Prepare release 1.6.0

sven1103 · web-flow · commit 413ef9a0fda0 · 2021-01-22T14:17:33.000+01:00
Release 1.6.0
diff --git a/drop-boxes/register-wf-16staxonomicprofiling/register-16staxonomic-dropbox.py b/drop-boxes/register-wf-16staxonomicprofiling/register-16staxonomic-dropbox.py
@@ -56,18 +56,12 @@ def process(transaction):
         space = nameSplit[0]
         project = pPattern.findall(nameSplit[1])[0]
         experiment_id = ePattern.findall(nameSplit[2])[0]
-        #sample_id = experiment_id+'.'
         sampleCode = nameSplit[-1]
+        sample_id = "/"+space+"/"+sampleCode
         if not experiment_id:
                 print "The identifier matching the pattern Q\w{4}E\[0-9]+ was not found in the fileName "+name
 
-        ss = transaction.getSearchService()
-
-        sc = SearchCriteria()
-        sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sampleCode))
-        foundSamples = ss.searchForSamples(sc)
-        samplehit = foundSamples[0]
-        sample = transaction.getSampleForUpdate(samplehit.getSampleIdentifier())
+        sample = transaction.getSampleForUpdate(sample_id)
 
         experiment = transaction.getExperimentForUpdate("/"+space+"/"+project+"/"+experiment_id)
         experiment.setPropertyValue("Q_WF_STATUS", "FINISHED")
diff --git a/drop-boxes/register-wf-epitopeprediction/register-epitopeprediction.py b/drop-boxes/register-wf-epitopeprediction/register-epitopeprediction.py
@@ -34,18 +34,14 @@ def process(transaction):
     project = pPattern.findall(nameSplit[1])[0]
     experiment_id = ePattern.findall(nameSplit[2])[0]
     sampleCode = nameSplit[-1]
+    sample_id = "/"+space+"/"+sampleCode
+
     if not experiment_id:
             print "The identifier matching the pattern Q\w{4}E\[0-9]+ was not found in the fileName "+name
 
-    ss = transaction.getSearchService()
-
-    sc = SearchCriteria()
-    sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sampleCode))
-    foundSamples = ss.searchForSamples(sc)
-    samplehit = foundSamples[0]
-    sample = transaction.getSampleForUpdate(samplehit.getSampleIdentifier())
-
-    parents = samplehit.getParentSampleIdentifiers()
+    sample = transaction.getSampleForUpdate(sample_id)
+    
+    parents = sample.getParentSampleIdentifiers()
     parentcodes = []
     for parent in parents:
         parentcodes.append(parent.split("/")[-1])
diff --git a/drop-boxes/register-wf-hlatyping/register-hlatyping.py b/drop-boxes/register-wf-hlatyping/register-hlatyping.py
@@ -57,18 +57,13 @@ def process(transaction):
     project = pPattern.findall(name)[0]
     experiment_id = ePattern.findall(name)[0]
     sampleCode = nameSplit[-1]
+    sample_id = "/"+space+"/"+sampleCode
     if not experiment_id:
             print "The identifier matching the pattern Q\w{4}E\[0-9]+ was not found in the fileName "+name
 
-    ss = transaction.getSearchService()
+    sample = transaction.getSampleForUpdate(sample_id)
 
-    sc = SearchCriteria()
-    sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sampleCode))
-    foundSamples = ss.searchForSamples(sc)
-    samplehit = foundSamples[0]
-    sample = transaction.getSampleForUpdate(samplehit.getSampleIdentifier())
-
-    parents = samplehit.getParentSampleIdentifiers()
+    parents = sample.getParentSampleIdentifiers()
     parentcodes = []
     for parent in parents:
         parentcodes.append(parent.split("/")[-1])
diff --git a/drop-boxes/register-wf-individualizedproteome/register-individualizedproteome-dropbox.py b/drop-boxes/register-wf-individualizedproteome/register-individualizedproteome-dropbox.py
@@ -41,20 +41,14 @@ def process(transaction):
         space = nameSplit[0]
         project = pPattern.findall(nameSplit[1])[0]
         experiment_id = ePattern.findall(nameSplit[2])[0]
-        #sample_id = experiment_id+'.'
         sampleCode = nameSplit[-1]
+        sample_id = "/"+space+"/"+sampleCode
+
         if not experiment_id:
                 print "The identifier matching the pattern Q\w{4}E\[0-9]+ was not found in the fileName "+name
 
