From fa025f686a042bd5ea8eae698bdc84ec655a037a Mon Sep 17 00:00:00 2001
From: juanf <juanf>
Date: Tue, 14 Apr 2015 12:30:14 +0000
Subject: [PATCH] SSDM-1728: YeastLab Data Curation - Report
SVN: 33821
---
.../stellingconsistency/consistency.py | 43 ++++++++++++-------
1 file changed, 28 insertions(+), 15 deletions(-)
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 71f36a5165e..5f9a373566a 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
@@ -8,11 +8,7 @@ import xml.etree.ElementTree as ET
## Definitions
##
-definitions = {
- "YEAST" : {},
- "POMBE" : {}
-};
-
+sampleTypesToVerify = ["YEAST","POMBE"];
logLevelsToPrint = ["ERROR", "REPORT", "MANUAL-FIX"];
##
@@ -20,10 +16,14 @@ logLevelsToPrint = ["ERROR", "REPORT", "MANUAL-FIX"];
##
numberOfManualFixes = 0;
+numberOfAutoFixes = 0;
def log(level, message):
if level == "MANUAL-FIX":
global numberOfManualFixes
numberOfManualFixes = numberOfManualFixes + 1
+ if level == "AUTO-FIX":
+ global numberOfAutoFixes
+ numberOfAutoFixes = numberOfAutoFixes + 1
if any(level in s for s in logLevelsToPrint):
print "[" + level + "] " + message;
@@ -66,24 +66,28 @@ def getSampleByPermId(tr, permId):
def process(tr):
log("REPORT", "START VERIFICATION REPORT!");
- for sampleType in definitions:
- properties = definitions[sampleType]
+ for sampleType in sampleTypesToVerify:
samples = getSamplesByType(tr, sampleType)
global currentCache
currentCache = samples
print sampleType + ": "+ str(len(samples))
for sample in samples:
- verify(tr, sample, properties)
+ verify(tr, sample)
global numberOfManualFixes
+ global numberOfAutoFixes
+ log("REPORT", "FOUND " + str(numberOfAutoFixes) + " AUTOMATIC FIXES!");
log("REPORT", "REQUIRED " + str(numberOfManualFixes) + " MANUAL FIXES!");
log("REPORT", "FINISH VERIFICATION REPORT!");
-def verify(tr, sample, properties):
+def verify(tr, sample):
annotationsRoot = getAnnotationsRootNodeFromSample(sample)
+ requiredAnnotationsFound = getRequiredAnnotations(sample)
+ #1.Annotations hierarchy
if annotationsRoot is not None:
for annotation in annotationsRoot:
annotatedSampleIdentifier = annotation.attrib["identifier"] #Identifier from annotated sample
+ requiredAnnotationsFound[annotatedSampleIdentifier] = True
try:
if isChild(sample, annotatedSampleIdentifier):
#This is an annotation from a parent, this is by default correct and don't needs further inspection.
@@ -95,17 +99,26 @@ def verify(tr, sample, properties):
if foundAnnotation is not None and foundAncestor is not None:
log("INFO", "BAD CHILD FOUND - " + sample.getSampleIdentifier() + " " + annotatedSampleIdentifier);
if areAnnotationsEqual(annotation, foundAnnotation):
- log("INFO", "GOOD REPEATED ANNOTATION THAT CAN BE DELETED - " + sample.getSampleIdentifier() + " " + annotatedSampleIdentifier);
+ log("AUTO-FIX", "CASE 1 - GOOD REPEATED ANNOTATION THAT CAN BE DELETED - " + sample.getSampleIdentifier() + " " + annotatedSampleIdentifier);
else:
- log("MANUAL-FIX", "THE ANNOTATION: " + annotatedSampleIdentifier + " IS DIFFERENT AT SAMPLE: " + sample.getSampleIdentifier() + " AND ORIGINAL ANCESTOR:" + foundAncestor.getSampleIdentifier());
+ log("MANUAL-FIX", "CASE 3 - THE ANNOTATION: " + annotatedSampleIdentifier + " IS DIFFERENT AT SAMPLE: " + sample.getSampleIdentifier() + " AND ORIGINAL ANCESTOR:" + foundAncestor.getSampleIdentifier());
elif foundAncestor is None:
- log("MANUAL-FIX", "THE ANNOTATED SAMPLE IS NOT AN ANCESTOR - FOR SAMPLE: " + sample.getSampleIdentifier() + " ANNOTATION WITH MISSING ANCESTOR:" + annotatedSampleIdentifier);
+ log("MANUAL-FIX", "CASE 1 - THE ANNOTATED SAMPLE IS NOT AN ANCESTOR - FOR SAMPLE: " + sample.getSampleIdentifier() + " ANNOTATION WITH MISSING ANCESTOR:" + annotatedSampleIdentifier);
elif foundAnnotation is None:
- log("MANUAL-FIX", "THE ANNOTATED SAMPLE IS NOT ANNOTATED WHERE IT SHOULD - FOR SAMPLE: " + sample.getSampleIdentifier() + " ANNOTATION: " + annotatedSampleIdentifier +" NOT AT " + 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());
except Exception:
log("ERROR", "PROCESSING ANNOTATIONS XML CHILD " + sample.getSampleIdentifier());
- else:
- pass #No valid annotations found
+ #2.Missing Annotations
+ for parentIdentifier in requiredAnnotationsFound:
+ if not requiredAnnotationsFound[parentIdentifier]:
+ log("MANUAL-FIX", "CASE 4 - MISSING ANNOTATIONS ON SAMPLE: " + sample.getSampleIdentifier() + " FOR PARENT:" + parentIdentifier);
+
+def getRequiredAnnotations(sample):
+ requiredAnnotationsFound = {}
+ for parentIdentifier in sample.getParentSampleIdentifiers():
+ if "/FRP" in parentIdentifier: #Only require Plasmids
+ requiredAnnotationsFound[parentIdentifier] = False;
+ return requiredAnnotationsFound;
def areAnnotationsEqual(annotationA, annotationB):
for key in annotationA.attrib:
--
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