diff --git a/plasmid/source/core-plugins/petermigration/1/as/definitions.py b/plasmid/source/core-plugins/petermigration/1/as/definitions.py
index 2499678ad13f11bb98fd311b7393c5a2a4160173..093b5af7d6d4d058105551280f67745023da3869 100644
--- a/plasmid/source/core-plugins/petermigration/1/as/definitions.py
+++ b/plasmid/source/core-plugins/petermigration/1/as/definitions.py
@@ -29,14 +29,21 @@ tmScriptName= "TM"
# Storage
#
numberOfStorageGroups = 15
-stogageGroupPropertyCodes = ["STORAGE_NAME", "STORAGE_ROW", "STORAGE_COLUMN", "STORAGE_BOX_NAME", "STORAGE_USER", "STORAGE_BOX_POSITION"] #This is duplicated below, needs cleanup
-storageGroupDefinition = [
- ["STORAGE_NAME_0", "Physical Storage 0", "location", DataType.CONTROLLEDVOCABULARY, "FREEZER", "Storage Name 0", None, None, False],
- ["STORAGE_ROW_0", "Physical Storage 0", "Storage Row", DataType.INTEGER, None, "Storage Row 0", None, None, False],
- ["STORAGE_COLUMN_0", "Physical Storage 0", "Storage Column", DataType.INTEGER, None, "Storage Column 0", None, None, False],
- ["STORAGE_BOX_NAME_0", "Physical Storage 0", "box label", DataType.VARCHAR, None, "Storage Box Name 0", None, None, False],
- ["STORAGE_USER_0", "Physical Storage 0", "frozen by", DataType.CONTROLLEDVOCABULARY, "ALL_LAB_MEMBERS", "Storage User Id 0", None, None, False],
- ["STORAGE_BOX_POSITION_0", "Physical Storage 0", "position", DataType.VARCHAR, None, "Storage Box Position 0", None, None, False]
+
+def getStorageGroupPropertyCodes():
+ propertyCodes = [];
+ for property in getStorageGroupDefinition():
+ propertyCodes.append(property[0]);
+ return propertyCodes;
+
+def getStorageGroupDefinition():
+ return [
+ ["STORAGE_NAME", "Physical Storage", "location", DataType.CONTROLLEDVOCABULARY, "FREEZER", "Storage Name", None, None, False],
+ ["STORAGE_ROW", "Physical Storage", "Storage Row", DataType.INTEGER, None, "Storage Row", None, None, False],
+ ["STORAGE_COLUMN", "Physical Storage", "Storage Column", DataType.INTEGER, None, "Storage Column", None, None, False],
+ ["STORAGE_BOX_NAME", "Physical Storage", "box label", DataType.VARCHAR, None, "Storage Box Name", None, None, False],
+ ["STORAGE_USER", "Physical Storage", "frozen by", DataType.CONTROLLEDVOCABULARY, "ALL_LAB_MEMBERS", "Storage User Id", None, None, False],
+ ["STORAGE_BOX_POSITION", "Physical Storage", "position", DataType.VARCHAR, None, "Storage Box Position", 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 2eadba2c48b138c303ea4c2d2d79eb4d9484df8c..7c21e80069e787679e1173c58629028511ed96b7 100644
--- a/plasmid/source/core-plugins/petermigration/1/as/definitionsVoc.py
+++ b/plasmid/source/core-plugins/petermigration/1/as/definitionsVoc.py
@@ -4,11 +4,11 @@
#
# Helper Methods
#
-def getVocaularyTermCodeForVocabularyAndTermLabel(vocabularyCode, termLabel):
+def getVocabularyTermCodeForVocabularyAndTermLabel(vocabularyCode, termLabel):
vocabulary = vocacbularyDefinitions[vocabularyCode]
for term in vocabulary:
if term[1] == termLabel:
- print repr("TERM NOT FOUND IN VOCABULARY LIST: " + unicode(vocabularyCode) + " : '" + unicode(termLabel) + "'")
+ #print repr("TERM NOT FOUND IN VOCABULARY LIST: " + unicode(vocabularyCode) + " : '" + unicode(termLabel) + "'")
return term[0]
return None