-        ss = transaction.getSearchService()
-
-        sc = SearchCriteria()
-        sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sampleCode))
-        foundSamples = ss.searchForSamples(sc)
-        samplehit = foundSamples[0]
-        sample = transaction.getSampleForUpdate(samplehit.getSampleIdentifier())
-
-        parents = samplehit.getParentSampleIdentifiers()
+        sample = transaction.getSampleForUpdate(sample_id)
+        parents = sample.getParentSampleIdentifiers()
         parentcodes = []
         for parent in parents:
                 parentcodes.append(parent.split("/")[-1])
diff --git a/drop-boxes/register-wf-ligandomicsid/register-ligandomicsid-dropbox.py b/drop-boxes/register-wf-ligandomicsid/register-ligandomicsid-dropbox.py
@@ -41,19 +41,12 @@ def process(transaction):
         space = nameSplit[0]
         project = pPattern.findall(nameSplit[1])[0]
         experiment_id = ePattern.findall(nameSplit[2])[0]
-        #sample_id = experiment_id+'.'
         sampleCode = nameSplit[-1]
+        sample_id = "/" + space + "/" + sampleCode
         if not experiment_id:
                 print "The identifier matching the pattern Q\w{4}E\[0-9]+ was not found in the fileName "+name
 
-        ss = transaction.getSearchService()
-
-        sc = SearchCriteria()
-        sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sampleCode))
-        foundSamples = ss.searchForSamples(sc)
-        samplehit = foundSamples[0]
-        sample = transaction.getSampleForUpdate(samplehit.getSampleIdentifier())
-
+        sample = transaction.getSampleForUpdate(sample_id)
         experiment = transaction.getExperimentForUpdate("/"+space+"/"+project+"/"+experiment_id)
         experiment.setPropertyValue("Q_WF_STATUS", "FINISHED")
 
diff --git a/drop-boxes/register-wf-ligandomicsqc/register-ligandomicsqc-dropbox.py b/drop-boxes/register-wf-ligandomicsqc/register-ligandomicsqc-dropbox.py
@@ -41,18 +41,12 @@ def process(transaction):
         space = nameSplit[0]
         project = pPattern.findall(nameSplit[1])[0]
         experiment_id = ePattern.findall(nameSplit[2])[0]
-        #sample_id = experiment_id+'.'
         sampleCode = nameSplit[-1]
+        sample_id = "/"+space+"/"+sampleCode
         if not experiment_id:
                 print "The identifier matching the pattern Q\w{4}E\[0-9]+ was not found in the fileName "+name
 
-        ss = transaction.getSearchService()
-
-        sc = SearchCriteria()
-        sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sampleCode))
-        foundSamples = ss.searchForSamples(sc)
-        samplehit = foundSamples[0]
-        sample = transaction.getSampleForUpdate(samplehit.getSampleIdentifier())
+        sample = transaction.getSampleForUpdate(sample_id)
 
         experiment = transaction.getExperimentForUpdate("/"+space+"/"+project+"/"+experiment_id)
         experiment.setPropertyValue("Q_WF_STATUS", "FINISHED")
diff --git a/drop-boxes/register-wf-mapping/register-mapping-dropbox.py b/drop-boxes/register-wf-mapping/register-mapping-dropbox.py
@@ -41,22 +41,16 @@ def process(transaction):
         space = nameSplit[0]
         project = pPattern.findall(nameSplit[1])[0]
         experiment_id = ePattern.findall(nameSplit[2])[0]
-        #sample_id = experiment_id+'.'
         sampleCode = nameSplit[-1]
+        sample_id = "/"+space+"/"+sampleCode
         if not experiment_id:
                 print "The identifier matching the pattern Q\w{4}E\[0-9]+ was not found in the fileName "+name
 
-        ss = transaction.getSearchService()
-
-        sc = SearchCriteria()
-        sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sampleCode))
-        foundSamples = ss.searchForSamples(sc)
-        samplehit = foundSamples[0]
-        sample = transaction.getSampleForUpdate(samplehit.getSampleIdentifier())
+        sample = transaction.getSampleForUpdate(sample_id)
 
         additionalInfo = sample.getPropertyValue("Q_ADDITIONAL_INFO")
 
