From cd11a9575f7a6b6610e705e1532b40498d4f312c Mon Sep 17 00:00:00 2001
From: barillac <barillac>
Date: Fri, 12 Dec 2014 10:40:40 +0000
Subject: [PATCH] new sample types + dynamic properties added
SVN: 33036
---
.../petermigration/1/as/definitions.py | 31 +++++---
.../1/as/initialize-master-data.py | 74 +++++++++++++++++--
.../1/compatibility/adenosine_count.py | 1 +
.../1/compatibility/cytosine_count.py | 1 +
.../petermigration/1/compatibility/gc.py | 9 +++
.../1/compatibility/guanosine_count.py | 1 +
.../petermigration/1/compatibility/length.py | 9 +++
.../1/compatibility/nucleotide_count.py | 9 +++
.../1/compatibility/thymidine_count.py | 1 +
.../petermigration/1/compatibility/tm.py | 9 +++
.../drop-boxes/petermigration/migration.py | 44 ++++++++++-
11 files changed, 168 insertions(+), 21 deletions(-)
create mode 100644 plasmid/source/core-plugins/petermigration/1/compatibility/adenosine_count.py
create mode 100644 plasmid/source/core-plugins/petermigration/1/compatibility/cytosine_count.py
create mode 100644 plasmid/source/core-plugins/petermigration/1/compatibility/gc.py
create mode 100644 plasmid/source/core-plugins/petermigration/1/compatibility/guanosine_count.py
create mode 100644 plasmid/source/core-plugins/petermigration/1/compatibility/length.py
create mode 100644 plasmid/source/core-plugins/petermigration/1/compatibility/nucleotide_count.py
create mode 100644 plasmid/source/core-plugins/petermigration/1/compatibility/thymidine_count.py
create mode 100644 plasmid/source/core-plugins/petermigration/1/compatibility/tm.py
diff --git a/plasmid/source/core-plugins/petermigration/1/as/definitions.py b/plasmid/source/core-plugins/petermigration/1/as/definitions.py
index 220f739068a..2499678ad13 100644
--- a/plasmid/source/core-plugins/petermigration/1/as/definitions.py
+++ b/plasmid/source/core-plugins/petermigration/1/as/definitions.py
@@ -16,6 +16,14 @@ def getPropertyDefinitionByCode(definition, code):
# Scripts
#
commentsScriptName = "COMMENTS";
+adenosineScriptName = "ADENOSINE_COUNT"
+cytosineScriptName= "CYTOSINE_COUNT"
+gcScriptName= "GC"
+guanosineScriptName= "GUANOSINE_COUNT"
+lengthScriptName= "SEQUENCE_LENGTH"
+nucelotideScriptName= "ONUCLEOTIDE_COUNT"
+thymidineScriptName= "THYMIDINE_COUNT"
+tmScriptName= "TM"
#
# Storage
@@ -90,7 +98,6 @@ antibodyDefinition = [
["FROZEN", "General", "frozen", DataType.TIMESTAMP, None, "", None, None, False]
];
-
cellDefinition = [
["CO2", "General", "%CO2", DataType.CONTROLLEDVOCABULARY, "CO2", "", None, None, False],
["ATCC_NUM", "General", "ATCC No.", DataType.VARCHAR, None, "", None, None, False],
@@ -207,7 +214,7 @@ strainDefinition = [
];
oligoDefinition = [
- #["ADENOSINE", "General", "adenosine", DataType.XML, None, "", adenineScriptName],
+ ["ADENOSINE", "Calculated fields", "adenosine", DataType.INTEGER, None, "", adenosineScriptName, None, False],
["AMOUNT", "General", "amount", DataType.REAL, None, "", None, None, False],
["BARCODE", "General", "barcode", DataType.VARCHAR, None, "", None, None, False],
["BARCODE_LABEL", "General", "barcode label", DataType.VARCHAR, None, "", None, None, False],
@@ -215,19 +222,19 @@ oligoDefinition = [
["CONCENTRATION", "General", "concentration", DataType.REAL, None, "", None, None, False],
