From cd5d428a5d3bb9484c6cd53565bacb54fe793e2f Mon Sep 17 00:00:00 2001
From: barillac <barillac>
Date: Tue, 17 Mar 2015 11:24:19 +0000
Subject: [PATCH] changed structure of inventory
SVN: 33671
---
.../drop-boxes/petermigration/migration.py | 49 +++++++++++++------
1 file changed, 34 insertions(+), 15 deletions(-)
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 2270da028c2..9504d20de32 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
@@ -169,7 +169,20 @@ def getSampleForUpdate(sampleIdentifier, sampleType, tr):
sample = tr.getSampleForUpdate(sampleIdentifier)
if sample is None and sampleType is not None:
#print "Cache Create " + sampleIdentifier + ":" + str(sampleType)
- experiment = getExperimentForUpdate("/INVENTORY/MATERIALS/" + sampleType, sampleType, tr)
+ if sampleType == "ANTIBODY":
+ experiment = getExperimentForUpdate("/MATERIALS/REAGENTS/ANTIBODIES", sampleType, tr)
+ elif sampleType == "CELL":
+ experiment = getExperimentForUpdate("/MATERIALS/CELL_LINES/CELL_LINE_COLLECTION_1", sampleType, tr)
+ elif sampleType == "STRAIN":
+ experiment = getExperimentForUpdate("/MATERIALS/YEASTS/YEAST_COLLECTION", sampleType, tr)
+ elif sampleType == "PLASMID":
+ experiment = getExperimentForUpdate("/MATERIALS/PLASMIDS/PLASMID_COLLECTION_1", sampleType, tr)
+ elif sampleType == "CHEMICAL":
+ experiment = getExperimentForUpdate("/MATERIALS/REAGENTS/CHEMICALS", sampleType, tr)
+ elif sampleType == "SIRNA":
+ experiment = getExperimentForUpdate("/MATERIALS/POLYNUCLEOTIDES/RNA_COLLECTION_1", sampleType, tr)
+ elif sampleType == "OLIGO":
+ experiment = getExperimentForUpdate("/MATERIALS/POLYNUCLEOTIDES/OLIGO_COLLECTION_1", sampleType, tr)
sample = tr.createNewSample(sampleIdentifier, sampleType)
sample.setExperiment(experiment)
if sample is not None:
@@ -217,7 +230,7 @@ class FMPeterOpenBISDTO(OpenBISDTO):
if (code is not None) and (' ' not in code):
if self.isSampleCacheable():
sampleID2Sample[self.values["NAME"]] = self.values
- sample = getSampleForUpdate("/INVENTORY/"+code, None, tr)
+ sample = getSampleForUpdate("/MATERIALS/"+code, None, tr)
if sample is not None:
lastModificationData = self.values["MODIFICATION_DATE"].strip()
lastModificationData = str(datetime.strptime(lastModificationData, "%Y-%m-%d"))[:10]
@@ -287,7 +300,7 @@ class FMPeterEntityBoxOpenBISDTO(OpenBISDTO):
return self.values["*CODE"]
def write(self, tr):
- sample = getSampleForUpdate("/INVENTORY/"+self.values["*CODE"], None, tr)
+ sample = getSampleForUpdate("/MATERIALS/"+self.values["*CODE"], None, tr)
print "* INFO Boxes size: " + str(len(self.values["*BOXESLIST"]))
#Delete old boxes
for boxNum in range(1, definitions.numberOfStorageGroups+1):
@@ -319,7 +332,7 @@ class FMPeterEntityBoxOpenBISDTO(OpenBISDTO):
sample.setPropertyValue(propertyCode + "_" + str(boxNum), propertyValue)
def isBoxPressent(self, boxSignature, tr):
- sample = getSampleForUpdate("/INVENTORY/"+self.values["*CODE"], None, tr)
+ sample = getSampleForUpdate("/MATERIALS/"+self.values["*CODE"], None, tr)
if sample is not None:
for boxNum in range(1, definitions.numberOfStorageGroups+1):
storedSignature = "";
@@ -363,7 +376,7 @@ class AntibodyAdaptor(FileMakerEntityAdaptor):
class AntibodyOpenBISDTO(FMPeterOpenBISDTO):
def write(self, tr):
- sample = getSampleForUpdate("/INVENTORY/"+self.values["ANTIBODY_ID_NR"],"ANTIBODY", tr)
+ sample = getSampleForUpdate("/MATERIALS/"+self.values["ANTIBODY_ID_NR"],"ANTIBODY", tr)
