diff --git a/plasmid/source/core-plugins/stellingmigration/1/dss/drop-boxes/stellingconsistency/consistency.py b/plasmid/source/core-plugins/stellingmigration/1/dss/drop-boxes/stellingconsistency/consistency.py
index 3d41b2b739cf9c449c34606d864070a14172ca35..35ead1ad3f2be7254b5f48f1f18aa2d3e85f849d 100644
--- a/plasmid/source/core-plugins/stellingmigration/1/dss/drop-boxes/stellingconsistency/consistency.py
+++ b/plasmid/source/core-plugins/stellingmigration/1/dss/drop-boxes/stellingconsistency/consistency.py
@@ -18,6 +18,7 @@ logLevelsToPrint = ["ERROR", "REPORT", "MANUAL-FIX"] #INFO not included, use it
numberOfManualFixes = 0
numberOfAutoFixesDeletes = 0
numberOfAutoFixesLost = 0
+numberOfCanBeUpdated = 0
def logManualFix(message, creator, sampleIdentifier, affectedSampleToBeAnnotated, creatorOfAncestor, ancestor):
log("MANUAL-FIX", message + "\t" + creator + "\t" + sampleIdentifier + "\t" + affectedSampleToBeAnnotated + "\t" + creatorOfAncestor + "\t" + ancestor)
@@ -85,12 +86,16 @@ def process(tr):
global numberOfManualFixes
global numberOfAutoFixesDeletes
global numberOfAutoFixesLost
+ global numberOfCanBeUpdated
log("REPORT", "FOUND " + str(numberOfAutoFixesDeletes) + " AUTOMATIC DELETE FIXES!")
log("REPORT", "FOUND " + str(numberOfAutoFixesLost) + " AUTOMATIC LOST FIXES!")
+ log("REPORT", "UPDATABLE " + str(numberOfCanBeUpdated) + " SAMPLES!")
log("REPORT", "REQUIRED " + str(numberOfManualFixes-1) + " MANUAL FIXES!") #-1 For the Header
log("REPORT", "FINISH VERIFICATION REPORT!")
def verify(tr, sample):
+ newAnnotations = [];
+ newAnnotationsReady = True;
annotationsRoot = getAnnotationsRootNodeFromSample(sample)
#1.Annotations hierarchy
requiredAnnotationsFound = getRequiredAnnotations(sample) #To detect case 4
@@ -103,6 +108,7 @@ def verify(tr, sample):
try:
if isChild(sample, annotatedSampleIdentifier):
#This is an annotation from a parent, this is by default correct and don't needs further inspection.
+ newAnnotations.append(getAnnotationMap(annotation));
log("INFO", "GOOT ANNOTATION AT SAMPLE: " + sample.getSampleIdentifier() + " ANNOTATION: " + annotatedSampleIdentifier)
else:
foundAnnotationAndAncestor = getAnnotationAndAncestor(annotatedSampleIdentifier, sample.getParentSampleIdentifiers())
@@ -113,31 +119,58 @@ def verify(tr, sample):
if areAnnotationsEqual(annotation, foundAnnotation) and areAnnotationsEqual(foundAnnotation, annotation):
log("AUTO-FIX", "CASE 1 - GOOD REPEATED ANNOTATION THAT CAN BE DELETED - AT SAMPLE: " + sample.getSampleIdentifier() + " FOR ANNOTATION: " + annotatedSampleIdentifier + " FOUND ORIGINAL AT: " + foundAncestor.getSampleIdentifier())
else:
- #log("MANUAL-FIX", "CASE 3 - THE ANNOTATION: " + annotatedSampleIdentifier + " IS DIFFERENT AT SAMPLE: " + sample.getSampleIdentifier() + " AND ORIGINAL ANCESTOR:" + foundAncestor.getSampleIdentifier())
logManualFix("Case 3 - The annotation is different on the sample and his ancestor.", sample.getSample().getRegistrator().getUserId(), sample.getSampleIdentifier(), annotatedSampleIdentifier, foundAncestor.getSample().getRegistrator().getUserId(), foundAncestor.getSampleIdentifier())
+ newAnnotationsReady = False
elif foundAncestor is None:
logManualFix("Case 1 - The annotated sample is not an ancestor, is missing on the hierarchy for some reason.", sample.getSample().getRegistrator().getUserId(), sample.getSampleIdentifier(), annotatedSampleIdentifier, "?", "?")