["CONCENTRATION_UNIT", "General", "concentration unit", DataType.CONTROLLEDVOCABULARY, "CONC_UNITS", "", None, None, False],
["CREATION_DATE", "General", "creation date", DataType.TIMESTAMP, None, "", None, None, False],
- # ["CYTOSINE", "General", "cytosine", DataType.XML, None, "", cytosineScriptName],
+ ["CYTOSINE", "Calculated fields", "cytosine", DataType.INTEGER, None, "", cytosineScriptName, None, False],
["DATE", "General", "date", DataType.VARCHAR, None, "", None, None, False],
["FROZEN", "General", "frozen", DataType.TIMESTAMP, None, "", None, None, False],
- #["GC", "General", "gc", DataType.XML, None, "", gcScriptName],
+ ["GC", "Calculated fields", "gc", DataType.REAL, None, "", gcScriptName, None, False],
["GENE_LOCUS", "General", "gene locus", DataType.VARCHAR, None, "", None, None, False],
["GRADE", "General", "grade", DataType.CONTROLLEDVOCABULARY, "OLIGO_GRADE", "", None, None, False],
- #["GUANOSINE", "General", "guanosine", DataType.XML, None, "", guanosineScriptName],
+ ["GUANOSINE", "Calculated fields", "guanosine", DataType.INTEGER, None, "", guanosineScriptName, None, False],
["COMMENTS", "General", "Info", DataType.VARCHAR, None, "", None, None, False],
["INVESTIGATOR", "General", "investigator", DataType.CONTROLLEDVOCABULARY, "ALL_LAB_MEMBERS", "", None, None, False],
- #["LENGTH", "General", "length", DataType.XML, None, "", lengthScriptName],
- ["MODIFICATION_DATE", "General", "modification date", DataType.TIMESTAMP, None, "", None, None, False],
- ["MODIFIED_BY", "General", "modified by", DataType.CONTROLLEDVOCABULARY, "ALL_LAB_MEMBERS", "", None, None, False],
- #["O_NUCLEOTIDE", "General", "O nucleotide", DataType.XML, None, "", nucelotideScriptName],
+ ["LENGTH", "Calculated fields", "length", DataType.INTEGER, None, "", lengthScriptName, None, False],
+ ["MODIFICATION_DATE", "General", "modification date", DataType.TIMESTAMP, None, "", None, None, False],
+ ["MODIFIED_BY", "General", "modified by", DataType.CONTROLLEDVOCABULARY, "ALL_LAB_MEMBERS", "", None, None, False],
+ ["O_NUCLEOTIDE", "Calculated fields", "O nucleotide", DataType.INTEGER, None, "", nucelotideScriptName, None, False],
["OD", "General", "od", DataType.INTEGER, None, "", None, None, False],
["NAME", "General", "oligo ID", DataType.INTEGER, None, "", None, None, False],
["OLIGO_ID_NR", "General", "oligo_id_nr", DataType.VARCHAR, None, "", None, None, False],
@@ -240,8 +247,8 @@ oligoDefinition = [
["RESTRICTION_SITE", "General", "restriction site", DataType.CONTROLLEDVOCABULARY, "RESTRICTION", "", None, None, False],
["SEQUENCE", "General", "sequence", DataType.VARCHAR, None, "", None, None, False],
["SERIAL_NUMBER", "General", "serial number", DataType.VARCHAR, None, "", None, None, False],
- #["THYMIDINE", "General", "thymidine", DataType.XML, None, "", thymidineScriptName],
- #["TM", "General", "tm", DataType.XML, None, "", tmScriptName],
+ ["THYMIDINE", "Calculated fields", "thymidine", DataType.INTEGER, None, "", thymidineScriptName, None, False],
+ ["TM", "Calculated fields", "tm", DataType.REAL, None, "", tmScriptName, None, False],
["USAGE", "General", "usage", DataType.CONTROLLEDVOCABULARY, "OLIGO_USAGE", "", None, None, False]
];
@@ -334,7 +341,7 @@ siRNADefinition = [