-        parents = samplehit.getParentSampleIdentifiers()
+        parents = sample.getParentSampleIdentifiers()
         parentcodes = []
         for parent in parents:
                 parentcodes.append(parent.split("/")[-1])
diff --git a/drop-boxes/register-wf-maqc/register-wf-maqc.py b/drop-boxes/register-wf-maqc/register-wf-maqc.py
@@ -41,20 +41,14 @@ def process(transaction):
 	space = nameSplit[0]
 	project = pPattern.findall(nameSplit[1])[0]
 	experiment_id = ePattern.findall(nameSplit[2])[0]
-	#sample_id = experiment_id+'.'
 	sampleCode = nameSplit[-1]
+        sample_id = "/"+space+"/"+sampleCode
 	if not experiment_id:
 		print "The identifier matching the pattern Q\w{4}E\[0-9]+ was not found in the fileName "+name
 
-	ss = transaction.getSearchService()
+        sample = transaction.getSampleForUpdate(sample_id)
 
-	sc = SearchCriteria()
-	sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sampleCode))
-	foundSamples = ss.searchForSamples(sc)
-	samplehit = foundSamples[0]
-	sample = transaction.getSampleForUpdate(samplehit.getSampleIdentifier())
-
-	parents = samplehit.getParentSampleIdentifiers()
+	parents = sample.getParentSampleIdentifiers()
 	if len(parents) > 6:
 		first = parents[0].split("/")[-1]
 		parentInfos = first+"_and_"+str(len(parents)-1)+"others"
diff --git a/drop-boxes/register-wf-maxquant/register-maxquant-dropbox.py b/drop-boxes/register-wf-maxquant/register-maxquant-dropbox.py
@@ -41,20 +41,14 @@ def process(transaction):
         space = nameSplit[0]
         project = pPattern.findall(nameSplit[1])[0]
         experiment_id = ePattern.findall(nameSplit[2])[0]
-        #sample_id = experiment_id+'.'
         sampleCode = nameSplit[-1]
+        sample_id = "/"+space+"/"+sampleCode
         if not experiment_id:
                 print "The identifier matching the pattern Q\w{4}E\[0-9]+ was not found in the fileName "+name
 
-        ss = transaction.getSearchService()
+        sample = transaction.getSampleForUpdate(sample_id)
 
-        sc = SearchCriteria()
-        sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sampleCode))
-        foundSamples = ss.searchForSamples(sc)
-        samplehit = foundSamples[0]
-        sample = transaction.getSampleForUpdate(samplehit.getSampleIdentifier())
-
-        parents = samplehit.getParentSampleIdentifiers()
+        parents = sample.getParentSampleIdentifiers()
         parentcodes = []
         for parent in parents:
                 parentcodes.append(parent.split("/")[-1])
diff --git a/drop-boxes/register-wf-mergenngsdata/register-mergengsdata.py b/drop-boxes/register-wf-mergenngsdata/register-mergengsdata.py
@@ -34,18 +34,13 @@ def process(transaction):
     project = pPattern.findall(nameSplit[1])[0]
     experiment_id = ePattern.findall(nameSplit[2])[0]
     sampleCode = nameSplit[-1]
+    sample_id = "/"+space+"/"+sampleCode
     if not experiment_id:
             print "The identifier matching the pattern Q\w{4}E\[0-9]+ was not found in the fileName "+name
 
-    ss = transaction.getSearchService()
+    sample = transaction.getSampleForUpdate(sample_id)
 
-    sc = SearchCriteria()
-    sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sampleCode))
-    foundSamples = ss.searchForSamples(sc)
-    samplehit = foundSamples[0]
-    sample = transaction.getSampleForUpdate(samplehit.getSampleIdentifier())
-
-    parents = samplehit.getParentSampleIdentifiers()
+    parents = sample.getParentSampleIdentifiers()
     parentcodes = []
     for parent in parents:
         parentcodes.append(parent.split("/")[-1])
diff --git a/drop-boxes/register-wf-msqc/register-wf-msqc.py b/drop-boxes/register-wf-msqc/register-wf-msqc.py
@@ -41,20 +41,14 @@ def process(transaction):
 	space = nameSplit[0]
 	project = pPattern.findall(nameSplit[1])[0]
 	experiment_id = ePattern.findall(nameSplit[2])[0]
-	#sample_id = experiment_id+'.'
 	sampleCode = nameSplit[-1]
+        sample_id = "/"+space+"/"+sampleCode
 	if not experiment_id:
 		print "The identifier matching the pattern Q\w{4}E\[0-9]+ was not found in the fileName "+name
 