setEntityProperties(tr, self.definition, sample, self.values);
def getIdentifier(self, tr):
@@ -391,7 +404,7 @@ class CellOpenBISDTO(FMPeterOpenBISDTO):
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)
+ sample = getSampleForUpdate("/MATERIALS/"+code,"CELL", tr)
setEntityProperties(tr, self.definition, sample, self.values);
def getIdentifier(self, tr):
@@ -420,7 +433,7 @@ class StrainOpenBISDTO(FMPeterOpenBISDTO):
def write(self, tr):
code = self.values["STRAIN_ID_NR"]
if code is not None:
- sample = getSampleForUpdate("/INVENTORY/"+code,"STRAIN", tr)
+ sample = getSampleForUpdate("/MATERIALS/"+code,"STRAIN", tr)
setEntityProperties(tr, self.definition, sample, self.values);
def getIdentifier(self, tr):
@@ -448,7 +461,7 @@ class PlasmidOpenBISDTO(FMPeterOpenBISDTO):
def write(self, tr):
code = self.values["PLASMID_ID_NR"]
if code is not None:
- sample = getSampleForUpdate("/INVENTORY/"+code,"PLASMID", tr)
+ sample = getSampleForUpdate("/MATERIALS/"+code,"PLASMID", tr)
setEntityProperties(tr, self.definition, sample, self.values);
def getIdentifier(self, tr):
@@ -477,7 +490,7 @@ class OligoOpenBISDTO(FMPeterOpenBISDTO):
def write(self, tr):
code = self.values["OLIGO_ID_NR"]
if code is not None:
- sample = getSampleForUpdate("/INVENTORY/"+code,"OLIGO", tr)
+ sample = getSampleForUpdate("/MATERIALS/"+code,"OLIGO", tr)
setEntityProperties(tr, self.definition, sample, self.values);
def getIdentifier(self, tr):
@@ -509,7 +522,7 @@ class ChemicalOpenBISDTO(FMPeterOpenBISDTO):
def write(self, tr):
code = "CHEM_" + self.values["RECORD_NUMBER"]
if code is not None:
- sample = getSampleForUpdate("/INVENTORY/"+code,"CHEMICAL", tr)
+ sample = getSampleForUpdate("/MATERIALS/"+code,"CHEMICAL", tr)
setEntityProperties(tr, self.definition, sample, self.values);
def getIdentifier(self, tr):
@@ -535,7 +548,7 @@ class SirnaOpenBISDTO(FMPeterOpenBISDTO):
def write(self, tr):
code = "SI_" + self.values["SIRNA_OLIGONUMBER"]
if code is not None:
- sample = getSampleForUpdate("/INVENTORY/"+code,"SIRNA", tr)
+ sample = getSampleForUpdate("/MATERIALS/"+code,"SIRNA", tr)
setEntityProperties(tr, self.definition, sample, self.values);
def getIdentifier(self, tr):
@@ -565,7 +578,7 @@ class DocumentsAdaptor(FileMakerEntityAdaptor):
class DocumentOpenBISDTO(OpenBISDTO):
def write(self, tr):
- sampleIdentifier = "/INVENTORY/"+self.values["ID_NR"];
+ sampleIdentifier = "/MATERIALS/"+self.values["ID_NR"];
dataSetSample = getSampleForUpdate(sampleIdentifier, None, tr)
if dataSetSample is not None and self.values["*DATA"] is not None and self.values["FILE"] is not None:
print "* INFO DATASET CREATION FOR SERIAL " + self.values["SERIAL"] + " WITH FILE " + self.values["FILE"]
@@ -629,7 +642,13 @@ adaptors = [ AntibodyAdaptor(fmConnString, fmUser, fmPass, "BOXIT_antibodies_Pet
def createDataHierarchy(tr):
- inventorySpace = tr.getSpace("INVENTORY")
+ inventorySpace = tr.getSpace("MATERIALS")
if inventorySpace == None:
- tr.createNewSpace("INVENTORY", None)
- tr.createNewProject("/INVENTORY/MATERIALS")
\ No newline at end of file
+ tr.createNewSpace("MATERIALS", None)
+ tr.createNewProject("/MATERIALS/REAGENTS")
+ tr.createNewProject("/MATERIALS/CELL_LINES")
+ tr.createNewProject("/MATERIALS/POLYNUCLEOTIDES")
+ tr.createNewProject("/MATERIALS/PLASMIDS")
+ tr.createNewProject("/MATERIALS/YEASTS")
+
+
\ No newline at end of file
--
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