["OFF_TARGET_EFFECTS", "General", "Off target effects", DataType.VARCHAR, None, "", None, None, False],
["INFO", "General", "Info", DataType.VARCHAR, None, "", None, None, False],
["SPECIFIC_SPLICE_VARIANT", "General", "Specific splice variant", DataType.VARCHAR, None, "", None, None, False],
- ["TRANSFECTION_AGENT", "General", "Transfection agent", DataType.VARCHAR, None, "", None, None, False],
+ ["TRANSFECTION_AGENT", "General", "Transfection agent", DataType.CONTROLLEDVOCABULARY, "TRANSFECTION_AGENT", "", None, None, False],
["PUBLISHED", "General", "Published", DataType.VARCHAR, None, "", None, None, False],
["LIBRARY", "General", "Library", DataType.VARCHAR, None, "", None, None, False],
["CHARACTERIZED_BY_COMPANY", "General", "Characterized by company", DataType.VARCHAR, None, "", None, None, False],
diff --git a/plasmid/source/core-plugins/petermigration/1/as/initialize-master-data.py b/plasmid/source/core-plugins/petermigration/1/as/initialize-master-data.py
index ebe35d1e62e..8227260d1e9 100644
--- a/plasmid/source/core-plugins/petermigration/1/as/initialize-master-data.py
+++ b/plasmid/source/core-plugins/petermigration/1/as/initialize-master-data.py
@@ -17,8 +17,8 @@
##
## Configuration
##
-PATH_TO_MANAGE_PROPERTIES_SCRIPTS = "/Users/juanf/Documents/workspace/openbis/source/core-plugins/petermigration/1/compatibility/";
-#PATH_TO_MANAGE_PROPERTIES_SCRIPTS = "/Users/barillac/openbis-peter/servers/core-plugins/petermigration/1/compatibility/";
+#PATH_TO_MANAGE_PROPERTIES_SCRIPTS = "/Users/juanf/Documents/workspace/openbis/source/core-plugins/petermigration/1/compatibility/";
+PATH_TO_MANAGE_PROPERTIES_SCRIPTS = "/Users/barillac/openbis-peter/servers/core-plugins/petermigration/1/compatibility/";
# MasterDataRegistrationTransaction Class
import definitions
@@ -133,7 +133,7 @@ def createScript(path, name, description, scriptType, entityType):
return script;
##
-## Manage properties scripts
+## Managed properties scripts
##
commentsScript = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "comments.py",
definitions.commentsScriptName,
@@ -141,6 +141,57 @@ commentsScript = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "comments.py",
"MANAGED_PROPERTY",
"SAMPLE");
+##
+## Dynamic properties scripts
+##
+adenosineScript = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "adenosine_count.py",
+ definitions.adenosineScriptName,
+ "Count number of adenosine in sequence",
+ "DYNAMIC_PROPERTY",
+ "SAMPLE");
+
+cytosineScript = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "cytosine_count.py",
+ definitions.cytosineScriptName,
+ "Count number of cytosine in sequence",
+ "DYNAMIC_PROPERTY",
+ "SAMPLE");
+
+gcScript = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "gc.py",
+ definitions.gcScriptName,
+ "(guanosine+cytosine)*100/length",
+ "DYNAMIC_PROPERTY",
+ "SAMPLE");
+
+guanosineScript = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "guanosine_count.py",
+ definitions.guanosineScriptName,
+ "Count number of guanosine in sequence",
+ "DYNAMIC_PROPERTY",
+ "SAMPLE");
+
+lengthScript = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "length.py",
+ definitions.lengthScriptName,
+ "Count total length of sequence (A+C+T+G+O_nucleotide)",
+ "DYNAMIC_PROPERTY",
+ "SAMPLE");
+
