARYDATASIZE.setLabel('primary Data Size')
+prop_type_PRIMARYDATASIZE.setManagedInternally(False)
+prop_type_PRIMARYDATASIZE.setInternalNamespace(False)
+
+
+prop_type_PRIMARYINDEXSIZE = tr.getOrCreateNewPropertyType('PRIMARYINDEXSIZE', DataType.INTEGER)
+prop_type_PRIMARYINDEXSIZE.setLabel('primary Index Size')
+prop_type_PRIMARYINDEXSIZE.setManagedInternally(False)
+prop_type_PRIMARYINDEXSIZE.setInternalNamespace(False)
+
+
+prop_type_PRINCIPAL_INVESTIGATOR_EMAIL = tr.getOrCreateNewPropertyType('PRINCIPAL_INVESTIGATOR_EMAIL', DataType.VARCHAR)
+prop_type_PRINCIPAL_INVESTIGATOR_EMAIL.setLabel('Email of Principal Investigator')
+prop_type_PRINCIPAL_INVESTIGATOR_EMAIL.setManagedInternally(False)
+prop_type_PRINCIPAL_INVESTIGATOR_EMAIL.setInternalNamespace(False)
+
+
+prop_type_PRINCIPAL_INVESTIGATOR_NAME = tr.getOrCreateNewPropertyType('PRINCIPAL_INVESTIGATOR_NAME', DataType.VARCHAR)
+prop_type_PRINCIPAL_INVESTIGATOR_NAME.setLabel('Name of Principal Investigator')
+prop_type_PRINCIPAL_INVESTIGATOR_NAME.setManagedInternally(False)
+prop_type_PRINCIPAL_INVESTIGATOR_NAME.setInternalNamespace(False)
+
+
+prop_type_QC_AT_DBSSE = tr.getOrCreateNewPropertyType('QC_AT_DBSSE', DataType.CONTROLLEDVOCABULARY)
+prop_type_QC_AT_DBSSE.setLabel('QC at D-BSSE')
+prop_type_QC_AT_DBSSE.setManagedInternally(False)
+prop_type_QC_AT_DBSSE.setInternalNamespace(False)
+
+prop_type_QC_AT_DBSSE.setVocabulary(vocabulary_YES_NO)
+
+prop_type_QC_REQUIRED = tr.getOrCreateNewPropertyType('QC_REQUIRED', DataType.CONTROLLEDVOCABULARY)
+prop_type_QC_REQUIRED.setLabel('QC required')
+prop_type_QC_REQUIRED.setManagedInternally(False)
+prop_type_QC_REQUIRED.setInternalNamespace(False)
+
+prop_type_QC_REQUIRED.setVocabulary(vocabulary_YES_NO)
+
+prop_type_RUNNINGTIME = tr.getOrCreateNewPropertyType('RUNNINGTIME', DataType.VARCHAR)
+prop_type_RUNNINGTIME.setLabel('Running Time')
+prop_type_RUNNINGTIME.setManagedInternally(False)
+prop_type_RUNNINGTIME.setInternalNamespace(False)
+
+
+prop_type_RUN_FOLDER_NAME = tr.getOrCreateNewPropertyType('RUN_FOLDER_NAME', DataType.VARCHAR)
+prop_type_RUN_FOLDER_NAME.setLabel('Run Folder Name')
+prop_type_RUN_FOLDER_NAME.setManagedInternally(False)
+prop_type_RUN_FOLDER_NAME.setInternalNamespace(False)
+
+
+prop_type_SAMPLE_KIND = tr.getOrCreateNewPropertyType('SAMPLE_KIND', DataType.CONTROLLEDVOCABULARY)
+prop_type_SAMPLE_KIND.setLabel('Sample Kind')
+prop_type_SAMPLE_KIND.setManagedInternally(False)
+prop_type_SAMPLE_KIND.setInternalNamespace(False)
+
+prop_type_SAMPLE_KIND.setVocabulary(vocabulary_SAMPLE_TYPE)
+
+prop_type_SAMTOOLS_FLAGSTAT = tr.getOrCreateNewPropertyType('SAMTOOLS_FLAGSTAT', DataType.MULTILINE_VARCHAR)
+prop_type_SAMTOOLS_FLAGSTAT.setLabel('Samtools Flagstat Output')
+prop_type_SAMTOOLS_FLAGSTAT.setManagedInternally(False)
+prop_type_SAMTOOLS_FLAGSTAT.setInternalNamespace(False)
+
+
+prop_type_SBS_KIT = tr.getOrCreateNewPropertyType('SBS_KIT', DataType.VARCHAR)
+prop_type_SBS_KIT.setLabel('SBS Kit')
+prop_type_SBS_KIT.setManagedInternally(False)
+prop_type_SBS_KIT.setInternalNamespace(False)
+
+
+prop_type_SBS_SEQUENCING_KIT_VERSION = tr.getOrCreateNewPropertyType('SBS_SEQUENCING_KIT_VERSION', DataType.CONTROLLEDVOCABULARY)
+prop_type_SBS_SEQUENCING_KIT_VERSION.setLabel('SBS Sequencing Kit Version')
+prop_type_SBS_SEQUENCING_KIT_VERSION.setManagedInternally(False)
+prop_type_SBS_SEQUENCING_KIT_VERSION.setInternalNamespace(False)
+
+prop_type_SBS_SEQUENCING_KIT_VERSION.setVocabulary(vocabulary_SBS_SEQUENCING_KIT_VERSION)
+
+prop_type_SEQUENCER = tr.getOrCreateNewPropertyType('SEQUENCER', DataType.CONTROLLEDVOCABULARY)
+prop_type_SEQUENCER.setLabel('Sequencer')
+prop_type_SEQUENCER.setManagedInternally(False)
+prop_type_SEQUENCER.setInternalNamespace(False)
+
+prop_type_SEQUENCER.setVocabulary(vocabulary_SEQUENCER)
+
+prop_type_SEQUENCER_FINISHED = tr.getOrCreateNewPropertyType('SEQUENCER_FINISHED', DataType.TIMESTAMP)
+prop_type_SEQUENCER_FINISHED.setLabel('Sequencer finished')
+prop_type_SEQUENCER_FINISHED.setManagedInternally(False)
+prop_type_SEQUENCER_FINISHED.setInternalNamespace(False)
+
+
+prop_type_STARTING_AMOUNT_OF_SAMPLE_IN_NG = tr.getOrCreateNewPropertyType('STARTING_AMOUNT_OF_SAMPLE_IN_NG', DataType.REAL)
+prop_type_STARTING_AMOUNT_OF_SAMPLE_IN_NG.setLabel('Starting amount of sample (ng)')
+prop_type_STARTING_AMOUNT_OF_SAMPLE_IN_NG.setManagedInternally(False)
+prop_type_STARTING_AMOUNT_OF_SAMPLE_IN_NG.setInternalNamespace(False)
+
+
+prop_type_STD = tr.getOrCreateNewPropertyType('STD', DataType.REAL)
+prop_type_STD.setLabel('Standard deviation')
+prop_type_STD.setManagedInternally(False)
+prop_type_STD.setInternalNamespace(False)
+
+
+prop_type_SURFACECOUNT = tr.getOrCreateNewPropertyType('SURFACECOUNT', DataType.INTEGER)
+prop_type_SURFACECOUNT.setLabel('Surface Count')
+prop_type_SURFACECOUNT.setManagedInternally(False)
+prop_type_SURFACECOUNT.setInternalNamespace(False)
+
+
+prop_type_SWATHCOUNT = tr.getOrCreateNewPropertyType('SWATHCOUNT', DataType.INTEGER)
+prop_type_SWATHCOUNT.setLabel('Swath Count')
+prop_type_SWATHCOUNT.setManagedInternally(False)
+prop_type_SWATHCOUNT.setInternalNamespace(False)
+
+
+prop_type_TILECOUNT = tr.getOrCreateNewPropertyType('TILECOUNT', DataType.INTEGER)
+prop_type_TILECOUNT.setLabel('Tile Count')
+prop_type_TILECOUNT.setManagedInternally(False)
+prop_type_TILECOUNT.setInternalNamespace(False)
+
+
+prop_type_TOTAL_READS = tr.getOrCreateNewPropertyType('TOTAL_READS', DataType.INTEGER)
+prop_type_TOTAL_READS.setLabel('Total reads')
+prop_type_TOTAL_READS.setManagedInternally(False)
+prop_type_TOTAL_READS.setInternalNamespace(False)
+
+
+prop_type_UL_DNA = tr.getOrCreateNewPropertyType('UL_DNA', DataType.REAL)
+prop_type_UL_DNA.setLabel('Calculated ul DNA for 2nM stock')
+prop_type_UL_DNA.setManagedInternally(False)
+prop_type_UL_DNA.setInternalNamespace(False)
+
+
+prop_type_UL_EB = tr.getOrCreateNewPropertyType('UL_EB', DataType.REAL)
+prop_type_UL_EB.setLabel('Calculated ul EB for 2nM stock ')
+prop_type_UL_EB.setManagedInternally(False)
+prop_type_UL_EB.setInternalNamespace(False)
+
+
+prop_type_UL_STOCK = tr.getOrCreateNewPropertyType('UL_STOCK', DataType.INTEGER)
+prop_type_UL_STOCK.setLabel('ul of 2nM stock')
+prop_type_UL_STOCK.setManagedInternally(False)
+prop_type_UL_STOCK.setInternalNamespace(False)
+
+
+prop_type_UNIQUE_BARCODES = tr.getOrCreateNewPropertyType('UNIQUE_BARCODES', DataType.VARCHAR)
+prop_type_UNIQUE_BARCODES.setLabel('Unique Barcodes in Pool?')
