From f4dd85a0892a2312344adbee1c805fd5ede4ed1c Mon Sep 17 00:00:00 2001
From: barillac <barillac>
Date: Thu, 11 Dec 2014 13:38:44 +0000
Subject: [PATCH] new sample types added
SVN: 33027
---
.../petermigration/1/as/definitions.py | 30 +--
.../petermigration/1/as/definitionsVoc.py | 28 ++-
.../drop-boxes/petermigration/migration.py | 197 +++++++++++++++++-
3 files changed, 231 insertions(+), 24 deletions(-)
diff --git a/plasmid/source/core-plugins/petermigration/1/as/definitions.py b/plasmid/source/core-plugins/petermigration/1/as/definitions.py
index 2f679851f7d..220f739068a 100644
--- a/plasmid/source/core-plugins/petermigration/1/as/definitions.py
+++ b/plasmid/source/core-plugins/petermigration/1/as/definitions.py
@@ -180,7 +180,7 @@ strainDefinition = [
["MODIFICATION_DATE", "General", "modification date", DataType.TIMESTAMP, None, "", None, None, False],
["MODIFIED_BY", "General", "modified by", DataType.CONTROLLEDVOCABULARY, "ALL_LAB_MEMBERS", "", None, None, False],
["NUMBER", "General", "number", DataType.VARCHAR, None, "", None, None, False],
- ["OBTAINED_FROM", "General", "obtained from", DataType.VARCHAR, None, "", None, None, False],
+ ["STRAIN_OBTAINED_FROM", "General", "obtained from", DataType.VARCHAR, None, "", None, None, False],
["ORF", "General", "orf", DataType.VARCHAR, None, "", None, None, False],
["PAGE_NUMBER", "General", "page number", DataType.VARCHAR, None, "", None, None, False],
["PARENTAL_CELL", "General", "parental cell", DataType.VARCHAR, None, "", None, None, False],
@@ -211,7 +211,7 @@ oligoDefinition = [
["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],
- ["COMPANY", "General", "company", DataType.CONTROLLEDVOCABULARY, "OLIGO_COMPANY", "", None, None, False],
+ ["OLIGO_COMPANY", "General", "company", DataType.CONTROLLEDVOCABULARY, "OLIGO_COMPANY", "", None, None, False],
["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],
@@ -232,7 +232,7 @@ oligoDefinition = [
["NAME", "General", "oligo ID", DataType.INTEGER, None, "", None, None, False],
["OLIGO_ID_NR", "General", "oligo_id_nr", DataType.VARCHAR, None, "", None, None, False],
["ORDER_DATE", "General", "order date", DataType.VARCHAR, None, "", None, None, False],
- ["ORGANISM", "General", "organism", DataType.CONTROLLEDVOCABULARY, "OLIGO_ORGANISM", "", None, None, False],
+ ["OLIGO_ORGANISM", "General", "organism", DataType.CONTROLLEDVOCABULARY, "OLIGO_ORGANISM", "", None, None, False],
["PAGE_NUMBER", "General", "page number", DataType.VARCHAR, None, "", None, None, False],
["PRIMER_PARTNER", "General", "primer partner", DataType.VARCHAR, None, "", None, None, False],
["PRIMER_POSITION", "General", "primer position", DataType.CONTROLLEDVOCABULARY, "PRIMER_POSITION", "", None, None, False],
@@ -285,9 +285,9 @@ plasmidDefinition = [
["ORIGIN_OF_REPLICATION", "General", "origin of replication", DataType.VARCHAR, None, "", None, None, False],
["OTHER_MARKER", "General", "other marker", DataType.VARCHAR, None, "", None, None, False],
["PAGE_NUMBER", "General", "page number", DataType.VARCHAR, None, "", None, None, False],
- ["PERSPLASMIDNUM", "General", "persPlasmidnum", DataType.INTEGER, None, "", None, None, False],
+ ["PERSPLASMIDNUM", "General", "persPlasmidnum", DataType.REAL, None, "", None, None, False],
["PETERPLASMIDNUM", "General", "PeterPlasmidNum", DataType.INTEGER, None, "", None, None, False],