+nucelotideScript = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "nucleotide_count.py",
+ definitions.nucelotideScriptName,
+ "Count number of r,y,m,k,s,w,h,b,d,x,N in sequence",
+ "DYNAMIC_PROPERTY",
+ "SAMPLE");
+
+thymidineScript = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "thymidine_count.py",
+ definitions.thymidineScriptName,
+ "Count number of thymidine in sequence",
+ "DYNAMIC_PROPERTY",
+ "SAMPLE");
+
+tmScript = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "tm.py",
+ definitions.tmScriptName,
+ "68.3 + (0.41 * gc) - (600/length)",
+ "DYNAMIC_PROPERTY",
+ "SAMPLE");
+
##
## Vocabulary Types
##
@@ -150,13 +201,26 @@ for vocabularyCode, vocabularyValues in definitionsVoc.vocacbularyDefinitions.it
##
## Experiment Types
##
-createExperimentTypeWithProperties("ANTIBODY", "BOX TO HOLD SAMPLES OF THIS TYPE FOR ORGANIZATIONAL PURPOSES", []);
createExperimentTypeWithProperties("DEFAULT_EXPERIMENT", "Default Experiment", definitions.experimentDefinition);
-
+createExperimentTypeWithProperties("ANTIBODY", "BOX TO HOLD SAMPLES OF THIS TYPE FOR ORGANIZATIONAL PURPOSES", []);
+createExperimentTypeWithProperties("CELL", "BOX TO HOLD SAMPLES OF THIS TYPE FOR ORGANIZATIONAL PURPOSES", []);
+createExperimentTypeWithProperties("STRAIN", "BOX TO HOLD SAMPLES OF THIS TYPE FOR ORGANIZATIONAL PURPOSES", []);
+createExperimentTypeWithProperties("PLASMID", "BOX TO HOLD SAMPLES OF THIS TYPE FOR ORGANIZATIONAL PURPOSES", []);
+createExperimentTypeWithProperties("CHEMICAL", "BOX TO HOLD SAMPLES OF THIS TYPE FOR ORGANIZATIONAL PURPOSES", []);
+createExperimentTypeWithProperties("SIRNA", "BOX TO HOLD SAMPLES OF THIS TYPE FOR ORGANIZATIONAL PURPOSES", []);
+createExperimentTypeWithProperties("OLIGO", "BOX TO HOLD SAMPLES OF THIS TYPE FOR ORGANIZATIONAL PURPOSES", []);
##
## Sample Types
##
createSampleTypeWithProperties("ANTIBODY", "", definitions.antibodyDefinition);
+createSampleTypeWithProperties("CELL", "", definitions.cellDefinition);
+createSampleTypeWithProperties("STRAIN", "", definitions.strainDefinition);
+createSampleTypeWithProperties("PLASMID", "", definitions.plasmidDefinition);
+createSampleTypeWithProperties("CHEMICAL", "", definitions.chemicalDefinition);
+createSampleTypeWithProperties("SIRNA", "", definitions.siRNADefinition);
+createSampleTypeWithProperties("OLIGO", "", definitions.oligoDefinition);
+
+
addStorageGroups(definitions.numberOfStorageGroups, "ANTIBODY");
diff --git a/plasmid/source/core-plugins/petermigration/1/compatibility/adenosine_count.py b/plasmid/source/core-plugins/petermigration/1/compatibility/adenosine_count.py
new file mode 100644
index 00000000000..58363afbe1c
--- /dev/null
+++ b/plasmid/source/core-plugins/petermigration/1/compatibility/adenosine_count.py
@@ -0,0 +1 @@
+entity.propertyValue('SEQUENCE').count('A')+entity.propertyValue('SEQUENCE').count('a')
\ No newline at end of file
diff --git a/plasmid/source/core-plugins/petermigration/1/compatibility/cytosine_count.py b/plasmid/source/core-plugins/petermigration/1/compatibility/cytosine_count.py
new file mode 100644
index 00000000000..faed851214f
--- /dev/null
+++ b/plasmid/source/core-plugins/petermigration/1/compatibility/cytosine_count.py
@@ -0,0 +1 @@
+entity.propertyValue('SEQUENCE').count('C')+entity.propertyValue('SEQUENCE').count('c')