+prop_type_UNIQUE_BARCODES.setManagedInternally(False)
+prop_type_UNIQUE_BARCODES.setInternalNamespace(False)
+
+
+prop_type_VERSION = tr.getOrCreateNewPropertyType('VERSION', DataType.VARCHAR)
+prop_type_VERSION.setLabel('Version')
+prop_type_VERSION.setManagedInternally(False)
+prop_type_VERSION.setInternalNamespace(False)
+
+
+prop_type_YIELD_MBASES = tr.getOrCreateNewPropertyType('YIELD_MBASES', DataType.INTEGER)
+prop_type_YIELD_MBASES.setLabel('Yield(Mbases)')
+prop_type_YIELD_MBASES.setManagedInternally(False)
+prop_type_YIELD_MBASES.setInternalNamespace(False)
+
+
+prop_type_ZOOMLEVELS = tr.getOrCreateNewPropertyType('ZOOMLEVELS', DataType.INTEGER)
+prop_type_ZOOMLEVELS.setLabel('zoom Levels')
+prop_type_ZOOMLEVELS.setManagedInternally(False)
+prop_type_ZOOMLEVELS.setInternalNamespace(False)
+
+
+print "Imported 92 Property Types"
+assignment_DATA_SET_ALIGNMENT_ALIGNMENT_SOFTWARE = tr.assignPropertyType(data_set_type_ALIGNMENT, prop_type_ALIGNMENT_SOFTWARE)
+assignment_DATA_SET_ALIGNMENT_ALIGNMENT_SOFTWARE.setMandatory(False)
+assignment_DATA_SET_ALIGNMENT_ALIGNMENT_SOFTWARE.setSection(None)
+assignment_DATA_SET_ALIGNMENT_ALIGNMENT_SOFTWARE.setPositionInForms(3)
+
+assignment_DATA_SET_ALIGNMENT_VERSION = tr.assignPropertyType(data_set_type_ALIGNMENT, prop_type_VERSION)
+assignment_DATA_SET_ALIGNMENT_VERSION.setMandatory(False)
+assignment_DATA_SET_ALIGNMENT_VERSION.setSection(None)
+assignment_DATA_SET_ALIGNMENT_VERSION.setPositionInForms(4)
+
+assignment_DATA_SET_ALIGNMENT_NOTES = tr.assignPropertyType(data_set_type_ALIGNMENT, prop_type_NOTES)
+assignment_DATA_SET_ALIGNMENT_NOTES.setMandatory(False)
+assignment_DATA_SET_ALIGNMENT_NOTES.setSection(None)
+assignment_DATA_SET_ALIGNMENT_NOTES.setPositionInForms(5)
+
+assignment_DATA_SET_ALIGNMENT_SAMTOOLS_FLAGSTAT = tr.assignPropertyType(data_set_type_ALIGNMENT, prop_type_SAMTOOLS_FLAGSTAT)
+assignment_DATA_SET_ALIGNMENT_SAMTOOLS_FLAGSTAT.setMandatory(False)
+assignment_DATA_SET_ALIGNMENT_SAMTOOLS_FLAGSTAT.setSection(None)
+assignment_DATA_SET_ALIGNMENT_SAMTOOLS_FLAGSTAT.setPositionInForms(6)
+
+assignment_DATA_SET_ALIGNMENT_MAPPED_READS = tr.assignPropertyType(data_set_type_ALIGNMENT, prop_type_MAPPED_READS)
+assignment_DATA_SET_ALIGNMENT_MAPPED_READS.setMandatory(False)
+assignment_DATA_SET_ALIGNMENT_MAPPED_READS.setSection(None)
+assignment_DATA_SET_ALIGNMENT_MAPPED_READS.setPositionInForms(7)
+
+assignment_DATA_SET_ALIGNMENT_TOTAL_READS = tr.assignPropertyType(data_set_type_ALIGNMENT, prop_type_TOTAL_READS)
+assignment_DATA_SET_ALIGNMENT_TOTAL_READS.setMandatory(False)
+assignment_DATA_SET_ALIGNMENT_TOTAL_READS.setSection(None)
+assignment_DATA_SET_ALIGNMENT_TOTAL_READS.setPositionInForms(8)
+
+assignment_DATA_SET_ALIGNMENT_ISSUED_COMMAND = tr.assignPropertyType(data_set_type_ALIGNMENT, prop_type_ISSUED_COMMAND)
+assignment_DATA_SET_ALIGNMENT_ISSUED_COMMAND.setMandatory(False)
+assignment_DATA_SET_ALIGNMENT_ISSUED_COMMAND.setSection(None)
+assignment_DATA_SET_ALIGNMENT_ISSUED_COMMAND.setPositionInForms(9)
+
+assignment_DATA_SET_BASECALL_STATS_MISMATCH_IN_INDEX = tr.assignPropertyType(data_set_type_BASECALL_STATS, prop_type_MISMATCH_IN_INDEX)
+assignment_DATA_SET_BASECALL_STATS_MISMATCH_IN_INDEX.setMandatory(False)
+assignment_DATA_SET_BASECALL_STATS_MISMATCH_IN_INDEX.setSection(None)
+assignment_DATA_SET_BASECALL_STATS_MISMATCH_IN_INDEX.setPositionInForms(3)
+
+assignment_DATA_SET_BIGWIGGLE_NOTES = tr.assignPropertyType(data_set_type_BIGWIGGLE, prop_type_NOTES)
+assignment_DATA_SET_BIGWIGGLE_NOTES.setMandatory(False)
+assignment_DATA_SET_BIGWIGGLE_NOTES.setSection(None)
+assignment_DATA_SET_BIGWIGGLE_NOTES.setPositionInForms(3)
+
+assignment_DATA_SET_BIGWIGGLE_VERSION = tr.assignPropertyType(data_set_type_BIGWIGGLE, prop_type_VERSION)
+assignment_DATA_SET_BIGWIGGLE_VERSION.setMandatory(False)
+assignment_DATA_SET_BIGWIGGLE_VERSION.setSection(None)
+assignment_DATA_SET_BIGWIGGLE_VERSION.setPositionInForms(4)
+
+assignment_DATA_SET_BIGWIGGLE_ISCOMPRESSED = tr.assignPropertyType(data_set_type_BIGWIGGLE, prop_type_ISCOMPRESSED)
+assignment_DATA_SET_BIGWIGGLE_ISCOMPRESSED.setMandatory(False)
+assignment_DATA_SET_BIGWIGGLE_ISCOMPRESSED.setSection(None)
+assignment_DATA_SET_BIGWIGGLE_ISCOMPRESSED.setPositionInForms(5)
+
+assignment_DATA_SET_BIGWIGGLE_ISSWAPPED = tr.assignPropertyType(data_set_type_BIGWIGGLE, prop_type_ISSWAPPED)
+assignment_DATA_SET_BIGWIGGLE_ISSWAPPED.setMandatory(False)
+assignment_DATA_SET_BIGWIGGLE_ISSWAPPED.setSection(None)
+assignment_DATA_SET_BIGWIGGLE_ISSWAPPED.setPositionInForms(6)
+
+assignment_DATA_SET_BIGWIGGLE_PRIMARYDATASIZE = tr.assignPropertyType(data_set_type_BIGWIGGLE, prop_type_PRIMARYDATASIZE)
+assignment_DATA_SET_BIGWIGGLE_PRIMARYDATASIZE.setMandatory(False)
+assignment_DATA_SET_BIGWIGGLE_PRIMARYDATASIZE.setSection(None)
+assignment_DATA_SET_BIGWIGGLE_PRIMARYDATASIZE.setPositionInForms(7)
+
+assignment_DATA_SET_BIGWIGGLE_PRIMARYINDEXSIZE = tr.assignPropertyType(data_set_type_BIGWIGGLE, prop_type_PRIMARYINDEXSIZE)
+assignment_DATA_SET_BIGWIGGLE_PRIMARYINDEXSIZE.setMandatory(False)
+assignment_DATA_SET_BIGWIGGLE_PRIMARYINDEXSIZE.setSection(None)
+assignment_DATA_SET_BIGWIGGLE_PRIMARYINDEXSIZE.setPositionInForms(8)
+
+assignment_DATA_SET_BIGWIGGLE_ZOOMLEVELS = tr.assignPropertyType(data_set_type_BIGWIGGLE, prop_type_ZOOMLEVELS)
+assignment_DATA_SET_BIGWIGGLE_ZOOMLEVELS.setMandatory(False)
+assignment_DATA_SET_BIGWIGGLE_ZOOMLEVELS.setSection(None)
+assignment_DATA_SET_BIGWIGGLE_ZOOMLEVELS.setPositionInForms(9)
+
+assignment_DATA_SET_BIGWIGGLE_CHROMCOUNT = tr.assignPropertyType(data_set_type_BIGWIGGLE, prop_type_CHROMCOUNT)
+assignment_DATA_SET_BIGWIGGLE_CHROMCOUNT.setMandatory(False)
+assignment_DATA_SET_BIGWIGGLE_CHROMCOUNT.setSection(None)
+assignment_DATA_SET_BIGWIGGLE_CHROMCOUNT.setPositionInForms(10)
+
+assignment_DATA_SET_BIGWIGGLE_BASESCOVERED = tr.assignPropertyType(data_set_type_BIGWIGGLE, prop_type_BASESCOVERED)
+assignment_DATA_SET_BIGWIGGLE_BASESCOVERED.setMandatory(False)
+assignment_DATA_SET_BIGWIGGLE_BASESCOVERED.setSection(None)
+assignment_DATA_SET_BIGWIGGLE_BASESCOVERED.setPositionInForms(11)
+
+assignment_DATA_SET_BIGWIGGLE_MEAN = tr.assignPropertyType(data_set_type_BIGWIGGLE, prop_type_MEAN)
+assignment_DATA_SET_BIGWIGGLE_MEAN.setMandatory(False)
+assignment_DATA_SET_BIGWIGGLE_MEAN.setSection(None)
+assignment_DATA_SET_BIGWIGGLE_MEAN.setPositionInForms(12)
+
+assignment_DATA_SET_BIGWIGGLE_MIN = tr.assignPropertyType(data_set_type_BIGWIGGLE, prop_type_MIN)
+assignment_DATA_SET_BIGWIGGLE_MIN.setMandatory(False)
+assignment_DATA_SET_BIGWIGGLE_MIN.setSection(None)
+assignment_DATA_SET_BIGWIGGLE_MIN.setPositionInForms(13)
+
+assignment_DATA_SET_BIGWIGGLE_MAX = tr.assignPropertyType(data_set_type_BIGWIGGLE, prop_type_MAX)
+assignment_DATA_SET_BIGWIGGLE_MAX.setMandatory(False)
+assignment_DATA_SET_BIGWIGGLE_MAX.setSection(None)
+assignment_DATA_SET_BIGWIGGLE_MAX.setPositionInForms(14)
+
+assignment_DATA_SET_BIGWIGGLE_STD = tr.assignPropertyType(data_set_type_BIGWIGGLE, prop_type_STD)
+assignment_DATA_SET_BIGWIGGLE_STD.setMandatory(False)
+assignment_DATA_SET_BIGWIGGLE_STD.setSection(None)
+assignment_DATA_SET_BIGWIGGLE_STD.setPositionInForms(15)
+
+assignment_DATA_SET_FASTQ_GZ_NOTES = tr.assignPropertyType(data_set_type_FASTQ_GZ, prop_type_NOTES)
+assignment_DATA_SET_FASTQ_GZ_NOTES.setMandatory(False)
+assignment_DATA_SET_FASTQ_GZ_NOTES.setSection(None)
+assignment_DATA_SET_FASTQ_GZ_NOTES.setPositionInForms(3)
+
+assignment_DATA_SET_FASTQ_GZ_YIELD_MBASES = tr.assignPropertyType(data_set_type_FASTQ_GZ, prop_type_YIELD_MBASES)
+assignment_DATA_SET_FASTQ_GZ_YIELD_MBASES.setMandatory(False)
+assignment_DATA_SET_FASTQ_GZ_YIELD_MBASES.setSection(None)
+assignment_DATA_SET_FASTQ_GZ_YIELD_MBASES.setPositionInForms(4)
+
+assignment_DATA_SET_FASTQ_GZ_PERCENTAGE_PASSED_FILTERING = tr.assignPropertyType(data_set_type_FASTQ_GZ, prop_type_PERCENTAGE_PASSED_FILTERING)
+assignment_DATA_SET_FASTQ_GZ_PERCENTAGE_PASSED_FILTERING.setMandatory(False)
+assignment_DATA_SET_FASTQ_GZ_PERCENTAGE_PASSED_FILTERING.setSection(None)
+assignment_DATA_SET_FASTQ_GZ_PERCENTAGE_PASSED_FILTERING.setPositionInForms(5)
+
+assignment_DATA_SET_FASTQ_GZ_INDEX1 = tr.assignPropertyType(data_set_type_FASTQ_GZ, prop_type_INDEX1)
+assignment_DATA_SET_FASTQ_GZ_INDEX1.setMandatory(False)
+assignment_DATA_SET_FASTQ_GZ_INDEX1.setSection(None)
+assignment_DATA_SET_FASTQ_GZ_INDEX1.setPositionInForms(6)
+
+assignment_DATA_SET_FASTQ_GZ_INDEX2 = tr.assignPropertyType(data_set_type_FASTQ_GZ, prop_type_INDEX2)
+assignment_DATA_SET_FASTQ_GZ_INDEX2.setMandatory(False)
+assignment_DATA_SET_FASTQ_GZ_INDEX2.setSection(None)
+assignment_DATA_SET_FASTQ_GZ_INDEX2.setPositionInForms(7)
+
+assignment_DATA_SET_FASTQ_GZ_PERCENTAGE_RAW_CLUSTERS_PER_LANE = tr.assignPropertyType(data_set_type_FASTQ_GZ, prop_type_PERCENTAGE_RAW_CLUSTERS_PER_LANE)
+assignment_DATA_SET_FASTQ_GZ_PERCENTAGE_RAW_CLUSTERS_PER_LANE.setMandatory(False)
+assignment_DATA_SET_FASTQ_GZ_PERCENTAGE_RAW_CLUSTERS_PER_LANE.setSection(None)
+assignment_DATA_SET_FASTQ_GZ_PERCENTAGE_RAW_CLUSTERS_PER_LANE.setPositionInForms(8)
+
+assignment_DATA_SET_FASTQ_GZ_PERCENTAGE_PERFECT_INDEX_READS = tr.assignPropertyType(data_set_type_FASTQ_GZ, prop_type_PERCENTAGE_PERFECT_INDEX_READS)
+assignment_DATA_SET_FASTQ_GZ_PERCENTAGE_PERFECT_INDEX_READS.setMandatory(False)
+assignment_DATA_SET_FASTQ_GZ_PERCENTAGE_PERFECT_INDEX_READS.setSection(None)
+assignment_DATA_SET_FASTQ_GZ_PERCENTAGE_PERFECT_INDEX_READS.setPositionInForms(9)
+