- ["PLASMID_ID", "General", "plasmid ID", DataType.VARCHAR, None, "", None, None, False],
+ ["NAME", "General", "plasmid ID", DataType.VARCHAR, None, "", None, None, False],
["PLASMID_ID_NR", "General", "plasmid_id_nr", DataType.VARCHAR, None, "", None, None, False],
["PLASMIDNAME", "General", "plasmidname", DataType.VARCHAR, None, "", None, None, False],
["PRIMERS", "General", "primers", DataType.VARCHAR, None, "", None, None, False],
@@ -302,8 +302,8 @@ plasmidDefinition = [
["SIZE_INSERT", "General", "size insert", DataType.REAL, None, "", None, None, False],
["SIZE_OF_INSERT", "General", "size of insert", DataType.VARCHAR, None, "", None, None, False],
["SIZE_VECTOR", "General", "size vector", DataType.REAL, None, "", None, None, False],
- ["SOURCE", "General", "source", DataType.VARCHAR, None, "", None, None, False],
- ["SPECIES", "General", "species", DataType.CONTROLLEDVOCABULARY, "PLASMID_ORGANISM", "", None, None, False],
+ ["PLASMID_SOURCE", "General", "source", DataType.VARCHAR, None, "", None, None, False],
+ ["PLASMID_SPECIES", "General", "species", DataType.CONTROLLEDVOCABULARY, "PLASMID_ORGANISM", "", None, None, False],
#["TUBES", "General", "TUBES", DataType.VARCHAR, None, "", None, None, False],
["URL", "General", "url", DataType.VARCHAR, None, "", None, None, False]
];
@@ -319,14 +319,14 @@ chemicalDefinition = [
siRNADefinition = [
["INVESTIGATOR", "General", "investigator", DataType.CONTROLLEDVOCABULARY, "ALL_LAB_MEMBERS", "", None, None, False],
["GENE_LOCUS", "General", "gene locus", DataType.VARCHAR, None, "", None, None, False],
- ["EXON_OR_THREE_PRIME", "General", "exon or three prime", DataType.VARCHAR, None, "", None, None, False],
- ["EXON", "General", "exon #", DataType.VARCHAR, None, "", None, None, False],
+ ["EXON_OR_THREE_PRIME", "General", "exon or three prime", DataType.CONTROLLEDVOCABULARY, "EXON_OR_THREE_PRIME", "", None, None, False],
+ ["EXON", "General", "exon #", DataType.INTEGER, None, "", None, None, False],
["3_PRIME_POSITION", "General", "3' position", DataType.VARCHAR, None, "", None, None, False],
- ["SPECIES", "General", "species", DataType.VARCHAR, None, "", None, None, False],
+ ["SIRNA_SPECIES", "General", "species", DataType.CONTROLLEDVOCABULARY, "SIRNA_SPECIES", "", None, None, False],
["SEQUENCE", "General", "SEQUENCE", DataType.VARCHAR, None, "", None, None, False],
- ["COMPANY", "General", "Company", DataType.VARCHAR, None, "", None, None, False],
- ["STOCK_CONCENTRATION", "General", "Stock concentration", DataType.VARCHAR, None, "", None, None, False],
- ["WORKING_CONCENTRATION", "General", "Working concentration", DataType.VARCHAR, None, "", None, None, False],
+ ["SIRNA_COMPANY", "General", "Company", DataType.CONTROLLEDVOCABULARY, "SIRNA_COMPANY", "", None, None, False],
+ ["STOCK_CONCENTRATION", "General", "Stock concentration", DataType.REAL, None, "", None, None, False],
+ ["WORKING_CONCENTRATION", "General", "Working concentration", DataType.REAL, None, "", None, None, False],
["EFFICIENCY", "General", "Efficiency", DataType.VARCHAR, None, "", None, None, False],
["EFFICIENCY_QPCR", "General", "Efficiency_qPCR", DataType.VARCHAR, None, "", None, None, False],
["EFFICIENCY_WESTERN", "General", "Efficiency_Western", DataType.VARCHAR, None, "", None, None, False],