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 8227260d1e9709108df94dec543b99f402e2ce4f..adfa8fb482bae0d9e8a8e0cd15450ec835d57f62 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
@@ -112,13 +112,12 @@ def createProperty(propertyCode, dataType, propertyLabel, propertyDescription, v
return property;
def addStorageGroups(numGroups, sampleType):
- storageGroup = copy.copy(definitions.storageGroupDefinition);
-
for storageIdx in range(1,(numGroups + 1)):
+ storageGroup = definitions.getStorageGroupDefinition();
for property in storageGroup:
- property[0] = property[0].replace(str(storageIdx-1), str(storageIdx));
- property[1] = property[1].replace(str(storageIdx-1), str(storageIdx));
- property[5] = property[5].replace(str(storageIdx-1), str(storageIdx));
+ property[0] = property[0] + "_" + str(storageIdx);
+ property[1] = property[1] + "_" + str(storageIdx);
+ property[5] = property[5] + "_" + str(storageIdx);
addPropertiesToSamples([sampleType], storageGroup);
#Valid Script Types: DYNAMIC_PROPERTY, MANAGED_PROPERTY, ENTITY_VALIDATION
@@ -213,17 +212,15 @@ createExperimentTypeWithProperties("OLIGO", "BOX TO HOLD SAMPLES OF THIS TYPE FO
## Sample Types
##
createSampleTypeWithProperties("ANTIBODY", "", definitions.antibodyDefinition);
+addStorageGroups(definitions.numberOfStorageGroups, "ANTIBODY");
createSampleTypeWithProperties("CELL", "", definitions.cellDefinition);
+addStorageGroups(definitions.numberOfStorageGroups, "CELL");
createSampleTypeWithProperties("STRAIN", "", definitions.strainDefinition);
createSampleTypeWithProperties("PLASMID", "", definitions.plasmidDefinition);
createSampleTypeWithProperties("CHEMICAL", "", definitions.chemicalDefinition);
createSampleTypeWithProperties("SIRNA", "", definitions.siRNADefinition);
createSampleTypeWithProperties("OLIGO", "", definitions.oligoDefinition);
-
-
-addStorageGroups(definitions.numberOfStorageGroups, "ANTIBODY");
-
##
## Data set Types
##
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 bdf94353e953e4b7a5daaf5911b557501db43d64..65a33a031031d62bd5cb4c4e3226f4417d50343c 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
@@ -42,7 +42,7 @@ def setEntityProperties(tr, definition, entity, properties):
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)
+ possiblePropertyValue = definitionsVoc.getVocabularyTermCodeForVocabularyAndTermLabel(propertyDefinition[4], propertyValue)
if possiblePropertyValue is not None:
propertyValue = possiblePropertyValue
else: #We rely on the Add Hock Terms if is None
@@ -183,7 +183,7 @@ class FileMakerEntityAdaptor(EntityAdaptor):
class FMPeterOpenBISDTO(OpenBISDTO):
def isInOpenBIS(self, tr):
code = self.getIdentifier(tr)
- if code is not None:
+ if (code is not None) and (' ' not in code):
sampleID2Sample[self.values["NAME"]] = self.values
sample = getSampleForUpdate("/INVENTORY/"+code, None, tr)
if sample is not None:
@@ -194,14 +194,17 @@ class FMPeterOpenBISDTO(OpenBISDTO):
else :
return False
else:
- print "Null Code found in: " + self.__class__.__name__
+ print "Invalid Code found '" + str(code) + "' for '" + self.__class__.__name__ + "'"
return True
class FMPeterBoxAdaptor(FileMakerEntityAdaptor):
selectBoxQuery = None
entityIdFieldName = None
entityCodeFieldName = None
-
+
+ def addEntity(self, values):