+assignment_DATA_SET_FASTQ_GZ_PERCENTAGE_ONE_MISMATCH_READS_INDEX = tr.assignPropertyType(data_set_type_FASTQ_GZ, prop_type_PERCENTAGE_ONE_MISMATCH_READS_INDEX)
+assignment_DATA_SET_FASTQ_GZ_PERCENTAGE_ONE_MISMATCH_READS_INDEX.setMandatory(False)
+assignment_DATA_SET_FASTQ_GZ_PERCENTAGE_ONE_MISMATCH_READS_INDEX.setSection(None)
+assignment_DATA_SET_FASTQ_GZ_PERCENTAGE_ONE_MISMATCH_READS_INDEX.setPositionInForms(10)
+
+assignment_EXPERIMENT_HT_SEQUENCING_EXPERIMENT_DESIGN = tr.assignPropertyType(exp_type_HT_SEQUENCING, prop_type_EXPERIMENT_DESIGN)
+assignment_EXPERIMENT_HT_SEQUENCING_EXPERIMENT_DESIGN.setMandatory(False)
+assignment_EXPERIMENT_HT_SEQUENCING_EXPERIMENT_DESIGN.setSection(None)
+assignment_EXPERIMENT_HT_SEQUENCING_EXPERIMENT_DESIGN.setPositionInForms(3)
+
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_RUN_FOLDER_NAME = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_CELL, prop_type_RUN_FOLDER_NAME)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_RUN_FOLDER_NAME.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_RUN_FOLDER_NAME.setSection(None)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_RUN_FOLDER_NAME.setPositionInForms(1)
+
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_SEQUENCER = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_CELL, prop_type_SEQUENCER)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_SEQUENCER.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_SEQUENCER.setSection(None)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_SEQUENCER.setPositionInForms(5)
+
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_END_TYPE = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_CELL, prop_type_END_TYPE)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_END_TYPE.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_END_TYPE.setSection(None)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_END_TYPE.setPositionInForms(7)
+
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_FLOW_CELL_SEQUENCED_ON = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_CELL, prop_type_FLOW_CELL_SEQUENCED_ON)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_FLOW_CELL_SEQUENCED_ON.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_FLOW_CELL_SEQUENCED_ON.setSection(None)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_FLOW_CELL_SEQUENCED_ON.setPositionInForms(8)
+
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_SEQUENCER_FINISHED = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_CELL, prop_type_SEQUENCER_FINISHED)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_SEQUENCER_FINISHED.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_SEQUENCER_FINISHED.setSection(None)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_SEQUENCER_FINISHED.setPositionInForms(9)
+
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_RUNNINGTIME = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_CELL, prop_type_RUNNINGTIME)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_RUNNINGTIME.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_RUNNINGTIME.setSection(None)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_RUNNINGTIME.setPositionInForms(10)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_RUNNINGTIME.setScriptName('Diff_time')
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_RUNNINGTIME.setDynamic(True)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_RUNNINGTIME.setManaged(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_RUNNINGTIME.setShownEdit(False)
+
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_ILLUMINA_PIPELINE_VERSION = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_CELL, prop_type_ILLUMINA_PIPELINE_VERSION)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_ILLUMINA_PIPELINE_VERSION.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_ILLUMINA_PIPELINE_VERSION.setSection(None)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_ILLUMINA_PIPELINE_VERSION.setPositionInForms(11)
+
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_CYCLES = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_CELL, prop_type_CYCLES)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_CYCLES.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_CYCLES.setSection(None)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_CYCLES.setPositionInForms(14)
+
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_INDEXREAD = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_CELL, prop_type_INDEXREAD)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_INDEXREAD.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_INDEXREAD.setSection(None)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_INDEXREAD.setPositionInForms(17)
+
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_INDEXREAD2 = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_CELL, prop_type_INDEXREAD2)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_INDEXREAD2.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_INDEXREAD2.setSection(None)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_INDEXREAD2.setPositionInForms(18)
+
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_CONTROL_LANE = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_CELL, prop_type_CONTROL_LANE)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_CONTROL_LANE.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_CONTROL_LANE.setSection(None)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_CONTROL_LANE.setPositionInForms(19)
+
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_FLOWCELLTYPE = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_CELL, prop_type_FLOWCELLTYPE)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_FLOWCELLTYPE.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_FLOWCELLTYPE.setSection(None)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_FLOWCELLTYPE.setPositionInForms(20)
+
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_LANECOUNT = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_CELL, prop_type_LANECOUNT)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_LANECOUNT.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_LANECOUNT.setSection(None)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_LANECOUNT.setPositionInForms(21)
+
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_SURFACECOUNT = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_CELL, prop_type_SURFACECOUNT)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_SURFACECOUNT.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_SURFACECOUNT.setSection(None)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_SURFACECOUNT.setPositionInForms(22)
+
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_SWATHCOUNT = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_CELL, prop_type_SWATHCOUNT)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_SWATHCOUNT.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_SWATHCOUNT.setSection(None)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_SWATHCOUNT.setPositionInForms(23)
+
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_TILECOUNT = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_CELL, prop_type_TILECOUNT)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_TILECOUNT.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_TILECOUNT.setSection(None)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_TILECOUNT.setPositionInForms(24)
+
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_SBS_KIT = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_CELL, prop_type_SBS_KIT)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_SBS_KIT.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_SBS_KIT.setSection(None)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_SBS_KIT.setPositionInForms(25)
+
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_PAIRED_END_KIT = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_CELL, prop_type_PAIRED_END_KIT)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_PAIRED_END_KIT.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_PAIRED_END_KIT.setSection(None)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_PAIRED_END_KIT.setPositionInForms(26)
+
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_CLUSTER_STATION = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_CELL, prop_type_CLUSTER_STATION)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_CLUSTER_STATION.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_CLUSTER_STATION.setSection('Clustering')
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_CLUSTER_STATION.setPositionInForms(27)
+
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_CREATED_ON_CS = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_CELL, prop_type_CREATED_ON_CS)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_CREATED_ON_CS.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_CREATED_ON_CS.setSection('Clustering')
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_CREATED_ON_CS.setPositionInForms(28)
+
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_CS_PROTOCOL_VERSION = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_CELL, prop_type_CS_PROTOCOL_VERSION)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_CS_PROTOCOL_VERSION.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_CS_PROTOCOL_VERSION.setSection('Clustering')
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_CS_PROTOCOL_VERSION.setPositionInForms(29)
+