-	ss = transaction.getSearchService()
+	sample = transaction.getSampleForUpdate(sample_id)
 
-	sc = SearchCriteria()
-	sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sampleCode))
-	foundSamples = ss.searchForSamples(sc)
-	samplehit = foundSamples[0]
-	sample = transaction.getSampleForUpdate(samplehit.getSampleIdentifier())
-
-	parents = samplehit.getParentSampleIdentifiers()
+	parents = sample.getParentSampleIdentifiers()
 	parentcodes = []
 	for parent in parents:
 		parentcodes.append(parent.split("/")[-1])
diff --git a/drop-boxes/register-wf-ngsqc/register-wf-ngsqc.py b/drop-boxes/register-wf-ngsqc/register-wf-ngsqc.py
@@ -41,18 +41,12 @@ def process(transaction):
 	space = nameSplit[0]
 	project = pPattern.findall(nameSplit[1])[0]
 	experiment_id = ePattern.findall(nameSplit[2])[0]
-	#sample_id = experiment_id+'.'
 	sampleCode = nameSplit[-1]
+        sample_id = "/"+space+"/"+sampleCode
 	if not experiment_id:
 		print "The identifier matching the pattern Q\w{4}E\[0-9]+ was not found in the fileName "+name
 
-	ss = transaction.getSearchService()
-
-	sc = SearchCriteria()
-	sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sampleCode))
-	foundSamples = ss.searchForSamples(sc)
-	samplehit = foundSamples[0]
-	sample = transaction.getSampleForUpdate(samplehit.getSampleIdentifier())
+	sample = transaction.getSampleForUpdate(sample_id)
 
 	experiment = transaction.getExperimentForUpdate("/"+space+"/"+project+"/"+experiment_id)
 
diff --git a/drop-boxes/register-wf-peakpicking/script.py b/drop-boxes/register-wf-peakpicking/script.py
@@ -54,16 +54,12 @@ def process(transaction):
 
         #Register logs
         wfSampleCode = nameSplit[-1]
+
+	sample_id = "/"+space+"/"+wfSampleCode
         if not experiment_id:
                 print "The identifier matching the pattern Q\w{4}E\[0-9]+ was not found in the fileName "+name
 
-        ss = transaction.getSearchService()
-
-        sc = SearchCriteria()
-        sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, wfSampleCode))
-        foundSamples = ss.searchForSamples(sc)
-        samplehit = foundSamples[0]
-        wfSample = transaction.getSampleForUpdate(samplehit.getSampleIdentifier())
+        wfSample = transaction.getSampleForUpdate(sample_id)
         
         experiment = transaction.getExperimentForUpdate("/"+space+"/"+project+"/"+experiment_id)
 
@@ -95,4 +91,4 @@ def process(transaction):
                 sa = transaction.getSampleForUpdate(sampleID)
                 dataSetRes = transaction.createNewDataSet('Q_MS_MZML_DATA')
                 dataSetRes.setSample(sa)
-                transaction.moveFile(mzmlPath, dataSetRes)
+                transaction.moveFile(mzmlPath, dataSetRes)
diff --git a/drop-boxes/register-wf-peptideid/register-wf-peptideid.py b/drop-boxes/register-wf-peptideid/register-wf-peptideid.py
@@ -41,22 +41,14 @@ def process(transaction):
 	space = nameSplit[0]
 	project = pPattern.findall(nameSplit[1])[0]
 	experiment_id = ePattern.findall(nameSplit[2])[0]
-	#sample_id = experiment_id+'.'
 	sampleCode = nameSplit[-1]
+        sample_id = "/"+space+"/"+sampleCode
 	if not experiment_id:
 		print "The identifier matching the pattern Q\w{4}E\[0-9]+ was not found in the fileName "+name
 
-	ss = transaction.getSearchService()
+        sample = transaction.getSampleForUpdate(sample_id)
 