\ No newline at end of file
diff --git a/plasmid/source/core-plugins/petermigration/1/compatibility/gc.py b/plasmid/source/core-plugins/petermigration/1/compatibility/gc.py
new file mode 100644
index 00000000000..5067337f62e
--- /dev/null
+++ b/plasmid/source/core-plugins/petermigration/1/compatibility/gc.py
@@ -0,0 +1,9 @@
+import re
+
+def calculate_Onuc():
+ result = (len(re.findall("G|g|C|c", entity.propertyValue('SEQUENCE'))) * 100)/len(re.findall("A|a|C|c|G|g|T|t|R|r|Y|y|M|m|K|k|S|s|W|w|H|h|b|B|D|d|X|x|n|N", entity.propertyValue('SEQUENCE')))
+
+ return result
+
+def calculate():
+ return calculate_Onuc()
diff --git a/plasmid/source/core-plugins/petermigration/1/compatibility/guanosine_count.py b/plasmid/source/core-plugins/petermigration/1/compatibility/guanosine_count.py
new file mode 100644
index 00000000000..913b9db58cc
--- /dev/null
+++ b/plasmid/source/core-plugins/petermigration/1/compatibility/guanosine_count.py
@@ -0,0 +1 @@
+entity.propertyValue('SEQUENCE').count('G')+entity.propertyValue('SEQUENCE').count('g')
\ No newline at end of file
diff --git a/plasmid/source/core-plugins/petermigration/1/compatibility/length.py b/plasmid/source/core-plugins/petermigration/1/compatibility/length.py
new file mode 100644
index 00000000000..13aedef6fbb
--- /dev/null
+++ b/plasmid/source/core-plugins/petermigration/1/compatibility/length.py
@@ -0,0 +1,9 @@
+import re
+
+def calculate_Onuc():
+ result = len(re.findall("A|a|C|c|G|g|T|t|R|r|Y|y|M|m|K|k|S|s|W|w|H|h|b|B|D|d|X|x|n|N", entity.propertyValue('SEQUENCE')))
+
+ return result
+
+def calculate():
+ return calculate_Onuc()
diff --git a/plasmid/source/core-plugins/petermigration/1/compatibility/nucleotide_count.py b/plasmid/source/core-plugins/petermigration/1/compatibility/nucleotide_count.py
new file mode 100644
index 00000000000..e7630820e04
--- /dev/null
+++ b/plasmid/source/core-plugins/petermigration/1/compatibility/nucleotide_count.py
@@ -0,0 +1,9 @@
+import re
+
+def calculate_Onuc():
+ result = len(re.findall("R|r|Y|y|M|m|K|k|S|s|W|w|H|h|b|B|D|d|X|x|n|N", entity.propertyValue('SEQUENCE')))
+
+ return result
+
+def calculate():
+ return calculate_Onuc()
diff --git a/plasmid/source/core-plugins/petermigration/1/compatibility/thymidine_count.py b/plasmid/source/core-plugins/petermigration/1/compatibility/thymidine_count.py
new file mode 100644
index 00000000000..9d9db9385a9
--- /dev/null
+++ b/plasmid/source/core-plugins/petermigration/1/compatibility/thymidine_count.py
@@ -0,0 +1 @@
+entity.propertyValue('SEQUENCE').count('T')+entity.propertyValue('SEQUENCE').count('t')
\ No newline at end of file
diff --git a/plasmid/source/core-plugins/petermigration/1/compatibility/tm.py b/plasmid/source/core-plugins/petermigration/1/compatibility/tm.py
new file mode 100644
index 00000000000..a841d384a32
--- /dev/null
+++ b/plasmid/source/core-plugins/petermigration/1/compatibility/tm.py
@@ -0,0 +1,9 @@
+import re
+
+def calculate_Onuc():
+ result =68.3+ (0.41* float(len(re.findall("G|g|C|c", entity.propertyValue('SEQUENCE'))) * 100)/float(len(re.findall("A|a|C|c|G|g|T|t|R|r|Y|y|M|m|K|k|S|s|W|w|H|h|b|B|D|d|X|x|n|N", entity.propertyValue('SEQUENCE'))))) -(600/float(len(re.findall("A|a|C|c|G|g|T|t|R|r|Y|y|M|m|K|k|S|s|W|w|H|h|b|B|D|d|X|x|n|N", entity.propertyValue('SEQUENCE')))))