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_CLUSTER_GENERATION_KIT_VERSION = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_CELL, prop_type_CLUSTER_GENERATION_KIT_VERSION)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_CLUSTER_GENERATION_KIT_VERSION.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_CLUSTER_GENERATION_KIT_VERSION.setSection('Clustering')
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_CLUSTER_GENERATION_KIT_VERSION.setPositionInForms(30)
+
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_SBS_SEQUENCING_KIT_VERSION = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_CELL, prop_type_SBS_SEQUENCING_KIT_VERSION)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_SBS_SEQUENCING_KIT_VERSION.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_SBS_SEQUENCING_KIT_VERSION.setSection(None)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_SBS_SEQUENCING_KIT_VERSION.setPositionInForms(32)
+
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_ANALYSIS_FINISHED = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_CELL, prop_type_ANALYSIS_FINISHED)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_ANALYSIS_FINISHED.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_ANALYSIS_FINISHED.setSection(None)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_ANALYSIS_FINISHED.setPositionInForms(34)
+
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_NOTES = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_CELL, prop_type_NOTES)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_NOTES.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_NOTES.setSection(None)
+assignment_SAMPLE_ILLUMINA_FLOW_CELL_NOTES.setPositionInForms(35)
+
+assignment_SAMPLE_ILLUMINA_FLOW_LANE_CONCENTRATION_FLOWLANE = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_LANE, prop_type_CONCENTRATION_FLOWLANE)
+assignment_SAMPLE_ILLUMINA_FLOW_LANE_CONCENTRATION_FLOWLANE.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_LANE_CONCENTRATION_FLOWLANE.setSection(None)
+assignment_SAMPLE_ILLUMINA_FLOW_LANE_CONCENTRATION_FLOWLANE.setPositionInForms(20)
+
+assignment_SAMPLE_ILLUMINA_FLOW_LANE_NOTES = tr.assignPropertyType(samp_type_ILLUMINA_FLOW_LANE, prop_type_NOTES)
+assignment_SAMPLE_ILLUMINA_FLOW_LANE_NOTES.setMandatory(False)
+assignment_SAMPLE_ILLUMINA_FLOW_LANE_NOTES.setSection(None)
+assignment_SAMPLE_ILLUMINA_FLOW_LANE_NOTES.setPositionInForms(23)
+
+assignment_DATA_SET_ILLUMINA_HISEQ_OUTPUT_CASAVA_VERSION = tr.assignPropertyType(data_set_type_ILLUMINA_HISEQ_OUTPUT, prop_type_CASAVA_VERSION)
+assignment_DATA_SET_ILLUMINA_HISEQ_OUTPUT_CASAVA_VERSION.setMandatory(False)
+assignment_DATA_SET_ILLUMINA_HISEQ_OUTPUT_CASAVA_VERSION.setSection(None)
+assignment_DATA_SET_ILLUMINA_HISEQ_OUTPUT_CASAVA_VERSION.setPositionInForms(3)
+
+assignment_SAMPLE_LIBRARY_EXTERNAL_SAMPLE_NAME = tr.assignPropertyType(samp_type_LIBRARY, prop_type_EXTERNAL_SAMPLE_NAME)
+assignment_SAMPLE_LIBRARY_EXTERNAL_SAMPLE_NAME.setMandatory(False)
+assignment_SAMPLE_LIBRARY_EXTERNAL_SAMPLE_NAME.setSection(None)
+assignment_SAMPLE_LIBRARY_EXTERNAL_SAMPLE_NAME.setPositionInForms(1)
+
+assignment_SAMPLE_LIBRARY_KIT = tr.assignPropertyType(samp_type_LIBRARY, prop_type_KIT)
+assignment_SAMPLE_LIBRARY_KIT.setMandatory(False)
+assignment_SAMPLE_LIBRARY_KIT.setSection(None)
+assignment_SAMPLE_LIBRARY_KIT.setPositionInForms(2)
+
+assignment_SAMPLE_LIBRARY_PREPARED_BY = tr.assignPropertyType(samp_type_LIBRARY, prop_type_PREPARED_BY)
+assignment_SAMPLE_LIBRARY_PREPARED_BY.setMandatory(False)
+assignment_SAMPLE_LIBRARY_PREPARED_BY.setSection(None)
+assignment_SAMPLE_LIBRARY_PREPARED_BY.setPositionInForms(3)
+
+assignment_SAMPLE_LIBRARY_STARTING_AMOUNT_OF_SAMPLE_IN_NG = tr.assignPropertyType(samp_type_LIBRARY, prop_type_STARTING_AMOUNT_OF_SAMPLE_IN_NG)
+assignment_SAMPLE_LIBRARY_STARTING_AMOUNT_OF_SAMPLE_IN_NG.setMandatory(False)
+assignment_SAMPLE_LIBRARY_STARTING_AMOUNT_OF_SAMPLE_IN_NG.setSection(None)
+assignment_SAMPLE_LIBRARY_STARTING_AMOUNT_OF_SAMPLE_IN_NG.setPositionInForms(4)
+
+assignment_SAMPLE_LIBRARY_INDEX1 = tr.assignPropertyType(samp_type_LIBRARY, prop_type_INDEX1)
+assignment_SAMPLE_LIBRARY_INDEX1.setMandatory(False)
+assignment_SAMPLE_LIBRARY_INDEX1.setSection(None)
+assignment_SAMPLE_LIBRARY_INDEX1.setPositionInForms(7)
+
+assignment_SAMPLE_LIBRARY_INDEX2 = tr.assignPropertyType(samp_type_LIBRARY, prop_type_INDEX2)
+assignment_SAMPLE_LIBRARY_INDEX2.setMandatory(False)
+assignment_SAMPLE_LIBRARY_INDEX2.setSection(None)
+assignment_SAMPLE_LIBRARY_INDEX2.setPositionInForms(8)
+
+assignment_SAMPLE_LIBRARY_LOT = tr.assignPropertyType(samp_type_LIBRARY, prop_type_LOT)
+assignment_SAMPLE_LIBRARY_LOT.setMandatory(False)
+assignment_SAMPLE_LIBRARY_LOT.setSection(None)
+assignment_SAMPLE_LIBRARY_LOT.setPositionInForms(9)
+
+assignment_SAMPLE_LIBRARY_AGILENT_KIT = tr.assignPropertyType(samp_type_LIBRARY, prop_type_AGILENT_KIT)
+assignment_SAMPLE_LIBRARY_AGILENT_KIT.setMandatory(False)
+assignment_SAMPLE_LIBRARY_AGILENT_KIT.setSection('QC Data')
+assignment_SAMPLE_LIBRARY_AGILENT_KIT.setPositionInForms(10)
+
+assignment_SAMPLE_LIBRARY_FRAGMENT_SIZE_PREPARED_ILLUMINA = tr.assignPropertyType(samp_type_LIBRARY, prop_type_FRAGMENT_SIZE_PREPARED_ILLUMINA)
+assignment_SAMPLE_LIBRARY_FRAGMENT_SIZE_PREPARED_ILLUMINA.setMandatory(False)
+assignment_SAMPLE_LIBRARY_FRAGMENT_SIZE_PREPARED_ILLUMINA.setSection('QC Data')
+assignment_SAMPLE_LIBRARY_FRAGMENT_SIZE_PREPARED_ILLUMINA.setPositionInForms(11)
+
+assignment_SAMPLE_LIBRARY_NANO_DROP = tr.assignPropertyType(samp_type_LIBRARY, prop_type_NANO_DROP)
+assignment_SAMPLE_LIBRARY_NANO_DROP.setMandatory(False)
+assignment_SAMPLE_LIBRARY_NANO_DROP.setSection('QC Data')
+assignment_SAMPLE_LIBRARY_NANO_DROP.setPositionInForms(12)
+
+assignment_SAMPLE_LIBRARY_CONCENTRATION_PREPARED_ILLUMINA = tr.assignPropertyType(samp_type_LIBRARY, prop_type_CONCENTRATION_PREPARED_ILLUMINA)
+assignment_SAMPLE_LIBRARY_CONCENTRATION_PREPARED_ILLUMINA.setMandatory(False)
+assignment_SAMPLE_LIBRARY_CONCENTRATION_PREPARED_ILLUMINA.setSection('QC Data')
+assignment_SAMPLE_LIBRARY_CONCENTRATION_PREPARED_ILLUMINA.setPositionInForms(13)
+
+assignment_SAMPLE_LIBRARY_DNA_CONCENTRATION_OF_LIBRARY = tr.assignPropertyType(samp_type_LIBRARY, prop_type_DNA_CONCENTRATION_OF_LIBRARY)
+assignment_SAMPLE_LIBRARY_DNA_CONCENTRATION_OF_LIBRARY.setMandatory(False)
+assignment_SAMPLE_LIBRARY_DNA_CONCENTRATION_OF_LIBRARY.setSection('QC Data')
+assignment_SAMPLE_LIBRARY_DNA_CONCENTRATION_OF_LIBRARY.setPositionInForms(14)
+
+assignment_SAMPLE_LIBRARY_LIBRARY_PROCESSING_SUCCESSFUL = tr.assignPropertyType(samp_type_LIBRARY, prop_type_LIBRARY_PROCESSING_SUCCESSFUL)
+assignment_SAMPLE_LIBRARY_LIBRARY_PROCESSING_SUCCESSFUL.setMandatory(False)
+assignment_SAMPLE_LIBRARY_LIBRARY_PROCESSING_SUCCESSFUL.setSection('QC Data')
+assignment_SAMPLE_LIBRARY_LIBRARY_PROCESSING_SUCCESSFUL.setPositionInForms(15)
+
+assignment_SAMPLE_LIBRARY_LIBRARY_PROCESSING_FAILED = tr.assignPropertyType(samp_type_LIBRARY, prop_type_LIBRARY_PROCESSING_FAILED)
+assignment_SAMPLE_LIBRARY_LIBRARY_PROCESSING_FAILED.setMandatory(False)
+assignment_SAMPLE_LIBRARY_LIBRARY_PROCESSING_FAILED.setSection('QC Data')
+assignment_SAMPLE_LIBRARY_LIBRARY_PROCESSING_FAILED.setPositionInForms(16)
+
+assignment_SAMPLE_LIBRARY_QC_AT_DBSSE = tr.assignPropertyType(samp_type_LIBRARY, prop_type_QC_AT_DBSSE)
+assignment_SAMPLE_LIBRARY_QC_AT_DBSSE.setMandatory(False)
+assignment_SAMPLE_LIBRARY_QC_AT_DBSSE.setSection('QC Data')
+assignment_SAMPLE_LIBRARY_QC_AT_DBSSE.setPositionInForms(17)
+
+assignment_SAMPLE_LIBRARY_KIT_PREPARED = tr.assignPropertyType(samp_type_LIBRARY, prop_type_KIT_PREPARED)
+assignment_SAMPLE_LIBRARY_KIT_PREPARED.setMandatory(False)
+assignment_SAMPLE_LIBRARY_KIT_PREPARED.setSection(None)
+assignment_SAMPLE_LIBRARY_KIT_PREPARED.setPositionInForms(18)
+
+assignment_SAMPLE_LIBRARY_DATA_TRANSFERRED = tr.assignPropertyType(samp_type_LIBRARY, prop_type_DATA_TRANSFERRED)
+assignment_SAMPLE_LIBRARY_DATA_TRANSFERRED.setMandatory(False)
+assignment_SAMPLE_LIBRARY_DATA_TRANSFERRED.setSection(None)
+assignment_SAMPLE_LIBRARY_DATA_TRANSFERRED.setPositionInForms(19)
+
+assignment_SAMPLE_LIBRARY_INVOICE = tr.assignPropertyType(samp_type_LIBRARY, prop_type_INVOICE)
+assignment_SAMPLE_LIBRARY_INVOICE.setMandatory(False)
+assignment_SAMPLE_LIBRARY_INVOICE.setSection(None)
+assignment_SAMPLE_LIBRARY_INVOICE.setPositionInForms(20)
+
+assignment_SAMPLE_LIBRARY_NOTES = tr.assignPropertyType(samp_type_LIBRARY, prop_type_NOTES)
+assignment_SAMPLE_LIBRARY_NOTES.setMandatory(False)
+assignment_SAMPLE_LIBRARY_NOTES.setSection(None)
+assignment_SAMPLE_LIBRARY_NOTES.setPositionInForms(33)
+
+assignment_SAMPLE_LIBRARY_POOL_EXTERNAL_SAMPLE_NAME = tr.assignPropertyType(samp_type_LIBRARY_POOL, prop_type_EXTERNAL_SAMPLE_NAME)
+assignment_SAMPLE_LIBRARY_POOL_EXTERNAL_SAMPLE_NAME.setMandatory(False)
+assignment_SAMPLE_LIBRARY_POOL_EXTERNAL_SAMPLE_NAME.setSection(None)
+assignment_SAMPLE_LIBRARY_POOL_EXTERNAL_SAMPLE_NAME.setPositionInForms(1)
+
+assignment_SAMPLE_LIBRARY_POOL_PREPARED_BY = tr.assignPropertyType(samp_type_LIBRARY_POOL, prop_type_PREPARED_BY)
+assignment_SAMPLE_LIBRARY_POOL_PREPARED_BY.setMandatory(False)
+assignment_SAMPLE_LIBRARY_POOL_PREPARED_BY.setSection(None)
+assignment_SAMPLE_LIBRARY_POOL_PREPARED_BY.setPositionInForms(2)
+
+assignment_SAMPLE_LIBRARY_POOL_DNA_CONCENTRATION_POOL = tr.assignPropertyType(samp_type_LIBRARY_POOL, prop_type_DNA_CONCENTRATION_POOL)
+assignment_SAMPLE_LIBRARY_POOL_DNA_CONCENTRATION_POOL.setMandatory(False)
+assignment_SAMPLE_LIBRARY_POOL_DNA_CONCENTRATION_POOL.setSection(None)
+assignment_SAMPLE_LIBRARY_POOL_DNA_CONCENTRATION_POOL.setPositionInForms(3)
+
