From 8640341c6b1471c20e3c4341cbdb706f1dd4a9f5 Mon Sep 17 00:00:00 2001
From: barillac <barillac>
Date: Thu, 2 Jul 2015 12:47:41 +0000
Subject: [PATCH] small fix
SVN: 34317
---
.../dss/drop-boxes/weismigration/migration.py | 53 +++++++++++--------
1 file changed, 30 insertions(+), 23 deletions(-)
diff --git a/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes/weismigration/migration.py b/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes/weismigration/migration.py
index 3ae7e6b3cf4..721ebf09466 100644
--- a/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes/weismigration/migration.py
+++ b/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes/weismigration/migration.py
@@ -81,7 +81,6 @@ def setEntityProperties(tr, definition, entity, properties):
possiblePropertyValue = definitionsVoc.getVocabularyTermCodeForVocabularyAndTermLabel(propertyDefinition[4], propertyValue)
if possiblePropertyValue is not None:
propertyValue = possiblePropertyValue
- print "EXISTING VALUE:", propertyValue
else:
print "MISSING VALUE FOR:", propertyValue
@@ -265,17 +264,17 @@ def getSampleForUpdate(sampleIdentifier, sampleType, tr):
if sample is None and sampleType is not None:
#print "Cache Create " + sampleIdentifier + ":" + str(sampleType)
if sampleType == "ANTIBODY":
- experiment = getExperimentForUpdate("/MATERIALS/REAGENTS/ANTIBODIES", sampleType, tr)
+ experiment = getExperimentForUpdate("/MATERIALS/REAGENTS/ANTIBODIES", sampleType, tr)
elif sampleType == "STRAIN":
- experiment = getExperimentForUpdate("/MATERIALS/YEASTS/YEAST_COLLECTION_1", sampleType, tr)
+ experiment = getExperimentForUpdate("/MATERIALS/YEASTS/YEAST_COLLECTION_1", sampleType, tr)
elif sampleType == "PLASMID":
- experiment = getExperimentForUpdate("/MATERIALS/PLASMIDS/PLASMID_COLLECTION_1", sampleType, tr)
+ experiment = getExperimentForUpdate("/MATERIALS/PLASMIDS/PLASMID_COLLECTION_1", sampleType, tr)
elif sampleType == "CHEMICAL":
- experiment = getExperimentForUpdate("/MATERIALS/REAGENTS/CHEMICALS", sampleType, tr)
+ experiment = getExperimentForUpdate("/MATERIALS/REAGENTS/CHEMICALS", sampleType, tr)
elif sampleType == "RESTRICTION_ENZYME":
- experiment = getExperimentForUpdate("/MATERIALS/REAGENTS/RESTRICTION_ENZYMES", sampleType, tr)
+ experiment = getExperimentForUpdate("/MATERIALS/REAGENTS/RESTRICTION_ENZYMES", sampleType, tr)
elif sampleType == "OLIGO":
- experiment = getExperimentForUpdate("/MATERIALS/POLYNUCLEOTIDES/OLIGO_COLLECTION_1", sampleType, tr)
+ experiment = getExperimentForUpdate("/MATERIALS/POLYNUCLEOTIDES/OLIGO_COLLECTION_1", sampleType, tr)
sample = tr.createNewSample(sampleIdentifier, sampleType)
sample.setExperiment(experiment)
if sample is not None:
@@ -462,14 +461,19 @@ class AntibodyOpenBISDTO(FMPeterOpenBISDTO):
return False
def write(self, tr):
- code = "AB_" + self.values["REF_NUM"]
- if code is not None:
- sample = getSampleForUpdate("/MATERIALS/"+code,"ANTIBODY", tr)
- setEntityProperties(tr, self.definition, sample, self.values);
+ if self.values["REF_NUM"] is not None:
+
+ code = "AB" + self.values["REF_NUM"]
+ if code is not None:
+ sample = getSampleForUpdate("/MATERIALS/"+code,"ANTIBODY", tr)
+ setEntityProperties(tr, self.definition, sample, self.values);
+ else:
+ print "Sample ", self.values["REF_NUM"], " does not have a REF_NUM"
def getIdentifier(self, tr):
- code = "AB_"+ self.values["REF_NUM"]
- return code
+ if self.values["REF_NUM"]:
+ code = "AB"+ self.values["REF_NUM"]
+ return code
@@ -493,6 +497,7 @@ class StrainOpenBISDTO(FMPeterOpenBISDTO):
sample = getSampleForUpdate("/MATERIALS/"+code,"STRAIN", tr)
setEntityProperties(tr, self.definition, sample, self.values)
print setEntityProperties(tr, self.definition, sample, self.values)
+
def getIdentifier(self, tr):
code = self.values["NAME"]
@@ -575,13 +580,13 @@ class ChemicalOpenBISDTO(FMPeterOpenBISDTO):
return False
def write(self, tr):
- code = "CHEM_" + self.values["ID"]
+ code = "CHEM" + self.values["ID"]
if code is not None:
sample = getSampleForUpdate("/MATERIALS/"+code,"CHEMICAL", tr)
setEntityProperties(tr, self.definition, sample, self.values);
def getIdentifier(self, tr):
- code = "CHEM_" + self.values["ID"]
+ code = "CHEM" + self.values["ID"]
return code
##
@@ -601,15 +606,17 @@ class EnzymeOpenBISDTO(FMPeterOpenBISDTO):
return False
def write(self, tr):
- code = self.values["NAME"]
+ for i in range(1,45):
+ code = "RE" + str(i)
- if code is not None:
+
sample = getSampleForUpdate("/MATERIALS/"+code,"RESTRICTION_ENZYME", tr)
setEntityProperties(tr, self.definition, sample, self.values);
def getIdentifier(self, tr):
- code = self.values["NAME"]
- return code
+ for i in range(1,45):
+ code = "RE" + str(i)
+ return code
@@ -635,13 +642,13 @@ fmPass = "nucleus"
adaptors = [
- EnzymeAdaptor(fmConnString, fmUser, fmPass, "Weis_Restriction_enzymes")
+ #EnzymeAdaptor(fmConnString, fmUser, fmPass, "Weis_Restriction_enzymes")
#ChemicalAdaptor(fmConnString, fmUser, fmPass, "Weis_Chemicals")
- #OligoAdaptor(fmConnString, fmUser, fmPass, "Weis_Oligos"),
#AntibodyAdaptor(fmConnString, fmUser, fmPass, "Weis _Antibodies")
+ #OligoAdaptor(fmConnString, fmUser, fmPass, "Weis_Oligos"),
#PlasmidAdaptor(fmConnString, fmUser, fmPass, "Weis_Plasmids")
- #StrainAdaptor(fmConnString, fmUser, fmPass, "Weis_Yeast_Strains"),
- #StrainMultipleValuesAdaptor(fmConnString, fmUser, fmPass, "Weis_Yeast_Strains")
+ StrainAdaptor(fmConnString, fmUser, fmPass, "Weis_Yeast_Strains"),
+ StrainMultipleValuesAdaptor(fmConnString, fmUser, fmPass, "Weis_Yeast_Strains")
]
--
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