+
+ return result
+
+def calculate():
+ return calculate_Onuc()
diff --git a/plasmid/source/core-plugins/petermigration/1/dss/drop-boxes/petermigration/migration.py b/plasmid/source/core-plugins/petermigration/1/dss/drop-boxes/petermigration/migration.py
index 2e0335b67a4..2a7969b7f4c 100644
--- a/plasmid/source/core-plugins/petermigration/1/dss/drop-boxes/petermigration/migration.py
+++ b/plasmid/source/core-plugins/petermigration/1/dss/drop-boxes/petermigration/migration.py
@@ -427,6 +427,41 @@ class PlasmidOpenBISDTO(OpenBISDTO):
else :
return False
+class OligoAdaptor(FileMakerEntityAdaptor):
+
+ def init(self):
+ self.selectQuery = "SELECT * FROM \"boxit oligos\""
+ self.definition = definitions.oligoDefinition
+ FileMakerEntityAdaptor.init(self)
+
+ def addEntity(self, values):
+ self.entities.append(OligoOpenBISDTO(values, self.definition))
+
+class OligoOpenBISDTO(OpenBISDTO):
+ def write(self, tr):
+ code = self.values["OLIGO_ID_NR"]
+ if code is not None:
+ sample = getSampleForUpdate("/INVENTORY/"+code,"OLIGO", tr)
+ setEntityProperties(tr, self.definition, sample, self.values);
+
+ def getIdentifier(self, tr):
+ code = self.values["OLIGO_ID_NR"]
+ return code
+
+ def isInOpenBIS(self, tr):
+ antibodyID2Antibody[self.values["NAME"]] = self.values
+ code = self.values["OLIGO_ID_NR"]
+ if code is not None:
+ sample = getSampleForUpdate("/INVENTORY/"+ code, None, tr)
+ if sample is not None:
+ lastModificationData = self.values["MODIFICATION_DATE"].strip()
+ lastModificationData = str(datetime.strptime(lastModificationData, "%Y-%m-%d"))[:10]
+ lastModificationOpenBIS = sample.getPropertyValue("MODIFICATION_DATE")[:10]
+ return lastModificationOpenBIS == lastModificationData
+ else :
+ return False
+
+
class ChemicalAdaptor(FileMakerEntityAdaptor):
def init(self):
@@ -472,17 +507,17 @@ class SirnaAdaptor(FileMakerEntityAdaptor):
class SirnaOpenBISDTO(OpenBISDTO):
def write(self, tr):
- code = self.values["SIRNA_OLIGONUMBER"]
+ code = "SI_" + self.values["SIRNA_OLIGONUMBER"]
if code is not None:
sample = getSampleForUpdate("/INVENTORY/"+code,"SIRNA", tr)
setEntityProperties(tr, self.definition, sample, self.values);
def getIdentifier(self, tr):
- code = self.values["SIRNA_OLIGONUMBER"]
+ code = "SI_" +self.values["SIRNA_OLIGONUMBER"]
return code
def isInOpenBIS(self, tr):
- code = self.values["SIRNA_OLIGONUMBER"]
+ code = "SI_" + self.values["SIRNA_OLIGONUMBER"]
if code is not None:
sample = getSampleForUpdate("/INVENTORY/"+ code, None, tr)
if sample is not None:
@@ -560,8 +595,9 @@ fmPassServer = "ibcimsb2014"
#CellAdaptor(fmConnString, fmUser, fmPass, "BOXIT_cells_Peter"),
#PlasmidAdaptor(fmConnString, fmUser, fmPass, "BOXIT_plasmids_Peter"),
#StrainAdaptor(fmConnString, fmUser, fmPass, "BOXIT_strains_Peter"),
+ #SirnaAdaptor(fmConnString, fmUser, fmPass, "BOXIT_Main_Menu_Peter"),
#ChemicalAdaptor(fmConnString, fmUser, fmPass, "BOXIT_Main_Menu_Peter"),]
-adaptors = [SirnaAdaptor(fmConnString, fmUser, fmPass, "BOXIT_Main_Menu_Peter"),
+adaptors = [OligoAdaptor(fmConnString, fmUser, fmPass, "BOXIT_oligos_Peter"),
DocumentsAdaptor(fmConnString, fmUser, fmPass, "BOXIT_documents_Peter")]
def createDataHierarchy(tr):
--
GitLab