@@ -338,12 +338,12 @@ siRNADefinition = [
["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],
- ["NUMBERINPOOL", "General", "NumberINpool", DataType.VARCHAR, None, "", None, None, False],
+ ["NUMBERINPOOL", "General", "NumberINpool", DataType.INTEGER, None, "", None, None, False],
["TEST", "General", "Test", DataType.VARCHAR, None, "", None, None, False],
["CHEMICAL_MODIFICATION", "General", "Chemical modification", DataType.VARCHAR, None, "", None, None, False],
["OLIGO_NAME", "General", "Oligo name", DataType.VARCHAR, None, "", None, None, False],
["SIRNA_OLIGONUMBER", "General", "siRNA_OligoNumber", DataType.VARCHAR, None, "", None, None, False],
- ["FREEZER_LOCATION", "General", "Freezer Location", DataType.VARCHAR, None, "", None, None, False],
+ ["SIRNA_FREEZER_LOCATION", "General", "Freezer Location", DataType.CONTROLLEDVOCABULARY, "SIRNA_FREEZER_LOCATION", "", None, None, False],
["DRAWER", "General", "Drawer", DataType.VARCHAR, None, "", None, None, False]
];
diff --git a/plasmid/source/core-plugins/petermigration/1/as/definitionsVoc.py b/plasmid/source/core-plugins/petermigration/1/as/definitionsVoc.py
index a65f8d07a59..a63b4f78643 100644
--- a/plasmid/source/core-plugins/petermigration/1/as/definitionsVoc.py
+++ b/plasmid/source/core-plugins/petermigration/1/as/definitionsVoc.py
@@ -736,8 +736,34 @@ vocacbularyDefinitions = {
["SV40", "SV40"],
["TET_ON", "tet on"],
["TET_OFF", "tet off"],
- ["RIM1", "rim1"],
+ ["RIM1", "rim1"]
],
+ "EXON_OR_THREE_PRIME" : [
+ ["EXON", "exon"],
+ ["3P", "3'"],
+ ["5P", "5'"]
+ ],
+ "SIRNA_SPECIES" : [
+ ["HUMAN", "Human"],
+ ["MOUSE", "Mouse'"]
+ ],
+ "SIRNA_COMPANY" : [
+ ["AMBION", "Ambion"],
+ ["DHARMACON", "Dharmacon'"],
+ ["INVITORGEN", "Invitrogen'"],
+ ["MICROSYNTH", "Microsynth'"],
+ ["QIAGEN", "Qiagen'"],
+ ["GIFT", "Gift'"]
+ ],
+ "SIRNA_FREEZER_LOCATION" : [
+ ["BIGLABFREEZER", "BigLab freezer"],
+ ["SMALLLAB_BIGFREEZER", "SmallLab Big freezer'"],
+ ["FREEZER_G17", "Freezer G17'"],
+ ["G93-FRANK", "G9.3--Frank'"],
+ ["FREEZER-G17_BOX_NATHALIE", "Freezer G17 Box Nathalie'"],
+ ["BOX-THIBAULT-BIGFREEZER-SMALLLAB", "Box thibault Big freezer small lab'"],
+ ["BOX-NATHALIE", "Box Nathalie'"]
+ ],
"FREEZER" : [
["G9_FRIDGE-1", "G9 Fridge 1"],
["G9_FRIDGE-2", "G9 Fridge 2"],
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 3bd8b0f3925..2e0335b67a4 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
@@ -36,6 +36,10 @@ def setEntityProperties(tr, definition, entity, properties):
propertyDefinition = definitions.getPropertyDefinitionByCode(definition, propertyCode)
if propertyValue is not None:
propertyValue = unicode(propertyValue)
+
+ if propertyDefinition is not None and propertyDefinition[3] == DataType.TIMESTAMP and propertyValue is not None:
+ date_val = datetime.strptime(propertyValue, "%Y")
+ propertyValue = datetime.strftime(date_val, "%Y-%m-%d")
if propertyDefinition is not None and propertyDefinition[3] == DataType.CONTROLLEDVOCABULARY and propertyValue is not None:
possiblePropertyValue = definitionsVoc.getVocaularyTermCodeForVocabularyAndTermLabel(propertyDefinition[4], propertyValue)
@@ -45,19 +49,19 @@ def setEntityProperties(tr, definition, entity, properties):
#Create new vocabulary term
vocabulary = tr.getVocabularyForUpdate(propertyDefinition[4])
term = tr.createNewVocabularyTerm()