-	sc = SearchCriteria()
-	#sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.TYPE, "Q_WF_MS_PEPTIDEID_RUN"))
-	sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sampleCode))
-	foundSamples = ss.searchForSamples(sc)
-	#sample = transaction.createNewSample("/"+space+"/"+sample_id + str(len(foundSamples)+1), "Q_WF_MS_PEPTIDEID_RUN")
-	samplehit = foundSamples[0]
-	sample = transaction.getSampleForUpdate(samplehit.getSampleIdentifier())
-
-	parents = samplehit.getParentSampleIdentifiers()
+	parents = sample.getParentSampleIdentifiers()
 	parentcodes = []
 	for parent in parents:
 		parentcodes.append(parent.split("/")[-1])
diff --git a/drop-boxes/register-wf-qedda/register-qedda.py b/drop-boxes/register-wf-qedda/register-qedda.py
@@ -34,16 +34,11 @@ def process(transaction):
     project = pPattern.findall(nameSplit[1])[0]
     experiment_id = ePattern.findall(nameSplit[2])[0]
     sampleCode = nameSplit[-1]
+    sample_id = "/"+space+"/"+sampleCode
     if not experiment_id:
             print "The identifier matching the pattern Q\w{4}E\[0-9]+ was not found in the fileName "+name
 
-    ss = transaction.getSearchService()
-
-    sc = SearchCriteria()
-    sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sampleCode))
-    foundSamples = ss.searchForSamples(sc)
-    sample = foundSamples[0]
-    sample = transaction.getSampleForUpdate(sample.getSampleIdentifier())
+    sample = transaction.getSampleForUpdate(sample_id)
  
     experiment = transaction.getExperimentForUpdate("/"+space+"/"+project+"/"+experiment_id)
 
diff --git a/drop-boxes/register-wf-rnaexpressionanalysis/register-wf-rnaexpranalysis.py b/drop-boxes/register-wf-rnaexpressionanalysis/register-wf-rnaexpranalysis.py
@@ -42,18 +42,13 @@ def process(transaction):
 	project = pPattern.findall(nameSplit[1])[0]
 	experiment_id = ePattern.findall(nameSplit[2])[0]
 	sampleCode = nameSplit[-1]
+        sample_id = "/"+space+"/"+sampleCode
 	if not experiment_id:
 		print "The identifier matching the pattern Q\w{4}E\[0-9]+ was not found in the fileName "+name
 
-	ss = transaction.getSearchService()
+	sample = transaction.getSampleForUpdate(sample_id)
 
-	sc = SearchCriteria()
-	sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sampleCode))
-	foundSamples = ss.searchForSamples(sc)
-	samplehit = foundSamples[0]
-	sample = transaction.getSampleForUpdate(samplehit.getSampleIdentifier())
-
-	parents = samplehit.getParentSampleIdentifiers()
+	parents = sample.getParentSampleIdentifiers()
 	parentcodes = []
 	for parent in parents:
 		parentcodes.append(parent.split("/")[-1])
diff --git a/drop-boxes/register-wf-shrna/register-shrna-dropbox.py b/drop-boxes/register-wf-shrna/register-shrna-dropbox.py
@@ -41,20 +41,14 @@ def process(transaction):
         space = nameSplit[0]
         project = pPattern.findall(nameSplit[1])[0]
         experiment_id = ePattern.findall(nameSplit[2])[0]
-        #sample_id = experiment_id+'.'
         sampleCode = nameSplit[-1]
+        sample_id = "/"+space+"/"+sampleCode
         if not experiment_id:
                 print "The identifier matching the pattern Q\w{4}E\[0-9]+ was not found in the fileName "+name
 
-        ss = transaction.getSearchService()
+        sample = transaction.getSampleForUpdate(sample_id)
 
-        sc = SearchCriteria()
-        sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sampleCode))
-        foundSamples = ss.searchForSamples(sc)
-        samplehit = foundSamples[0]
-        sample = transaction.getSampleForUpdate(samplehit.getSampleIdentifier())
-
-        parents = samplehit.getParentSampleIdentifiers()
+        parents = sample.getParentSampleIdentifiers()
         parentcodes = []
         for parent in parents:
                 parentcodes.append(parent.split("/")[-1])
diff --git a/drop-boxes/register-wf-variantannotation/register-variantannotation.py b/drop-boxes/register-wf-variantannotation/register-variantannotation.py
diff --git a/drop-boxes/register-wf-variantcalling/register-wf-variantcalling.py b/drop-boxes/register-wf-variantcalling/register-wf-variantcalling.py