+assignment_SAMPLE_LIBRARY_POOL_QC_REQUIRED = tr.assignPropertyType(samp_type_LIBRARY_POOL, prop_type_QC_REQUIRED)
+assignment_SAMPLE_LIBRARY_POOL_QC_REQUIRED.setMandatory(False)
+assignment_SAMPLE_LIBRARY_POOL_QC_REQUIRED.setSection(None)
+assignment_SAMPLE_LIBRARY_POOL_QC_REQUIRED.setPositionInForms(4)
+
+assignment_SAMPLE_LIBRARY_POOL_AGILENT_KIT = tr.assignPropertyType(samp_type_LIBRARY_POOL, prop_type_AGILENT_KIT)
+assignment_SAMPLE_LIBRARY_POOL_AGILENT_KIT.setMandatory(False)
+assignment_SAMPLE_LIBRARY_POOL_AGILENT_KIT.setSection('QC Data')
+assignment_SAMPLE_LIBRARY_POOL_AGILENT_KIT.setPositionInForms(5)
+
+assignment_SAMPLE_LIBRARY_POOL_FRAGMENT_SIZE_BASE_PAIRS = tr.assignPropertyType(samp_type_LIBRARY_POOL, prop_type_FRAGMENT_SIZE_BASE_PAIRS)
+assignment_SAMPLE_LIBRARY_POOL_FRAGMENT_SIZE_BASE_PAIRS.setMandatory(False)
+assignment_SAMPLE_LIBRARY_POOL_FRAGMENT_SIZE_BASE_PAIRS.setSection('QC Data')
+assignment_SAMPLE_LIBRARY_POOL_FRAGMENT_SIZE_BASE_PAIRS.setPositionInForms(6)
+
+assignment_SAMPLE_LIBRARY_POOL_NANO_DROP = tr.assignPropertyType(samp_type_LIBRARY_POOL, prop_type_NANO_DROP)
+assignment_SAMPLE_LIBRARY_POOL_NANO_DROP.setMandatory(False)
+assignment_SAMPLE_LIBRARY_POOL_NANO_DROP.setSection('QC Data')
+assignment_SAMPLE_LIBRARY_POOL_NANO_DROP.setPositionInForms(7)
+
+assignment_SAMPLE_LIBRARY_POOL_CONCENTRATION = tr.assignPropertyType(samp_type_LIBRARY_POOL, prop_type_CONCENTRATION)
+assignment_SAMPLE_LIBRARY_POOL_CONCENTRATION.setMandatory(False)
+assignment_SAMPLE_LIBRARY_POOL_CONCENTRATION.setSection('QC Data')
+assignment_SAMPLE_LIBRARY_POOL_CONCENTRATION.setPositionInForms(8)
+
+assignment_SAMPLE_LIBRARY_POOL_DNA_CONCENTRATION_QGF = tr.assignPropertyType(samp_type_LIBRARY_POOL, prop_type_DNA_CONCENTRATION_QGF)
+assignment_SAMPLE_LIBRARY_POOL_DNA_CONCENTRATION_QGF.setMandatory(False)
+assignment_SAMPLE_LIBRARY_POOL_DNA_CONCENTRATION_QGF.setSection('QC Data')
+assignment_SAMPLE_LIBRARY_POOL_DNA_CONCENTRATION_QGF.setPositionInForms(9)
+
+assignment_SAMPLE_LIBRARY_POOL_INVOICE = tr.assignPropertyType(samp_type_LIBRARY_POOL, prop_type_INVOICE)
+assignment_SAMPLE_LIBRARY_POOL_INVOICE.setMandatory(False)
+assignment_SAMPLE_LIBRARY_POOL_INVOICE.setSection(None)
+assignment_SAMPLE_LIBRARY_POOL_INVOICE.setPositionInForms(10)
+
+assignment_SAMPLE_LIBRARY_POOL_NOTES = tr.assignPropertyType(samp_type_LIBRARY_POOL, prop_type_NOTES)
+assignment_SAMPLE_LIBRARY_POOL_NOTES.setMandatory(False)
+assignment_SAMPLE_LIBRARY_POOL_NOTES.setSection(None)
+assignment_SAMPLE_LIBRARY_POOL_NOTES.setPositionInForms(11)
+
+assignment_DATA_SET_MACS_OUTPUT_MACS_VERSION = tr.assignPropertyType(data_set_type_MACS_OUTPUT, prop_type_MACS_VERSION)
+assignment_DATA_SET_MACS_OUTPUT_MACS_VERSION.setMandatory(False)
+assignment_DATA_SET_MACS_OUTPUT_MACS_VERSION.setSection(None)
+assignment_DATA_SET_MACS_OUTPUT_MACS_VERSION.setPositionInForms(3)
+
+assignment_DATA_SET_MACS_OUTPUT_NOTES = tr.assignPropertyType(data_set_type_MACS_OUTPUT, prop_type_NOTES)
+assignment_DATA_SET_MACS_OUTPUT_NOTES.setMandatory(False)
+assignment_DATA_SET_MACS_OUTPUT_NOTES.setSection(None)
+assignment_DATA_SET_MACS_OUTPUT_NOTES.setPositionInForms(4)
+
+assignment_SAMPLE_MASTER_SAMPLE_BIOLOGICAL_SAMPLE_ARRIVED = tr.assignPropertyType(samp_type_MASTER_SAMPLE, prop_type_BIOLOGICAL_SAMPLE_ARRIVED)
+assignment_SAMPLE_MASTER_SAMPLE_BIOLOGICAL_SAMPLE_ARRIVED.setMandatory(True)
+assignment_SAMPLE_MASTER_SAMPLE_BIOLOGICAL_SAMPLE_ARRIVED.setSection(None)
+assignment_SAMPLE_MASTER_SAMPLE_BIOLOGICAL_SAMPLE_ARRIVED.setPositionInForms(1)
+
+assignment_SAMPLE_MASTER_SAMPLE_CONTACT_PERSON_EMAIL = tr.assignPropertyType(samp_type_MASTER_SAMPLE, prop_type_CONTACT_PERSON_EMAIL)
+assignment_SAMPLE_MASTER_SAMPLE_CONTACT_PERSON_EMAIL.setMandatory(True)
+assignment_SAMPLE_MASTER_SAMPLE_CONTACT_PERSON_EMAIL.setSection(None)
+assignment_SAMPLE_MASTER_SAMPLE_CONTACT_PERSON_EMAIL.setPositionInForms(2)
+
+assignment_SAMPLE_MASTER_SAMPLE_CONTACT_PERSON_NAME = tr.assignPropertyType(samp_type_MASTER_SAMPLE, prop_type_CONTACT_PERSON_NAME)
+assignment_SAMPLE_MASTER_SAMPLE_CONTACT_PERSON_NAME.setMandatory(True)
+assignment_SAMPLE_MASTER_SAMPLE_CONTACT_PERSON_NAME.setSection(None)
+assignment_SAMPLE_MASTER_SAMPLE_CONTACT_PERSON_NAME.setPositionInForms(3)
+
+assignment_SAMPLE_MASTER_SAMPLE_PRINCIPAL_INVESTIGATOR_EMAIL = tr.assignPropertyType(samp_type_MASTER_SAMPLE, prop_type_PRINCIPAL_INVESTIGATOR_EMAIL)
+assignment_SAMPLE_MASTER_SAMPLE_PRINCIPAL_INVESTIGATOR_EMAIL.setMandatory(True)
+assignment_SAMPLE_MASTER_SAMPLE_PRINCIPAL_INVESTIGATOR_EMAIL.setSection(None)
+assignment_SAMPLE_MASTER_SAMPLE_PRINCIPAL_INVESTIGATOR_EMAIL.setPositionInForms(4)
+
+assignment_SAMPLE_MASTER_SAMPLE_PRINCIPAL_INVESTIGATOR_NAME = tr.assignPropertyType(samp_type_MASTER_SAMPLE, prop_type_PRINCIPAL_INVESTIGATOR_NAME)
+assignment_SAMPLE_MASTER_SAMPLE_PRINCIPAL_INVESTIGATOR_NAME.setMandatory(True)
+assignment_SAMPLE_MASTER_SAMPLE_PRINCIPAL_INVESTIGATOR_NAME.setSection(None)
+assignment_SAMPLE_MASTER_SAMPLE_PRINCIPAL_INVESTIGATOR_NAME.setPositionInForms(5)
+
+assignment_SAMPLE_MASTER_SAMPLE_NCBI_ORGANISM_TAXONOMY = tr.assignPropertyType(samp_type_MASTER_SAMPLE, prop_type_NCBI_ORGANISM_TAXONOMY)
+assignment_SAMPLE_MASTER_SAMPLE_NCBI_ORGANISM_TAXONOMY.setMandatory(True)
+assignment_SAMPLE_MASTER_SAMPLE_NCBI_ORGANISM_TAXONOMY.setSection(None)
+assignment_SAMPLE_MASTER_SAMPLE_NCBI_ORGANISM_TAXONOMY.setPositionInForms(7)
+
+assignment_SAMPLE_MASTER_SAMPLE_SAMPLE_KIND = tr.assignPropertyType(samp_type_MASTER_SAMPLE, prop_type_SAMPLE_KIND)
+assignment_SAMPLE_MASTER_SAMPLE_SAMPLE_KIND.setMandatory(True)
+assignment_SAMPLE_MASTER_SAMPLE_SAMPLE_KIND.setSection(None)
+assignment_SAMPLE_MASTER_SAMPLE_SAMPLE_KIND.setPositionInForms(21)
+
+assignment_SAMPLE_MASTER_SAMPLE_NOTES = tr.assignPropertyType(samp_type_MASTER_SAMPLE, prop_type_NOTES)
+assignment_SAMPLE_MASTER_SAMPLE_NOTES.setMandatory(False)
+assignment_SAMPLE_MASTER_SAMPLE_NOTES.setSection(None)
+assignment_SAMPLE_MASTER_SAMPLE_NOTES.setPositionInForms(22)
+
+assignment_SAMPLE_RAW_SAMPLE_EXTERNAL_SAMPLE_NAME = tr.assignPropertyType(samp_type_RAW_SAMPLE, prop_type_EXTERNAL_SAMPLE_NAME)
+assignment_SAMPLE_RAW_SAMPLE_EXTERNAL_SAMPLE_NAME.setMandatory(False)
+assignment_SAMPLE_RAW_SAMPLE_EXTERNAL_SAMPLE_NAME.setSection(None)
+assignment_SAMPLE_RAW_SAMPLE_EXTERNAL_SAMPLE_NAME.setPositionInForms(1)
+
+assignment_SAMPLE_RAW_SAMPLE_CONCENTRATION_ORIGINAL_ILLUMINA = tr.assignPropertyType(samp_type_RAW_SAMPLE, prop_type_CONCENTRATION_ORIGINAL_ILLUMINA)
+assignment_SAMPLE_RAW_SAMPLE_CONCENTRATION_ORIGINAL_ILLUMINA.setMandatory(False)
+assignment_SAMPLE_RAW_SAMPLE_CONCENTRATION_ORIGINAL_ILLUMINA.setSection(None)
+assignment_SAMPLE_RAW_SAMPLE_CONCENTRATION_ORIGINAL_ILLUMINA.setPositionInForms(4)
+
+assignment_SAMPLE_RAW_SAMPLE_PREPARED_BY = tr.assignPropertyType(samp_type_RAW_SAMPLE, prop_type_PREPARED_BY)
+assignment_SAMPLE_RAW_SAMPLE_PREPARED_BY.setMandatory(False)
+assignment_SAMPLE_RAW_SAMPLE_PREPARED_BY.setSection(None)
+assignment_SAMPLE_RAW_SAMPLE_PREPARED_BY.setPositionInForms(8)
+
+assignment_SAMPLE_RAW_SAMPLE_KIT_PREPARED = tr.assignPropertyType(samp_type_RAW_SAMPLE, prop_type_KIT_PREPARED)
+assignment_SAMPLE_RAW_SAMPLE_KIT_PREPARED.setMandatory(False)
+assignment_SAMPLE_RAW_SAMPLE_KIT_PREPARED.setSection(None)
+assignment_SAMPLE_RAW_SAMPLE_KIT_PREPARED.setPositionInForms(9)
+
+assignment_SAMPLE_RAW_SAMPLE_LIBRARY_PROCESSING_POSSIBLE_YES_NO = tr.assignPropertyType(samp_type_RAW_SAMPLE, prop_type_LIBRARY_PROCESSING_POSSIBLE_YES_NO)
+assignment_SAMPLE_RAW_SAMPLE_LIBRARY_PROCESSING_POSSIBLE_YES_NO.setMandatory(False)
+assignment_SAMPLE_RAW_SAMPLE_LIBRARY_PROCESSING_POSSIBLE_YES_NO.setSection(None)
+assignment_SAMPLE_RAW_SAMPLE_LIBRARY_PROCESSING_POSSIBLE_YES_NO.setPositionInForms(10)
+
+assignment_SAMPLE_RAW_SAMPLE_NOTES = tr.assignPropertyType(samp_type_RAW_SAMPLE, prop_type_NOTES)
+assignment_SAMPLE_RAW_SAMPLE_NOTES.setMandatory(False)
+assignment_SAMPLE_RAW_SAMPLE_NOTES.setSection(None)
+assignment_SAMPLE_RAW_SAMPLE_NOTES.setPositionInForms(13)
+
+print "Imported 104 Property Assignments"
+print "Imported 0 External DMSs"
+print ("Import of Master Data finished.")
\ No newline at end of file
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/data-sources/.gitignore b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/data-sources/.gitignore
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/create-flowcell-hiseq/create-flowcell-hiseq.py b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/create-flowcell-hiseq/create-flowcell-hiseq.py
new file mode 100644
index 00000000000..c65531875bd
--- /dev/null
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/create-flowcell-hiseq/create-flowcell-hiseq.py
@@ -0,0 +1,209 @@
+'''
+@copyright:
+2013 ETH Zuerich, CISD
+
+@license:
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+@description:
+Parses the two Illumina provided files 'runParameters.xml' and 'RunInfo.xml'
+and creates one Sample of type 'ILLUMINA_FLOW_CELL' and sets Sample properties
+from those two XML files. Additionally the number of lanes are read out and
+are created as contained samples of type 'ILLUMINA_FLOW_LANE'.
+
+@note:
+print statements go to: <openBIS_HOME>/datastore_server/log/startup_log.txt
+expected incoming Name for HiSeq runs: 110715_SN792_0054_BC035RACXX
+
+structure:
+110715_SN792_0054_BC035RACXX/
+ runParameters.xml
+ RunInfo.xml
+
+The run folder created by the HiSeq sequencer is used to create a new
+ILLUMINA_FLOW_CELL in openBIS. The properties are then set by parsing the
+two XML files in this folder.
+
+@author:
+Manuel Kohler
+'''
+
+import os
+import shutil
+from time import *
+from datetime import *
+import xml.etree.ElementTree as etree
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
+
+RUNPARAMETERS = 'runParameters.xml'
+RUNINFO = 'RunInfo.xml'
+FLOWCELL_SPACE='BSSE_FLOWCELLS'
+FLOWCELL_PROJECT='FLOWCELLS'
+EXPERIMENT_TYPE_CODE='HT_SEQUENCING'
+FLOW_CELL='ILLUMINA_FLOW_CELL'
+FLOW_LANE='ILLUMINA_FLOW_LANE'
+
+FLOWCELL_PROJECT_ID = "/%(FLOWCELL_SPACE)s/%(FLOWCELL_PROJECT)s" % vars()
+
+# Mapping between XML file naming and used in here
+RUNPARAMETERS_XML = {'FLOWCELL':'Flowcell', 'RTAVERSION':'RTAVersion',
+ 'CONTROLLANE':'ControlLane', 'SBS':'Sbs', 'INDEX':'Index',
+ 'CYCLES':'Read1', 'PE':'Pe'}
+RUNINFO_XML = {'LANECOUNT':'LaneCount', 'SURFACECOUNT':'SurfaceCount',
+ 'SWATHCOUNT':'SwathCount', 'TILECOUNT':'TileCount'}
+
+class parseXmlFile:
+
+ def __init__(self, xmlFile):
+ self.xmlFile = xmlFile
+ self.tree = etree.parse(self.xmlFile)
+ self.root = self.tree.getroot()
+
+ def getXmlElement (self, elementName):
+ '''
+ Returns the text value of a given XML element
+ '''
+ for e in self.root.getchildren():
+ element = e.find(elementName)
+ if element is None:
+ return 'None'
+ else:
+ return element.text
+
+ def getAllchildren (self, elementName):
+ '''
+ finds all children of a given XML Element and returns them as list
+ '''
+ for e in self.root.getchildren():
+ # the '//' means look recursively for all children not only direct ones
+ childList = self.tree.findall('//' + elementName)
+ return childList
+
+# -----------------------------------------------------------------------------
+
+def create_openbis_timestamp ():
+ '''
+ Create an openBIS conform timestamp
+ '''
+ tz=localtime()[3]-gmtime()[3]
+ d=datetime.now()
+ return d.strftime("%Y-%m-%d %H:%M:%S GMT"+"%+.2d" % tz+":00")
+
+# -----------------------------------------------------------------------------
+
+def registerFlowLane(transaction, a_lane, flowCellName, newFlowCell):
+ '''
+ Registers a new Flow lane
+ '''
+ newFlowLane = transaction.createNewSample('/' + FLOWCELL_SPACE + '/' + flowCellName +
+ ':' + str(a_lane), FLOW_LANE)
+ newFlowLane.setContainer(newFlowCell)
+
+# -----------------------------------------------------------------------------
+
+def extractFlowCellName (runFolderName):
+ return runFolderName.split('_')[-1][1:]
+
+# -----------------------------------------------------------------------------
+
+def searchFlowCell (transaction, flowCellName):
+ '''
+ Search for the sample and check if there is already sample with this name
+ '''
+ search_service = transaction.getSearchService()
+ sc = SearchCriteria()
+ sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch( \
+ SearchCriteria.MatchClauseAttribute.CODE, flowCellName));
+ foundSamples = search_service.searchForSamples(sc)
+ if foundSamples.size() > 0:
+ raise NameError('Already found a flow cell with the following name: '+ flowCellName)
+ return foundSamples
+
+# -----------------------------------------------------------------------------
+
+def process(transaction):
+
+ incoming = transaction.getIncoming()
+ incomingPath = incoming.getAbsolutePath()
+
+ runFolderName = incoming.getName()
+ flowCellName = runFolderName.split('_')[-1][1:]
+
+ searchFlowCell (transaction, flowCellName)
+
+ # Parse the RunInfo.xml file
+ runInfo = parseXmlFile(incomingPath + '/' + RUNINFO)
+
+ # Create a new Flow Cell and set the experiment
+ project = transaction.getProject(FLOWCELL_PROJECT_ID)
+ if project == None:
+ space = transaction.getSpace(FLOWCELL_SPACE)
+ if space == None:
+ space = transaction.createNewSpace(FLOWCELL_SPACE, None)
+ project = transaction.createNewProject(FLOWCELL_PROJECT_ID)
+ expID = FLOWCELL_PROJECT_ID + '/' + datetime.now().strftime("%Y.%m")
+ exp = transaction.getExperiment(expID)
+ if exp == None:
+ exp = transaction.createNewExperiment(expID, EXPERIMENT_TYPE_CODE)
+ newFlowCell = transaction.createNewSample('/' + FLOWCELL_SPACE + '/' + flowCellName, FLOW_CELL)
+ newFlowCell.setExperiment(exp)
+
+ run = runInfo.getAllchildren('Run')[0].attrib
+ if (extractFlowCellName(run['Id']) != flowCellName):
+ raise NameError('Flowcell names do not match between directory name '+ flowCellName +
+ ' and ' + RUNINFO + 'property file: ' + extractFlowCellName(run['Id']))
+
+
+ # The HiSeq is providing more infos in the runParameters.xml, which we will parse here:
+ runParameters = parseXmlFile(incomingPath + '/' + RUNPARAMETERS)
+
+ newFlowCell.setPropertyValue("RUN_FOLDER_NAME", runFolderName)
+ newFlowCell.setPropertyValue("ILLUMINA_PIPELINE_VERSION", runParameters.getXmlElement(RUNPARAMETERS_XML['RTAVERSION']))
+ newFlowCell.setPropertyValue("FLOWCELLTYPE", runParameters.getXmlElement(RUNPARAMETERS_XML['FLOWCELL']))
+ newFlowCell.setPropertyValue("CONTROL_LANE", runParameters.getXmlElement(RUNPARAMETERS_XML['CONTROLLANE']))
+ newFlowCell.setPropertyValue("SBS_KIT", runParameters.getXmlElement(RUNPARAMETERS_XML['SBS']))
+
+ read1 = runParameters.getAllchildren('Read1')
+ newFlowCell.setPropertyValue("CYCLES", read1[0].text)
+
+ read2 = runParameters.getAllchildren('Read2')
+ if (str(read2[0].text) == '0'):
+ newFlowCell.setPropertyValue("END_TYPE", "SINGLE_READ")
+ else:
+ newFlowCell.setPropertyValue("END_TYPE", "PAIRED_END")
+ newFlowCell.setPropertyValue("PAIRED_END_KIT", runParameters.getXmlElement(RUNPARAMETERS_XML['PE']))
+
+ indexRead1 = runParameters.getAllchildren('IndexRead1')
+ newFlowCell.setPropertyValue("INDEXREAD", indexRead1[0].text)
+
+ indexRead2 = runParameters.getAllchildren('IndexRead2')
+ newFlowCell.setPropertyValue("INDEXREAD2", indexRead2[0].text)
+
+ def setFcProperty(searchId, dict):
+ children = runInfo.getAllchildren(searchId)
+ for element in (dict):
+ if (element <> '') and (dict[element] <> ''):
+ newFlowCell.setPropertyValue(element, children[0].attrib[dict[element]])
+
+ setFcProperty('FlowcellLayout', RUNINFO_XML)
+
+ sequencer = runInfo.getAllchildren('Instrument')
+ newFlowCell.setPropertyValue("SEQUENCER", sequencer[0].text)
+
+ newFlowCell.setPropertyValue("FLOW_CELL_SEQUENCED_ON", create_openbis_timestamp())
+ try:
+ maxLanes = runInfo.getAllchildren('FlowcellLayout')[0].attrib[RUNINFO_XML['LANECOUNT']]
+ except:
+ maxLanes = len(runInfo.getAllchildren('Tiles')[0])
+
+ [registerFlowLane(transaction, lane, flowCellName, newFlowCell) for lane in range(1,int(maxLanes)+1)]
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/create-flowcell-hiseq/plugin.properties b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/create-flowcell-hiseq/plugin.properties
new file mode 100644
index 00000000000..5c56666b206
--- /dev/null
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/create-flowcell-hiseq/plugin.properties
@@ -0,0 +1,12 @@
+#
+# Drop box for creating a flow cell based on runParameters.xml and RunInfo.xml created by an
+# Illumina HiSeq
+#
+# Variables:
+# incoming-root-dir
+# Path to the directory which contains incoming directories for drop boxes.
+incoming-dir = ${incoming-root-dir}/create-flowcell-hiseq
+incoming-data-completeness-condition = marker-file
+top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
+script-path = create-flowcell-hiseq.py
+storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/read-rta-timestamp/plugin.properties b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/read-rta-timestamp/plugin.properties
new file mode 100644
index 00000000000..ef56111b768
--- /dev/null
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/read-rta-timestamp/plugin.properties
@@ -0,0 +1,11 @@
+#
+# Drop box for registering a flow cell output as a data set
+#
+# Variables:
+# incoming-root-dir
+# Path to the directory which contains incoming directories for drop boxes.
+incoming-dir = ${incoming-root-dir}/read-rta-timestamp
+incoming-data-completeness-condition = marker-file
+top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
+script-path = read-rta-timestamp.py
+storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/read-rta-timestamp/read-rta-timestamp.py b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/read-rta-timestamp/read-rta-timestamp.py
new file mode 100644
index 00000000000..2b1687925ad
--- /dev/null
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/read-rta-timestamp/read-rta-timestamp.py
@@ -0,0 +1,76 @@
+'''
+@copyright:
+2013 ETH Zuerich, CISD
+
+@license:
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+@description:
+Reads out the time stamp of the file 'RTAComplete.txt' and sets the
+property for a finished sequencer called 'SEQUENCER_FINISHED' to the
+time stamp of this file.
+
+@note:
+print statements go to: <openBIS_HOME>/datastore_server/log/startup_log.txt
+expected incoming Name for HiSeq runs: 110715_SN792_0054_BC035RACXX
+
+structure:
+110715_SN792_0054_BC035RACXX/
+ RTAComplete.txt
+
+@author:
+Manuel Kohler
+'''
+
+import os
+import shutil
+from time import *
+from datetime import *
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
+
+MarkerHiSeqComplete = 'RTAComplete.txt'
+
+def createOpenbisTimeStamp(file):
+ '''
+ Creates a openBIS compatible time stamp of a file time stamp
+ '''
+ mtime = os.path.getmtime(file)
+ lt = localtime(mtime)
+ tz = localtime().tm_hour - gmtime().tm_hour
+ return (strftime("%Y-%m-%d %H:%M:%S GMT" + "%+.2d" % tz + ":00", lt))
+
+# -----------------------------------------------------------------------------
+
+def extractFlowCellName (runFolderName):
+ return runFolderName.split('_')[-1][1:]
+
+# -----------------------------------------------------------------------------
+
+def process(transaction):
+
+ incomingPath = transaction.getIncoming().getAbsolutePath()
+ # Get the incoming name
+ runFolderName = transaction.getIncoming().getName()
+ flowCellName = extractFlowCellName(runFolderName)
+
+ Markerfile = incomingPath + "/" + MarkerHiSeqComplete
+
+ # Search for the sample and check if there is already sample with this name
+ search_service = transaction.getSearchService()
+ sc = SearchCriteria()
+ sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, flowCellName));
+ foundSamples = search_service.searchForSamples(sc)
+
+ if foundSamples.size() > 0:
+ sa = transaction.getSampleForUpdate(foundSamples[0].getSampleIdentifier())
+ sa.setPropertyValue("SEQUENCER_FINISHED", createOpenbisTimeStamp(Markerfile))
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-basecall-stats/plugin.properties b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-basecall-stats/plugin.properties
new file mode 100644
index 00000000000..d6e67945db5
--- /dev/null
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-basecall-stats/plugin.properties
@@ -0,0 +1,11 @@
+#
+# Drop box for registering a flow cell output as a data set
+#
+# Variables:
+# incoming-root-dir
+# Path to the directory which contains incoming directories for drop boxes.
+incoming-dir = ${incoming-root-dir}/register-basecall-stats
+incoming-data-completeness-condition = marker-file
+top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
+script-path = register-basecall-stats.py
+storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-basecall-stats/register-basecall-stats.py b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-basecall-stats/register-basecall-stats.py
new file mode 100644
index 00000000000..4c47f6a072d
--- /dev/null
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-basecall-stats/register-basecall-stats.py
@@ -0,0 +1,62 @@
+'''
+@copyright:
+2013 ETH Zuerich, CISD
+
+@license:
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+@description:
+Registers an incoming directory as a 'BASECALL_STATS' data set in openBIS.
+The name of the directory is used to search for the matching sample.
+
+@note:
+print statements go to: <openBIS_HOME>/datastore_server/log/startup_log.txt
+expected incoming Name for HiSeq runs: C035RACXX_1
+expected incoming Name for MiSeq runs: A0T19_1
+
+@author:
+Manuel Kohler
+'''
+
+import os
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchSubCriteria
+
+# -----------------------------------------------------------------------------
+
+def extractFlowCellName (runFolderName):
+ flowCell, flowLane = runFolderName.split('_')
+ return flowCell, flowLane
+
+# -----------------------------------------------------------------------------
+
+def process(transaction):
+
+ runFolderName = transaction.getIncoming().getName()
+ incomingPath = transaction.getIncoming().getPath()
+ flowCellName, flowLaneName = extractFlowCellName(runFolderName)
+
+ # Create a data set and set type
+ dataSet = transaction.createNewDataSet("BASECALL_STATS")
+ dataSet.setMeasuredData(False)
+
+ dataSet.setPropertyValue("MISMATCH_IN_INDEX", "NONE")
+
+ search_service = transaction.getSearchService()
+ transaction.moveFile(incomingPath, dataSet)
+ sc = SearchCriteria()
+ sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, flowCellName + ':' + flowLaneName))
+ foundSamples = search_service.searchForSamples(sc)
+
+ if foundSamples.size() > 0:
+ dataSet.setSample(foundSamples[0])
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-flowcell/plugin.properties b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-flowcell/plugin.properties
new file mode 100644
index 00000000000..697c1d5d3cb
--- /dev/null
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-flowcell/plugin.properties
@@ -0,0 +1,11 @@
+#
+# Drop box for registering a flow cell output as a data set
+#
+# Variables:
+# incoming-root-dir
+# Path to the directory which contains incoming directories for drop boxes.