+ self.entities.append(FMPeterEntityBoxOpenBISDTO(values, self.definition))
+
def init(self):
print "Reading boxes for: " + self.__class__.__name__
emptyBox = 0
@@ -236,7 +239,7 @@ class FMPeterBoxAdaptor(FileMakerEntityAdaptor):
#The antibody is not there. What the *#%$&
emptyBox += 1
- print "Not found: " + str(emptyBox)
+ print "Boxes positions with empty entityId for " + self.__class__.__name__ + ":" + str(emptyBox)
for entiyCode, allBoxes in boxes.iteritems():
self.addEntity({
@@ -247,42 +250,14 @@ class FMPeterBoxAdaptor(FileMakerEntityAdaptor):
result.close()
preparedStatement.close()
-##
-## Antibodies
-##
-class AntibodyAdaptor(FileMakerEntityAdaptor):
-
- def init(self):
- self.selectQuery = "SELECT * FROM \"boxit antibodies\""
- self.definition = definitions.antibodyDefinition
- FileMakerEntityAdaptor.init(self)
-
- def addEntity(self, values):
- self.entities.append(AntibodyOpenBISDTO(values, self.definition))
-
-class AntibodyOpenBISDTO(FMPeterOpenBISDTO):
- def write(self, tr):
- sample = getSampleForUpdate("/INVENTORY/"+self.values["ANTIBODY_ID_NR"],"ANTIBODY", tr)
- setEntityProperties(tr, self.definition, sample, self.values);
-
- def getIdentifier(self, tr):
- return self.values["ANTIBODY_ID_NR"]
-
-class AntibodyBoxAdaptor(FMPeterBoxAdaptor):
- selectBoxQuery = "SELECT * FROM \"antibody boxes\""
- entityIdFieldName = "antibody ID"
- entityCodeFieldName = "ANTIBODY_ID_NR"
-
- def addEntity(self, values):
- self.entities.append(AntibodyBoxOpenBISDTO(values, self.definition))
-
-class AntibodyBoxOpenBISDTO(OpenBISDTO):
+class FMPeterEntityBoxOpenBISDTO(OpenBISDTO):
def write(self, tr):
sample = getSampleForUpdate("/INVENTORY/"+self.values["*CODE"], None, tr)
+ print "BOXES SIZE: " + self.values["*CODE"] + " " + str(len(self.values["*BOXESLIST"]))
#Delete old boxes
for boxNum in range(1, definitions.numberOfStorageGroups+1):
- for propertyCode in definitions.stogageGroupPropertyCodes:
+ for propertyCode in definitions.getStorageGroupPropertyCodes():
sample.setPropertyValue(propertyCode + "_" + str(boxNum), None)
#Add new boxes
boxNum = 1
@@ -290,14 +265,14 @@ class AntibodyBoxOpenBISDTO(OpenBISDTO):
boxNum += 1
for propertyCode, propertyValue in box.iteritems():
if propertyCode == "STORAGE_NAME":
- freezerName = definitionsVoc.getVocaularyTermCodeForVocabularyAndTermLabel("FREEZER", propertyValue)
+ freezerName = definitionsVoc.getVocabularyTermCodeForVocabularyAndTermLabel("FREEZER", propertyValue)
if freezerName is None:
#print repr("NOT FOUND FEEZER: " + self.values["ANTIBODY_ID_NR"] + " : '" + unicode(propertyValue) + "'")
propertyValue = None
else:
propertyValue = freezerName
if propertyCode == "STORAGE_USER":
- storageUser = definitionsVoc.getVocaularyTermCodeForVocabularyAndTermLabel("ALL_LAB_MEMBERS", propertyValue)
+ storageUser = definitionsVoc.getVocabularyTermCodeForVocabularyAndTermLabel("ALL_LAB_MEMBERS", propertyValue)
if storageUser is None:
#print repr("NOT FOUND USER: " + self.values["ANTIBODY_ID_NR"] + " : '" + unicode(propertyValue) + "'")
propertyValue = None
@@ -313,7 +288,7 @@ class AntibodyBoxOpenBISDTO(OpenBISDTO):
if sample is not None:
for boxNum in range(1, definitions.numberOfStorageGroups+1):
storedSignature = "";
- for propertyCode in definitions.stogageGroupPropertyCodes:
