From de1b85b87ee2035fc9de6ba280b5677caeaabcf2 Mon Sep 17 00:00:00 2001
From: juanf <juanf>
Date: Wed, 10 Dec 2014 13:49:34 +0000
Subject: [PATCH] SSDM-1285 : ELN - Peter Lab Migration
SVN: 33014
---
.../petermigration/1/as/definitions.py | 1 -
.../drop-boxes/petermigration/migration.py | 152 +++++++++++++-----
2 files changed, 112 insertions(+), 41 deletions(-)
diff --git a/plasmid/source/core-plugins/petermigration/1/as/definitions.py b/plasmid/source/core-plugins/petermigration/1/as/definitions.py
index 1693894fdc3..2f679851f7d 100644
--- a/plasmid/source/core-plugins/petermigration/1/as/definitions.py
+++ b/plasmid/source/core-plugins/petermigration/1/as/definitions.py
@@ -351,7 +351,6 @@ siRNADefinition = [
# Data Set Types
#
documentDefinition = [
- ["NOTES", "General", "Notes", DataType.MULTILINE_VARCHAR, None, "", None, None, False],
["CREATION_DATE", "General", "date created", DataType.TIMESTAMP, None, "", None, None, False],
["MODIFICATION_DATE", "General", "date modified", DataType.TIMESTAMP, None, "", None, None, False],
["INFO", "General", "info", DataType.VARCHAR, None, "", None, None, False],
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 1f045369161..d7674e43958 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
@@ -5,17 +5,11 @@ import definitionsVoc
import re
import random
from datetime import datetime
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria, SearchSubCriteria
import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.DataType as DataType
-
import java.lang.Class as Class
-import java.sql.Connection as Connection
import java.sql.DriverManager as DriverManager
-import java.sql.PreparedStatement as PreparedStatement
-import java.sql.ResultSet as ResultSet
-import java.sql.SQLException as SQLException
-import java.util.ArrayList as ArrayList
-import java.util.List as List
##
## Generic Process Method
@@ -35,7 +29,41 @@ def process(tr):
print "FINISH!"
##
-## Generic Adaptor Pattern
+## Help Methods
+##
+def setEntityProperties(tr, definition, entity, properties):
+ for propertyCode, propertyValue in properties.iteritems():
+ propertyDefinition = definitions.getPropertyDefinitionByCode(definition, propertyCode)
+ if propertyValue is not None:
+ propertyValue = unicode(propertyValue)
+
+ if propertyDefinition is not None and propertyDefinition[3] == DataType.CONTROLLEDVOCABULARY and propertyValue is not None:
+ possiblePropertyValue = definitionsVoc.getVocaularyTermCodeForVocabularyAndTermLabel(propertyDefinition[4], propertyValue)
+ if possiblePropertyValue is not None:
+ propertyValue = possiblePropertyValue
+ else: #We rely on the Add Hock Terms if is None
+ #Create new vocabulary term
+ vocabulary = tr.getVocabularyForUpdate(propertyDefinition[4])
+ term = tr.createNewVocabularyTerm()
+ 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]
+ 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
+
+ if propertyDefinition is not None: #Sometimes special fields are added for other purposes, these should not be set
+ entity.setPropertyValue(propertyCode, propertyValue)
+
+##
+## Generic Pattern
##
class EntityAdaptor:
entities = None
@@ -82,17 +110,36 @@ class OpenBISDTO:
##
## Costumer specific logic
##
+experimentCache = {}
sampleCache = {}
antibodyID2Antibody = {}
+def getExperimentForUpdate(experimentIdentifier, experimentType, tr):
+ if experimentIdentifier not in experimentCache:
+ #print "Cache failed " + experimentIdentifier + ":" + str(experimentType)
+ experiment = tr.getExperimentForUpdate(experimentIdentifier)
+ if experiment is None and experimentType is not None:
+ #print "Cache Create " + experimentIdentifier + ":" + str(experimentType)
+ experiment = tr.createNewExperiment(experimentIdentifier, experimentType)
+ if experiment is not None:
+ experimentCache[experimentIdentifier] = experiment
+ else:
+ pass
+ #print "Cache hit " + experimentIdentifier + ":" + str(experimentType)
+ if experimentIdentifier not in experimentCache:
+ return None
+ else:
+ return experimentCache[experimentIdentifier]
+
def getSampleForUpdate(sampleIdentifier, sampleType, tr):
if sampleIdentifier not in sampleCache:
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)
+ experiment = getExperimentForUpdate("/INVENTORY/MATERIALS/" + sampleType, sampleType, tr)
sample = tr.createNewSample(sampleIdentifier, sampleType)
-
+ sample.setExperiment(experiment)
if sample is not None:
sampleCache[sampleIdentifier] = sample
else:
@@ -139,34 +186,7 @@ class AntibodyAdaptor(FileMakerEntityAdaptor):
class AntibodyOpenBISDTO(OpenBISDTO):
def write(self, tr):
sample = getSampleForUpdate("/INVENTORY/"+self.values["ANTIBODY_ID_NR"],"ANTIBODY", tr)
-
- for propertyCode, propertyValue in self.values.iteritems():
- propertyDefinition = definitions.getPropertyDefinitionByCode(self.definition, propertyCode)
- if propertyValue is not None:
- propertyValue = unicode(propertyValue)
-
- if propertyDefinition[3] == DataType.CONTROLLEDVOCABULARY and propertyValue is not None:
- posiblePropertyValue = definitionsVoc.getVocaularyTermCodeForVocabularyAndTermLabel(propertyDefinition[4], propertyValue)
- if posiblePropertyValue is not None:
- propertyValue = posiblePropertyValue
- else: #We rely on the Add Hock Terms if is None
- #Create new vocabulary term
- vocabulary = tr.getVocabularyForUpdate(propertyDefinition[4])
- term = tr.createNewVocabularyTerm()
- 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]
- 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
- sample.setPropertyValue(propertyCode, propertyValue)
+ setEntityProperties(tr, self.definition, sample, self.values);
def getIdentifier(self, tr):
return self.values["ANTIBODY_ID_NR"]
@@ -298,6 +318,57 @@ class AntibodyBoxOpenBISDTO(OpenBISDTO):
return False
return True
+class DocumentsAdaptor(FileMakerEntityAdaptor):
+
+ def init(self):
+ self.selectQuery = "SELECT * FROM documents"
+ self.definition = definitions.documentDefinition
+ FileMakerEntityAdaptor.init(self)
+
+ def addEntity(self, values):
+ preparedStatement = self.connection.prepareStatement("SELECT GetAs(file, 'FILE') AS fileData FROM documents WHERE serial = ?");
+ preparedStatement.setString(1, values["SERIAL"]);
+ result = preparedStatement.executeQuery();
+
+ if result.next():
+ fileData = result.getBytes("fileData");
+ if fileData is not None:
+ values["*DATA"] = fileData
+
+ self.entities.append(DocumentOpenBISDTO(values, self.definition))
+
+class DocumentOpenBISDTO(OpenBISDTO):
+ def write(self, tr):
+ sampleIdentifier = "/INVENTORY/"+self.values["ID_NR"];
+ dataSetSample = getSampleForUpdate(sampleIdentifier, None, tr)
+ if dataSetSample is not None:
+ dataSet = tr.createNewDataSet("DOCUMENT")
+ dataSet.setSample(dataSetSample)
+ setEntityProperties(tr, self.definition, dataSet, self.values)
+ tr.createNewFile(dataSet, "Test")
+ #incoming = tr.getIncoming()
+ #tr.moveFile(incoming.getAbsolutePath(), dataSet)
+ else:
+ print "Document missing sample: " + sampleIdentifier
+
+ def getIdentifier(self, tr):
+ return self.values["SERIAL"]
+
+ def getDocumentBySerial(self, tr, serial):
+ criteria = SearchCriteria()
+ criteria.setOperator(criteria.SearchOperator.MATCH_ANY_CLAUSES)
+ criteria.addMatchClause(criteria.MatchClause.createAttributeMatch(criteria.MatchClauseAttribute.TYPE, "DOCUMENT"))
+ criteria.addMatchClause(criteria.MatchClause.createPropertyMatch("SERIAL", serial))
+ datasets = tr.getSearchService().searchForDataSets(criteria)
+ if datasets:
+ return datasets[0]
+ else:
+ return None
+
+ def isInOpenBIS(self, tr):
+ dataset = self.getDocumentBySerial(tr, self.values["SERIAL"])
+ return dataset is not None
+
fmConnString = "jdbc:filemaker://127.0.0.1/"
fmUser = "designer"
fmPass = "seattle"
@@ -306,11 +377,12 @@ fmConnStringServer = "jdbc:filemaker://fm.ethz.ch/"
fmUserServer= "sistemp"
fmPassServer = "ibcimsb2014"
-adaptors = [AntibodyAdaptor(fmConnString, fmUser, fmPass, "BOXIT_antibodies_Peter.fmp12"), AntibodyBoxAdaptor(fmConnString, fmUser, fmPass, "BOXIT_antibody_boxes_Peter")]
+adaptors = [AntibodyAdaptor(fmConnString, fmUser, fmPass, "BOXIT_antibodies_Peter"),
+ AntibodyBoxAdaptor(fmConnString, fmUser, fmPass, "BOXIT_antibody_boxes_Peter"),
+ DocumentsAdaptor(fmConnString, fmUser, fmPass, "BOXIT_documents_Peter")]
def createDataHierarchy(tr):
inventorySpace = tr.getSpace("INVENTORY")
if inventorySpace == None:
tr.createNewSpace("INVENTORY", None)
- tr.createNewProject("/INVENTORY/MATERIALS")
- tr.createNewExperiment("/INVENTORY/MATERIALS/ANTIBODY", "ANTIBODY")
\ No newline at end of file
+ tr.createNewProject("/INVENTORY/MATERIALS")
\ No newline at end of file
--
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