+incoming-dir = ${incoming-root-dir}/register-flowcell-hiseq
+incoming-data-completeness-condition = marker-file
+top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
+script-path = register-flowcell-hiseq.py
+storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-flowcell/register-flowcell-hiseq.py b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-flowcell/register-flowcell-hiseq.py
new file mode 100644
index 00000000000..4b2251d72bc
--- /dev/null
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-flowcell/register-flowcell-hiseq.py
@@ -0,0 +1,138 @@
+'''
+@copyright:
+2013 ETH Zuerich, CISD
+
+@license:
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+@description:
+Registers an incoming directory as a data set in openBIS. The name of the directory is used to
+search for the matching sample.
+
+@note:
+print statements go to: <openBIS_HOME>/datastore_server/log/startup_log.txt
+expected incoming Name for HiSeq runs: 110715_SN792_0054_BC035RACXX
+expected incoming Name for GAII runs: 110812_6353WAAXX
+
+@author:
+Manuel Kohler
+'''
+
+import os
+import shutil
+import glob
+import xml.etree.ElementTree as etree
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
+
+REGEX_RUNINFO_SAMPLE = '/Data/Status*'
+REGEX_RUNINFO_REPORTS = '/Data/reports'
+MARKER_STRING = '.MARKER_is_finished_'
+RUNSTATISTICS_DROPBOX = 'register-runstatistics'
+
+# -----------------------------------------------------------------------------
+
+def extractRunData (runFolderName, transaction):
+ '''
+ Splits the incoming folder name and extracts infos out of it
+ HiSeq example:
+ ['130227', 'SN792', '0211', 'BC1RPGACXX']
+ MiSeq example:
+ ['130227', 'M00721', '0036', '000000000-A3BAV']
+ '''
+ runDataDict = {}
+ date, sequencerID, runningNumber, flowCellId = runFolderName.split('_')
+ runDataDict['date'] = date
+ runDataDict['sequencerID'] = sequencerID
+ runDataDict['runningNumber'] = runningNumber
+
+ if not sequencerID.startswith('M'):
+ runDataDict['compartment'] = flowCellId[0]
+ runDataDict['flowCellId'] = flowCellId[1:]
+ dataSet = transaction.createNewDataSet("ILLUMINA_HISEQ_OUTPUT")
+ else:
+ runDataDict['flowCellId'] = flowCellId
+ dataSet = transaction.createNewDataSet("ILLUMINA_MISEQ_OUTPUT")
+ return runDataDict, dataSet
+
+# -----------------------------------------------------------------------------
+
+def touch_markerfile(filename):
+ try:
+ # do a touch
+ open(filename, 'w').close()
+ except:
+ print('Could not touch ' + filename)
+
+# -----------------------------------------------------------------------------
+
+def moveFiles(incomingPath, runDataDict, runStatisticsFolder):
+ #move RunInfo into a different drop box
+ runInfoSample=glob.glob(incomingPath + REGEX_RUNINFO_SAMPLE)
+ runInfoReport=glob.glob(incomingPath + REGEX_RUNINFO_REPORTS)
+ runInfoList = runInfoSample + runInfoReport
+
+ newPath = runStatisticsFolder + '/' + runDataDict['flowCellId'] + '/Data/'
+
+ os.makedirs(newPath)
+ for runInfo in runInfoList:
+ try:
+ if os.path.isdir(runInfo):
+ shutil.copytree(runInfo, newPath + os.path.basename(runInfo))
+ else:
+ shutil.copy2(runInfo, newPath)
+ except (IOError, os.error), why:
+ print (runInfo, newPath, str(why))
+
+# -----------------------------------------------------------------------------
+
+def getThreadProperties(transaction):
+
+ threadPropertyDict = {}
+ threadProperties = transaction.getGlobalState().getThreadParameters().getThreadProperties()
+
+ for key in threadProperties:
+ try:
+ threadPropertyDict[key] = threadProperties.getProperty(key)
+ except:
+ pass
+ return threadPropertyDict
+
+# -----------------------------------------------------------------------------
+
+def process(transaction):
+
+ threadPropertyDict = getThreadProperties(transaction)
+
+ incomingPath = transaction.getIncoming().getPath()
+ runFolderName = transaction.getIncoming().getName()
+ runDataDict, dataSet = extractRunData(runFolderName, transaction)
+
+ incomingRootDir = threadPropertyDict[u'incoming-root-dir']
+ runStatisticsFolder = incomingRootDir + '/' + RUNSTATISTICS_DROPBOX
+
+ moveFiles(incomingPath, runDataDict, runStatisticsFolder)
+
+ touch_markerfile( runStatisticsFolder + '/' + MARKER_STRING + runDataDict['flowCellId'])
+
+ dataSet.setMeasuredData(False)
+
+ search_service = transaction.getSearchService()
+ sc = SearchCriteria()
+ sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch( \
+ SearchCriteria.MatchClauseAttribute.CODE, runDataDict['flowCellId']));
+ foundSamples = search_service.searchForSamples(sc)
+
+ if foundSamples.size() > 0:
+ # Add the incoming file into the data set
+ transaction.moveFile(incomingPath, dataSet)
+ dataSet.setSample(foundSamples[0])
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-lane-hiseq/plugin.properties b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-lane-hiseq/plugin.properties
new file mode 100644
index 00000000000..f7523f7cdec
--- /dev/null
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-lane-hiseq/plugin.properties
@@ -0,0 +1,12 @@
+#
+# Drop box for registering a flow cell output as a data set
+#
+# Variables:
+# incoming-root-dir
+# Path to the directory which contains incoming directories for drop boxes.
+incoming-dir = ${incoming-root-dir}/register-lane-hiseq
+incoming-data-completeness-condition = marker-file
+top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
+script-path = register-lane-hiseq.py
+storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-lane-hiseq/register-lane-hiseq.py b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-lane-hiseq/register-lane-hiseq.py
new file mode 100755
index 00000000000..848fd08ad3b
--- /dev/null
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-lane-hiseq/register-lane-hiseq.py
@@ -0,0 +1,223 @@
+'''
+@copyright:
+2013 ETH Zuerich, CISD
+
+@license:
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+@description:
+Processes each flow lane of a Sequencing run and attaches the fastq files to
+the correct corresponding library samples
+
+@note:
+print statements go to: <openBIS_HOME>/datastore_server/log/startup_log.txt
+Expects as incoming folder:
+Project_<Flow Cell>_<Lane>
+e.g.Project_110715_SN792_0054_BC035RACXX_1
+
+
+@author:
+Manuel Kohler
+
+Note:
+print statements go to: ~openbis/sprint/datastore_server/log/startup_log.txt
+'''
+
+import os
+import fnmatch
+import time
+import shutil
+from time import *
+from datetime import *
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
+
+FASTQ_GZ_PATTERN = "*.fastq.gz"
+METADATA_FILE_SUFFIX = "_metadata.tsv"
+INDEX1='INDEX1'
+INDEX2='INDEX2'
+EXTERNAL_SAMPLE_NAME='EXTERNAL_SAMPLE_NAME'
+
+DEFAULT_INDEX='NoIndex'
+
+# -------------------------------------------------------------------------------
+
+def getFileNames(path):
+ '''
+ Gets all files matching a PATTERN in a path recursively
+ and returns the result as a list
+ '''
+ matches = []
+ for root, dirnames, filenames in os.walk(path):
+ for filename in fnmatch.filter(filenames, FASTQ_GZ_PATTERN):
+ matches.append(os.path.join(root, filename))
+ matches.sort()
+ return(matches)
+
+# -------------------------------------------------------------------------------
+
+def writeMetadataFile (fileName, parentPropertyTypes, parentPropertiesMap, fcMetaDataDict, fcMetaDataList):
+ '''
+ Writes a file of meta date related to one sample
+ '''
+ try:
+ metaDataFile = open(fileName,'w')
+ for propertyType in parentPropertyTypes:
+ metaDataFile.write(propertyType.encode('utf-8') + "\t" +
+ parentPropertiesMap[propertyType].tryGetAsString().encode('utf-8') + "\n")
+
+ metaDataFile.write("\nFLOWCELL PROPERTIES\n".encode('utf-8'))
+
+ for fcMetaData in fcMetaDataList:
+ metaDataFile.write(fcMetaData.encode('utf-8') + "\t" +
+ fcMetaDataDict[fcMetaData].tryGetAsString().encode('utf-8') + "\n")
+ pass
+ except IOError:
+ print ('File error, could not write '+ fileName)
+ finally:
+ metaDataFile.close()
+
+# -------------------------------------------------------------------------------
+
+def create_openbis_timestamp ():
+ '''
+ Create an openBIS conform timestamp
+ '''
+ tz=localtime()[3]-gmtime()[3]
+ d=datetime.now()
+ return d.strftime("%Y-%m-%d %H:%M:%S GMT"+"%+.2d" % tz+":00")
+
+# -------------------------------------------------------------------------------
+
+def getFlowCellMetaData (transaction, flowCellId):
+
+ def sortedDictValues(adict):
+ keys = adict.keys()
+ keys.sort()
+ return map(adict.get, keys)
+
+ search = transaction.getSearchService()
+ sc = SearchCriteria()
+ print('Searching FlowCell: '+ str(flowCellId))
+ sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, flowCellId));
+ foundFlowCells = search.searchForSamples(sc)
+
+ try:
+ assert foundFlowCells.size() == 1
+ except AssertionError:
+ print (str(foundFlowCells.size()) + ' flow cells found which match the criterias: '+ flowCellId)
+
+ fcPropertiesDict = {}
+ fcPropertyTypes = []
+
+ fcProperties = foundFlowCells[0].getSample().getProperties()
+ for property in fcProperties:
+ code = property.getPropertyType().getSimpleCode()
+ fcPropertyTypes.append(code)
+ fcPropertiesDict[code] = property
+
+ fcPropertyTypes.sort()
+ return fcPropertiesDict, fcPropertyTypes
+
+# -------------------------------------------------------------------------------
+
+def searchSample(search_service, sampleCode):
+
+ sc = SearchCriteria()
+ sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sampleCode));
+ foundSamples = search_service.searchForSamples(sc)
+
+ # there should be only one sample because it is unique
+ if (len(foundSamples) > 1):
+ raise Exception("More than one sample found! No unique code: " + sampleCode)
+ elif (len(foundSamples) == 0):
+ raise Exception("No matching sample found for: " + sampleCode)
+ else :
+ sample = foundSamples[0]
+ return sample
+
+# -------------------------------------------------------------------------------
+def process(transaction):
+
+ # useful for debugging:
+ print ("\n")
+ print(datetime.now())
+
+ search_service = transaction.getSearchService()
+
+ incomingPath = transaction.getIncoming().getAbsolutePath()
+ name = transaction.getIncoming().getName()
+
+ folders=[]
+ folders=os.listdir(incomingPath)
+
+ # expected incoming Name, e.g.: Project_110715_SN792_0054_BC035RACXX_1
+ split=name.split("_")
+ if (len(split) == 6):
+ runningDate = split[1]
+ sequencerId = split[2]
+ sequentialNumber = split[3]
+ hiseqTray = split[4][0]
+ flowCellId = split[4][1:]
+ flowLane = split[-1]
+ incoming_sample = flowCellId + ':' + flowLane
+ # expected Project_120112_63537AAXX_1
+ if (len(split) == 4):
+ runningDate = split[1]
+ flowCellId = split[2]
+ flowLane = split[-1]
+ incoming_sample = flowCellId + ':' + flowLane
+
+ # Search for the incoming_sample which is a Flow Lane
+ sc = SearchCriteria()
+ print('Processing sample: '+ str(incoming_sample))
+ sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, incoming_sample));
+ foundSamples = search_service.searchForSamples(sc)
+
+ # there should be only one sample because it is unique within one Flow Cell
+ if (len(foundSamples) > 1):
+ raise Exception("More than one sample found! No unique code: " + incoming_sample)
+ elif (len(foundSamples) == 0):
+ raise Exception("No matching sample found for: " + incoming_sample)
+ else :
+ sample = foundSamples[0].getSample()
+ parents = sample.getParents()
+
+ # -------------------------------------------------------------------------------
+
+ # loop over each Sample folder within a lane
+ for f in range(0,len(folders)):
+ # Create a data set and set type
+ dataSet = transaction.createNewDataSet("FASTQ_GZ")
+ dataSet.setMeasuredData(False)
+ dataSet.setPropertyValue(INDEX1, DEFAULT_INDEX)
+ dataSet.setPropertyValue(INDEX2, DEFAULT_INDEX)
+ dirName = transaction.createNewDirectory(dataSet,folders[f])
+
+ # if multiplexed samples then there is more than one folder
+ pathPerLane = incomingPath + '/' + folders[f]
+
+ # get all fastqs in this dataSet
+ fastqFileList=getFileNames(pathPerLane)
+
+ # put the files into the dataSet
+ for file in fastqFileList:
+ sampleCode = '-'.join(file.split('/')[-1].split('_')[:4])
+ print "Searching for " + sampleCode
+ sample = searchSample(search_service, sampleCode)
+
+ # finally add the files to the data set
+ transaction.moveFile(file , dataSet, folders[f])
+
+ #sa = transaction.getSampleForUpdate(sample.getSampleIdentifier())
+ #sa.setPropertyValue("DATA_TRANSFERRED", create_openbis_timestamp())
+ dataSet.setSample(sample)
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-runstatistics/plugin.properties b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-runstatistics/plugin.properties
new file mode 100644
index 00000000000..8572688f224
--- /dev/null
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-runstatistics/plugin.properties
@@ -0,0 +1,11 @@
+#
+# Drop box for registering a flow cell output as a data set
+#
+# Variables:
+# incoming-root-dir
+# Path to the directory which contains incoming directories for drop boxes.