+ for propertyCode in definitions.getStorageGroupPropertyCodes():
propertyValue = sample.getPropertyValue(propertyCode + "_" + str(boxNum))
if propertyValue is not None:
propertyValue = unicode(propertyValue)
@@ -326,12 +301,12 @@ class AntibodyBoxOpenBISDTO(OpenBISDTO):
def isInOpenBIS(self, tr):
for box in self.values["*BOXESLIST"]:
boxSignature = "";
- for propertyCode in definitions.stogageGroupPropertyCodes:
+ for propertyCode in definitions.getStorageGroupPropertyCodes():
propertyValue = box[propertyCode]
if propertyCode == "STORAGE_NAME":
- propertyValue = definitionsVoc.getVocaularyTermCodeForVocabularyAndTermLabel("FREEZER", propertyValue)
+ propertyValue = definitionsVoc.getVocabularyTermCodeForVocabularyAndTermLabel("FREEZER", propertyValue)
if propertyCode == "STORAGE_USER":
- propertyValue = definitionsVoc.getVocaularyTermCodeForVocabularyAndTermLabel("LAB_MEMBERS_INITIALS", propertyValue)
+ propertyValue = definitionsVoc.getVocabularyTermCodeForVocabularyAndTermLabel("LAB_MEMBERS_INITIALS", propertyValue)
if propertyValue is not None:
propertyValue = unicode(propertyValue)
@@ -339,6 +314,30 @@ class AntibodyBoxOpenBISDTO(OpenBISDTO):
if not self.isBoxPressent(boxSignature, tr):
return False
return True
+##
+## Antibodies
+##
+class AntibodyAdaptor(FileMakerEntityAdaptor):
+ def init(self):
+ self.selectQuery = "SELECT * FROM \"boxit antibodies\""
+ self.definition = definitions.antibodyDefinition
+ FileMakerEntityAdaptor.init(self)
+
+ def addEntity(self, values):
+ self.entities.append(AntibodyOpenBISDTO(values, self.definition))
+
+class AntibodyOpenBISDTO(FMPeterOpenBISDTO):
+ def write(self, tr):
+ sample = getSampleForUpdate("/INVENTORY/"+self.values["ANTIBODY_ID_NR"],"ANTIBODY", tr)
+ setEntityProperties(tr, self.definition, sample, self.values);
+
+ def getIdentifier(self, tr):
+ return self.values["ANTIBODY_ID_NR"]
+
+class AntibodyBoxAdaptor(FMPeterBoxAdaptor):
+ selectBoxQuery = "SELECT * FROM \"antibody boxes\""
+ entityIdFieldName = "antibody ID"
+ entityCodeFieldName = "ANTIBODY_ID_NR"
##
## Cells
@@ -364,6 +363,11 @@ class CellOpenBISDTO(FMPeterOpenBISDTO):
code = self.values["CELL_ID_NR_COPY"]
return code
+class CellBoxAdaptor(FMPeterBoxAdaptor):
+ selectBoxQuery = "SELECT * FROM \"cell boxes\""
+ entityIdFieldName = "cell ID"
+ entityCodeFieldName = "CELL_ID_NR_COPY"
+
##
## Strains
##
@@ -548,16 +552,18 @@ 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"),
- #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"),
- #OligoAdaptor(fmConnString, fmUser, fmPass, "BOXIT_oligos_Peter"),
- DocumentsAdaptor(fmConnString, fmUser, fmPass, "BOXIT_documents_Peter")]
+# AntibodyAdaptor(fmConnString, fmUser, fmPass, "BOXIT_antibodies_Peter"),
+# AntibodyBoxAdaptor(fmConnString, fmUser, fmPass, "BOXIT_antibody_boxes_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"),
+# OligoAdaptor(fmConnString, fmUser, fmPass, "BOXIT_oligos_Peter"),
+adaptors = [CellAdaptor(fmConnString, fmUser, fmPass, "BOXIT_cells_Peter"),
+ CellBoxAdaptor(fmConnString, fmUser, fmPass, "BOXIT_cell_boxes_Peter"),
+ DocumentsAdaptor(fmConnString, fmUser, fmPass, "BOXIT_documents_Peter")]
+
def createDataHierarchy(tr):
inventorySpace = tr.getSpace("INVENTORY")
if inventorySpace == None: