From f20cd35d924c20ca238fee95b8c477869ff44591 Mon Sep 17 00:00:00 2001
From: juanf <juanf>
Date: Thu, 2 Apr 2015 12:21:50 +0000
Subject: [PATCH] Fixing Non Parents found using the default transaction API
SVN: 33782
---
.../reporting-plugins/newbrowserapi/script.py | 30 +++++++++++++++----
1 file changed, 25 insertions(+), 5 deletions(-)
diff --git a/plasmid/source/core-plugins/newbrowser/1/dss/reporting-plugins/newbrowserapi/script.py b/plasmid/source/core-plugins/newbrowser/1/dss/reporting-plugins/newbrowserapi/script.py
index 720e0004284..4659107eed0 100644
--- a/plasmid/source/core-plugins/newbrowser/1/dss/reporting-plugins/newbrowserapi/script.py
+++ b/plasmid/source/core-plugins/newbrowser/1/dss/reporting-plugins/newbrowserapi/script.py
@@ -21,10 +21,30 @@ from java.io import File
from java.io import FileOutputStream
from java.lang import System
from net.lingala.zip4j.core import ZipFile
+from ch.systemsx.cisd.common.exceptions import UserFailureException
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria import MatchClause, SearchOperator, MatchClauseAttribute
+
import time
import subprocess
import os.path
+def getSampleByIdentifierForUpdate(tr, identifier):
+ space = identifier.split("/")[1];
+ code = identifier.split("/")[2];
+
+ criteria = SearchCriteria();
+ criteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.SPACE, space));
+ criteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, code));
+ criteria.setOperator(SearchOperator.MATCH_ALL_CLAUSES);
+
+ searchService = tr.getSearchService();
+ found = list(searchService.searchForSamples(criteria));
+ if len(found) == 1:
+ return tr.makeSampleMutable(found[0]);
+ else:
+ raise UserFailureException(identifier + " Not found by search service.");
+
def process(tr, parameters, tableBuilder):
method = parameters.get("method");
@@ -178,7 +198,7 @@ def insertDataSet(tr, parameters, tableBuilder):
metadata = parameters.get("metadata"); #java.util.LinkedHashMap<String, String> where the key is the name
#Create Dataset
- dataSetSample = tr.getSample(sampleIdentifier);
+ dataSetSample = getSampleByIdentifierForUpdate(tr, sampleIdentifier);
dataSet = tr.createNewDataSet(dataSetType);
dataSet.setSample(dataSetSample);
@@ -248,7 +268,7 @@ def copySample(tr, parameters, tableBuilder):
#Copy children and attach to Sample
if sampleChildren != None:
for sampleChildIdentifier in sampleChildren:
- child = tr.getSample(sampleChildIdentifier); #Retrieve Sample child to copy
+ child = getSampleByIdentifierForUpdate(tr, sampleChildIdentifier); #Retrieve Sample child to copy
copyChildCode = None
try: #For autogenerated children that have the code as sufix
@@ -316,7 +336,7 @@ def insertUpdateSample(tr, parameters, tableBuilder):
sample = tr.createNewSample(sampleIdentifier, sampleType); #Create Sample given his id
if method == "updateSample":
- sample = tr.getSampleForUpdate(sampleIdentifier); #Retrieve Sample
+ sample = getSampleByIdentifierForUpdate(tr, sampleIdentifier); #Retrieve Sample
#Obtain space
space = None;
@@ -362,7 +382,7 @@ def insertUpdateSample(tr, parameters, tableBuilder):
#Add sample children
if sampleChildren != None:
for sampleChildIdentifier in sampleChildren:
- child = tr.getSampleForUpdate(sampleChildIdentifier); #Retrieve Sample
+ child = getSampleByIdentifierForUpdate(tr, sampleChildIdentifier); #Retrieve Sample
if child != None: #The new created ones will not be found
childParents = child.getParentSampleIdentifiers();
childParents.add(sampleIdentifier);
@@ -371,7 +391,7 @@ def insertUpdateSample(tr, parameters, tableBuilder):
#Remove sample children
if sampleChildrenRemoved != None:
for sampleChildIdentifier in sampleChildrenRemoved:
- child = tr.getSampleForUpdate(sampleChildIdentifier); #Retrieve Sample
+ child = getSampleByIdentifierForUpdate(tr, sampleChildIdentifier); #Retrieve Sample
if child != None: #The new created ones will not be found
childParents = child.getParentSampleIdentifiers();
childParents.remove(sampleIdentifier);
--
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