+incoming-dir = ${incoming-root-dir}/register-runstatistics
+incoming-data-completeness-condition = marker-file
+top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
+script-path = register-runstatistics.py
+storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-runstatistics/register-runstatistics.py b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-runstatistics/register-runstatistics.py
new file mode 100644
index 00000000000..c3fc98d03a4
--- /dev/null
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-runstatistics/register-runstatistics.py
@@ -0,0 +1,57 @@
+'''
+@copyright:
+2013 ETH Zuerich, CISD
+
+@license:
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+@description:
+Registers an incoming directory as a data set in openBIS. The name of
+the directory is used to search for the matching sample.
+
+@note:
+print statements go to: <openBIS_HOME>/datastore_server/log/startup_log.txt
+
+@author:
+Manuel Kohler
+'''
+
+import os
+import shutil
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchSubCriteria
+
+def process(transaction):
+
+ incomingPath = transaction.getIncoming().getPath()
+ incomingFolder = transaction.getIncoming().getName()
+
+ search_service = transaction.getSearchService()
+ sc = SearchCriteria()
+ sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, incomingFolder));
+ foundSamples = search_service.searchForSamples(sc)
+
+ if foundSamples.size() > 0:
+
+ # Search for another data set of the same sample and make it a child of it
+ sampleSc = SearchCriteria()
+ sampleSc.addSubCriteria(SearchSubCriteria.createSampleContainerCriteria(sc))
+ foundContainedSamples = search_service.searchForSamples(sampleSc)
+ if foundContainedSamples.size() > 0:
+ for fcs in range(0,foundContainedSamples.size()):
+ dataSet = transaction.createNewDataSet("RUNINFO")
+ dataSet.setMeasuredData(False)
+ dataSet.setSample(foundContainedSamples[fcs])
+ # Add the incoming file into the data set
+ shutil.copytree(incomingPath, incomingPath + "_" + str(fcs+1))
+ transaction.moveFile(incomingPath + "_" + str(fcs+1), dataSet)
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-unaligned/plugin.properties b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-unaligned/plugin.properties
new file mode 100644
index 00000000000..9c8c317b60d
--- /dev/null
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-unaligned/plugin.properties
@@ -0,0 +1,11 @@
+#
+# Drop box for registering a flow cell output as a data set
+#
+# Variables:
+# incoming-root-dir
+# Path to the directory which contains incoming directories for drop boxes.
+incoming-dir = ${incoming-root-dir}/register-unaligned
+incoming-data-completeness-condition = marker-file
+top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
+script-path = register-unaligned.py
+storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-unaligned/register-unaligned.py b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-unaligned/register-unaligned.py
new file mode 100755
index 00000000000..d9e6b77c95f
--- /dev/null
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/drop-boxes/register-unaligned/register-unaligned.py
@@ -0,0 +1,185 @@
+'''
+@copyright:
+2013 ETH Zuerich, CISD
+
+@license:
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+@description:
+Splits up this complex data set into two different data sets and
+moves the corresponding file into those drop boxes
+
+@note:
+Expects as incoming folder: <FlowCell>/Unaligned_no_mismatch
+
+@author:
+Manuel Kohler
+'''
+
+import os
+import glob
+import shutil
+import time
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchSubCriteria
+
+BASECALL_STATS_FOLDER = 'Basecall_Stats_'
+REGEX_FILES = '*.*'
+REGEX_MAKEFILE = 'Make*'
+REGEX_LANES='/P*'
+REGEX_UNDETERMINED = '/U*/Sample*'
+UNALIGNED_FOLDER='Unaligned_'
+LANE_DROPBOX='register-lane-hiseq'
+BASECALL_DROPBOX='register-basecall-stats'
+MARKER_STRING='.MARKER_is_finished_'
+
+# -----------------------------------------------------------------------------
+
+def touch_markerfile(filename):
+ try:
+ # do a touch
+ open(filename, 'w').close()
+ except:
+ print('Could not touch ' + filename)
+
+# -----------------------------------------------------------------------------
+
+def searchForLaneParents(transaction, sampleCode):
+
+ search_service = transaction.getSearchService()
+ sc = SearchCriteria()
+ sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sampleCode))
+ foundSamples = search_service.searchForSamples(sc)
+ # there should be only one sample because it is unique within one Flow Cell
+ if (len(foundSamples) > 1):
+ raise Exception("More than one sample found! No unique code: " + sampleCode)
+ elif (len(foundSamples) == 0):
+ raise Exception("No matching sample found for: " + sampleCode)
+ else :
+ sample = foundSamples[0].getSample()
+ parents = sample.getParents()
+
+ # search for the parents
+ sc = SearchCriteria()
+ # set the Search Criteria to an OR condition, default is AND
+ sc.setOperator(SearchCriteria.SearchOperator.MATCH_ANY_CLAUSES)
+ # Get the codes for all parents
+ for parent in parents:
+ parentSubCode = parent.getSubCode()
+ sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, parentSubCode));
+ # all parents of the flow lane
+ foundParents = search_service.searchForSamples(sc)
+
+ parentCodeList = []
+
+ for foundParent in foundParents:
+ parent = foundParent.getSample()
+ # ArrayList
+ parentProperties = parent.getProperties()
+ # just get the current code
+ parentCode = parent.getCode()
+ parentCodeList.append(parentCode)
+ #print("Found parent code: "+ parentCode)
+
+ return parentCodeList
+
+# -----------------------------------------------------------------------------
+
+def renameFiles(transaction, dir, flowcellName):
+ # Limit of Samples when the Sample Code is still used in the renaming. If Number of Samples is
+ # bigger than this number, we just write the number in the file name.
+
+ MAX_SAMPLES = 20
+ FACILITY_CODE = "BSSE_QGF_"
+
+ for root, dirs, files in os.walk(dir):
+ for file in files:
+ lane = file.split("_")[0][-1]
+ if lane.isdigit():
+ sampleCode = flowcellName + ":" + lane
+ print sampleCode
+ parentCodeList = searchForLaneParents(transaction, sampleCode)
+ print parentCodeList
+ length = len(parentCodeList)
+ if length > MAX_SAMPLES:
+ # BSSE_QGF_96_samples_C1A8YACXX_Undetermined_L008_R1_001.fastq.gz
+ os.rename(root + '/' + file, root + "/" + FACILITY_CODE + str(length) + "_samples_" + flowcellName + "_" + file)
+ else:
+ # BSSE_QGF_10001_10002_10003_10004_C1A8YACXX_Undetermined_L008_R1_001.fastq.gz
+ SampleCodeString = "_".join([(e.split("-")[-1]) for e in parentCodeList])
+ os.rename(root + '/' + file, root + "/" + FACILITY_CODE + SampleCodeString + "_" + flowcellName + "_" + file)
+
+
+# -----------------------------------------------------------------------------
+
+def getThreadProperties(transaction):
+
+ threadPropertyDict = {}
+ threadProperties = transaction.getGlobalState().getThreadParameters().getThreadProperties()
+
+ for key in threadProperties:
+ try:
+ threadPropertyDict[key] = threadProperties.getProperty(key)
+ except:
+ pass
+ return threadPropertyDict
+
+# -----------------------------------------------------------------------------
+
+def extractFlowCellName (runFolderName):
+ return runFolderName.split('_')[-1][1:]
+
+# -----------------------------------------------------------------------------
+
+def process(transaction):
+
+ threadPropertyDict = getThreadProperties(transaction)
+ incomingRootDir = threadPropertyDict[u'incoming-root-dir']
+ laneFolder = incomingRootDir + '/' + LANE_DROPBOX + '/'
+ basecallStatsFolder = incomingRootDir + '/' + BASECALL_DROPBOX + '/'
+
+ incomingPath = transaction.getIncoming().getPath()
+ runFolderName = transaction.getIncoming().getName()
+ fcName = extractFlowCellName(runFolderName)
+
+ # -----------------------------------------------------------------------------
+ # move Lanes into a different drop box
+ laneList=glob.glob(incomingPath + '/'+ UNALIGNED_FOLDER + '*' + REGEX_LANES)
+ laneList.sort()
+
+ undeterminedList=glob.glob(incomingPath + '/'+ UNALIGNED_FOLDER + '*' + REGEX_UNDETERMINED)
+ undeterminedList.sort()
+
+ # add the Flow Cell Name to the Undetermined FASTQ files
+ [renameFiles(transaction, dir, fcName) for dir in undeterminedList]
+
+ # Multiplexing:
+ # First move the Undetermined reads to the other ones
+ [shutil.move(undeterminedLane, laneList[int(undeterminedLane.split('/')[-1][-1])-1] +'/' + undeterminedLane.split('/')[-1]) for undeterminedLane in undeterminedList]
+
+ [shutil.move(lane, laneFolder + lane.split('/')[-1]) for lane in laneList]
+ markerFileList = [touch_markerfile(laneFolder + MARKER_STRING+lane.split('/')[-1]) for lane in laneList]
+
+ # -----------------------------------------------------------------------------
+ # move Basecall Stats into a different drop box
+
+ # Build up a list of file which are part of the data set
+ for lane in xrange(1, len(laneList)+1):
+ path = incomingPath + '/'+ UNALIGNED_FOLDER + str(lane) + '/'
+ fileList=glob.glob(path + REGEX_FILES)
+ [fileList.append(i) for i in glob.glob(path + REGEX_MAKEFILE)]
+
+ dest = fcName + '_' + str(lane)
+ shutil.copytree(path + BASECALL_STATS_FOLDER + fcName , basecallStatsFolder + dest + '/' + BASECALL_STATS_FOLDER + fcName)
+ [shutil.move(file, basecallStatsFolder + dest) for file in fileList]
+ touch_markerfile(basecallStatsFolder + MARKER_STRING + dest)
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/maintenance-tasks/.gitignore b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/maintenance-tasks/.gitignore
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/reporting-plugins/.gitignore b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/reporting-plugins/.gitignore
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/services/.gitignore b/deep_sequencing_unit/source/core-plugins/illumina-ngs/2/dss/services/.gitignore
new file mode 100644
index 00000000000..e69de29bb2d
--
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