- codeToUse = re.sub(r'\W+','',propertyValue)
+ codeToUse = re.sub(r'\W+','_',propertyValue)
labelToUse = propertyValue
if len(codeToUse) is 0:
codeToUse = "None" + str(random.random())
if len(codeToUse) > 60:
- codeToUse = codeToUse[:60]
+ codeToUse = codeToUse[:50]
term.setCode(codeToUse)
term.setLabel(labelToUse)
term.setOrdinal(vocabulary.getTerms().size())
vocabulary.addTerm(term)
#Uses new vocabulary term
propertyValue = codeToUse
- #print "CREATED FOR VOCABULARY " + propertyDefinition[4] + " NEW TERM WITH CODE " + codeToUse
+ print repr(entity.getCode() + ", CREATED FOR VOCABULARY: " + propertyDefinition[4] + ", FOUND VALUE: " + labelToUse + ", NEW TERM WITH CODE: " + codeToUse)
if propertyDefinition is not None: #Sometimes special fields are added for other purposes, these should not be set
entity.setPropertyValue(propertyCode, propertyValue)
@@ -108,7 +112,7 @@ class OpenBISDTO:
pass
##
-## Costumer specific logic
+## Costumer specific logic: generic part
##
experimentCache = {}
sampleCache = {}
@@ -133,7 +137,7 @@ def getExperimentForUpdate(experimentIdentifier, experimentType, tr):
def getSampleForUpdate(sampleIdentifier, sampleType, tr):
if sampleIdentifier not in sampleCache:
- print "Cache failed " + sampleIdentifier + ":" + str(sampleType)
+ #print "Cache failed " + sampleIdentifier + ":" + str(sampleType)
sample = tr.getSampleForUpdate(sampleIdentifier)
if sample is None and sampleType is not None:
#print "Cache Create " + sampleIdentifier + ":" + str(sampleType)
@@ -172,7 +176,10 @@ class FileMakerEntityAdaptor(EntityAdaptor):
self.addEntity(values)
result.close()
preparedStatement.close()
-
+
+##
+## Customer specific logic: different sample types
+##
class AntibodyAdaptor(FileMakerEntityAdaptor):
def init(self):
@@ -317,6 +324,175 @@ class AntibodyBoxOpenBISDTO(OpenBISDTO):
if not self.isBoxPressent(boxSignature, tr):
return False
return True
+
+class CellAdaptor(FileMakerEntityAdaptor):
+
+ def init(self):
+ self.selectQuery = "SELECT * FROM \"boxit cells\""
+ self.definition = definitions.cellDefinition
+ FileMakerEntityAdaptor.init(self)
+
+ def addEntity(self, values):
+ self.entities.append(CellOpenBISDTO(values, self.definition))
+
+class CellOpenBISDTO(OpenBISDTO):
+ def write(self, tr):
+ code = self.values["CELL_ID_NR_COPY"]
+ if code is not None and code.startswith("c_"):
+ sample = getSampleForUpdate("/INVENTORY/"+code,"CELL", tr)
+ setEntityProperties(tr, self.definition, sample, self.values);
+
+ def getIdentifier(self, tr):
+ code = self.values["CELL_ID_NR_COPY"]
+ return code
+
+ def isInOpenBIS(self, tr):
+ antibodyID2Antibody[self.values["NAME"]] = self.values
+ code = self.values["CELL_ID_NR_COPY"]
+ if code is not None and code.startswith("c_"):
+ 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 StrainAdaptor(FileMakerEntityAdaptor):
+
+ def init(self):
+ self.selectQuery = "SELECT * FROM \"boxit strains\""
+ self.definition = definitions.strainDefinition
+ FileMakerEntityAdaptor.init(self)
+
+ def addEntity(self, values):
+ self.entities.append(StrainOpenBISDTO(values, self.definition))
+
+class StrainOpenBISDTO(OpenBISDTO):
+ def write(self, tr):
+ code = self.values["STRAIN_ID_NR"]
+ if code is not None:
+ sample = getSampleForUpdate("/INVENTORY/"+code,"STRAIN", tr)
+ setEntityProperties(tr, self.definition, sample, self.values);
+