- #log("MANUAL-FIX", "CASE 1 - THE ANNOTATED SAMPLE IS NOT AN ANCESTOR - FOR SAMPLE: " + sample.getSampleIdentifier() + " ANNOTATION WITH MISSING ANCESTOR:" + annotatedSampleIdentifier)
+ newAnnotationsReady = False
elif foundAnnotation is None:
logManualFix("Case 2 - The annotated sample is not annotated on the appropriate ancestor.", sample.getSample().getRegistrator().getUserId(), sample.getSampleIdentifier(), annotatedSampleIdentifier, foundAncestor.getSample().getRegistrator().getUserId(), foundAncestor.getSampleIdentifier())
- #log("MANUAL-FIX", "CASE 2 - THE ANNOTATED SAMPLE IS NOT ANNOTATED WHERE IT SHOULD - FOR SAMPLE: " + sample.getSampleIdentifier() + " ANNOTATION: " + annotatedSampleIdentifier +" NOT AT " + foundAncestor.getSampleIdentifier())
+ newAnnotationsReady = False
except Exception, err:
log("ERROR", "PROCESSING ANNOTATIONS XML CHILD " + sample.getSampleIdentifier() + " ERR: " + str(err))
#2.Missing Parents Annotations
for parentIdentifier in requiredAnnotationsFound:
if not requiredAnnotationsFound[parentIdentifier]:
- #log("MANUAL-FIX", "CASE 4 - MISSING ANNOTATIONS ON SAMPLE: " + sample.getSampleIdentifier() + " FOR PARENT:" + parentIdentifier)
logManualFix("Case 4 - Missing annotation on sample for parent.", sample.getSample().getRegistrator().getUserId(), sample.getSampleIdentifier(), parentIdentifier, "-", "-")
+ newAnnotationsReady = False
#3.Missing Annotations LOST
for parentAnnotationIdentifier in requiredAnnotationsFromParents:
if not requiredAnnotationsFromParents[parentAnnotationIdentifier]:
+ lostPermId = getRequiredAnnotationsFromParentsPermId(sample, parentAnnotationIdentifier)
+ if lostPermId is None:
+ raise Exception("Lost PermId Not Found");
+ newAnnotations.append({ "permId" : lostPermId, "identifier" : parentAnnotationIdentifier, "PLASMID_RELATIONSHIP" : "LOT" });
log("AUTO-FIX-2", "CASE 2 - MISSING LOST ANNOTATIONS ON SAMPLE: " + sample.getSampleIdentifier() + " FOR LOST ANNOTATION: " + parentAnnotationIdentifier + " PRESENT INTO ONE OF THE PARENTS")
#4 Check parents from contained
expectedParents = getContainedFromAnnotations(sample)
lostParents = areParentsPresent(sample, expectedParents)
if len(lostParents) > 0:
logManualFix("Case 5 - Missing Parents present in Contained: ", sample.getSample().getRegistrator().getUserId(), sample.getSampleIdentifier(), str(lostParents), "?", "?")
-
+ newAnnotationsReady = False
+ #5 Check repeated parents in annotations
+ if areAnnotationDuplicated(sample):
+ logManualFix("Case 6 - Same annotation coming from different parents: ", sample.getSample().getRegistrator().getUserId(), sample.getSampleIdentifier(), "?", "?", "?")
+ newAnnotationsReady = False
+ if newAnnotationsReady:
+ global numberOfCanBeUpdated;
+ numberOfCanBeUpdated = numberOfCanBeUpdated + 1;
+ #1. Create new annotations XML
+
+ #2. Add LOST parents
+
+def areAnnotationDuplicated(sample):
+ annotated = {}; #They should be parents of the sample and not been missing
+ annotationsRoot = getAnnotationsRootNodeFromSample(sample);
+ if annotationsRoot is not None:
+ for annotation in annotationsRoot:
+ permId = getValueOrNull(annotation.attrib, "permId");
+ if permId in annotated:
+ return True
+ else:
+ annotated[permId] = True
+ return False
+
def getContainedFromAnnotations(sample):
contained = []; #They should be parents of the sample and not been missing
annotationsRoot = getAnnotationsRootNodeFromSample(sample);
@@ -156,6 +189,19 @@ def areParentsPresent(sample, parents):
notPresent.append(parent);
return notPresent
+def getRequiredAnnotationsFromParentsPermId(sample, identifier):
+ for parentIdentifier in sample.getParentSampleIdentifiers():
+ if ("/FRY" in parentIdentifier) or ("/FRS" in parentIdentifier): #Only check Yeast and Pombe Parents
+ parent = getSampleFromCache(parentIdentifier)
+ parentAnnotationsRoot = getAnnotationsRootNodeFromSample(parent)
+ if parentAnnotationsRoot is not None:
+ for parentAnnotation in parentAnnotationsRoot:
+ parentAnnotationIdentifier = parentAnnotation.attrib["identifier"]
+ if "/FRP" in parentAnnotationIdentifier: #Only require Plasmids
+ if identifier == parentAnnotationIdentifier:
+ return parentAnnotation.attrib["permId"]
+ return None
+
def getRequiredAnnotationsFromParents(sample):
requiredAnnotationsFromParents = {}
for parentIdentifier in sample.getParentSampleIdentifiers():
@@ -176,6 +222,13 @@ def getRequiredAnnotations(sample):
requiredAnnotationsFound[parentIdentifier] = False
return requiredAnnotationsFound
+def getAnnotationMap(annotation):
+ map = {};
+ for key in annotation.attrib:
+ value = getValueOrNull(annotation.attrib, key)
+ map[key] = value;
+ return map
+
def areAnnotationsEqual(annotationA, annotationB):
for key in annotationA.attrib:
value = getValueOrNull(annotationA.attrib, key)