+ def getIdentifier(self, tr):
+ code = self.values["STRAIN_ID_NR"]
+ return code
+
+ def isInOpenBIS(self, tr):
+ antibodyID2Antibody[self.values["NAME"]] = self.values
+ code = self.values["STRAIN_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 PlasmidAdaptor(FileMakerEntityAdaptor):
+
+ def init(self):
+ self.selectQuery = "SELECT * FROM \"boxit plasmids\""
+ self.definition = definitions.plasmidDefinition
+ FileMakerEntityAdaptor.init(self)
+
+ def addEntity(self, values):
+ self.entities.append(PlasmidOpenBISDTO(values, self.definition))
+
+class PlasmidOpenBISDTO(OpenBISDTO):
+ def write(self, tr):
+ code = self.values["PLASMID_ID_NR"]
+ if code is not None:
+ sample = getSampleForUpdate("/INVENTORY/"+code,"PLASMID", tr)
+ setEntityProperties(tr, self.definition, sample, self.values);
+
+ def getIdentifier(self, tr):
+ code = self.values["PLASMID_ID_NR"]
+ return code
+
+ def isInOpenBIS(self, tr):
+ antibodyID2Antibody[self.values["NAME"]] = self.values
+ code = self.values["PLASMID_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):
+ self.selectQuery = "SELECT * FROM \"Chemicals\""
+ self.definition = definitions.chemicalDefinition
+ FileMakerEntityAdaptor.init(self)
+
+ def addEntity(self, values):
+ self.entities.append(ChemicalOpenBISDTO(values, self.definition))
+
+class ChemicalOpenBISDTO(OpenBISDTO):
+ def write(self, tr):
+ code = "CHEM_" + self.values["RECORD_NUMBER"]
+ if code is not None:
+ sample = getSampleForUpdate("/INVENTORY/"+code,"CHEMICAL", tr)
+ setEntityProperties(tr, self.definition, sample, self.values);
+
+ def getIdentifier(self, tr):
+ code = "CHEM_" + self.values["RECORD_NUMBER"]
+ return code
+
+ def isInOpenBIS(self, tr):
+ code = "CHEM_" + self.values["RECORD_NUMBER"]
+ 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 SirnaAdaptor(FileMakerEntityAdaptor):
+
+ def init(self):
+ self.selectQuery = "SELECT * FROM \"siRNA\""
+ self.definition = definitions.siRNADefinition
+ FileMakerEntityAdaptor.init(self)
+
+ def addEntity(self, values):
+ self.entities.append(SirnaOpenBISDTO(values, self.definition))
+
+class SirnaOpenBISDTO(OpenBISDTO):
+ def write(self, tr):
+ code = 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"]
+ return code
+
+ def isInOpenBIS(self, tr):
+ code = self.values["SIRNA_OLIGONUMBER"]
+ 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 DocumentsAdaptor(FileMakerEntityAdaptor):
@@ -379,8 +555,13 @@ fmConnStringServer = "jdbc:filemaker://fm.ethz.ch/"
fmUserServer= "sistemp"
fmPassServer = "ibcimsb2014"
-adaptors = [AntibodyAdaptor(fmConnString, fmUser, fmPass, "BOXIT_antibodies_Peter"),
- AntibodyBoxAdaptor(fmConnString, fmUser, fmPass, "BOXIT_antibody_boxes_Peter"),
+#adaptors = [#AntibodyAdaptor(fmConnString, fmUser, fmPass, "BOXIT_antibodies_Peter"),
+ #AntibodyBoxAdaptor(fmConnString, fmUser, fmPass, "BOXIT_antibody_boxes_Peter"),
+ #CellAdaptor(fmConnString, fmUser, fmPass, "BOXIT_cells_Peter"),
+ #PlasmidAdaptor(fmConnString, fmUser, fmPass, "BOXIT_plasmids_Peter"),
+ #StrainAdaptor(fmConnString, fmUser, fmPass, "BOXIT_strains_Peter"),
+ #ChemicalAdaptor(fmConnString, fmUser, fmPass, "BOXIT_Main_Menu_Peter"),]
+adaptors = [SirnaAdaptor(fmConnString, fmUser, fmPass, "BOXIT_Main_Menu_Peter"),
DocumentsAdaptor(fmConnString, fmUser, fmPass, "BOXIT_documents_Peter")]
def createDataHierarchy(tr):
--
GitLab