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Commit b084fc35 authored by barillac's avatar barillac
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small fix 

SVN: 34458
parent 1363ed04
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plasmid/source/core-plugins/weismigration/1/dss/drop-boxes/add_strain_parents/add_strain_parents.py
+ 57
− 30
View file @ b084fc35
......@@ -27,11 +27,12 @@ def update_sample_with_parents(tr, sample_dict):
space_code = "MATERIALS"
project_code = "YEASTS"
# The dictionary keys come from the CSV file
sample_id = sample_dict['identifier']
sample_id = "/MATERIALS/" + sample_dict['Code']
yeast_parent_code = sample_dict['derived from']
yeast_parent_code_split = re.split("and|,|\&|\+|x|/|-|\?|\(|\)", yeast_parent_code)
print sample_id, yeast_parent_code_split
parents_code_list=[]
#e.split("/|-|\?|\(|\)"
# insert=sample_dict['Insert']
# insert_split=re.split("/|-|\?|\(|\|+)", insert)
......@@ -46,35 +47,61 @@ def update_sample_with_parents(tr, sample_dict):
# if
for name in yeast_parent_code_split:
sample = tr.getSample(sample_id)
sample_for_update = tr.makeSampleMutable(sample)
if re.search ("kwy ", name):
yeast_parent_id = "/MATERIALS/"+name.replace("kwy ","KWY").strip()
sample_for_update.setParentSampleIdentifiers([yeast_parent_id])
elif re.search ("pKW", name):
yeast_parent_id = "/MATERIALS/"+name.replace("pKW","PKW").strip()
sample_for_update.setParentSampleIdentifiers([yeast_parent_id])
elif re.search ("PKW", name):
yeast_parent_id = "/MATERIALS/"+name
sample_for_update.setParentSampleIdentifiers([yeast_parent_id])
elif re.search ("kwy", name):
yeast_parent_id = "/MATERIALS/"+name.replace("kwy","KWY").strip()
sample_for_update.setParentSampleIdentifiers([yeast_parent_id])
elif re.search ("KWY ", name):
yeast_parent_id = "/MATERIALS/"+name.replace("KWY ","KWY").strip()
sample_for_update.setParentSampleIdentifiers([yeast_parent_id])
elif re.match ("KW\d+", name):
yeast_parent_id = "/MATERIALS/"+name.replace("KW","KWY").strip()
sample_for_update.setParentSampleIdentifiers([yeast_parent_id])
elif re.search ("k", name):
yeast_parent_id = "/MATERIALS/"+name.replace("k","KWY").strip()
sample_for_update.setParentSampleIdentifiers([yeast_parent_id])
elif re.search ("KWYY", name):
yeast_parent_id = "/MATERIALS/"+name.replace("KWYY","KWY").strip()
sample_for_update.setParentSampleIdentifiers([yeast_parent_id])
elif re.search ("KWy", name):
yeast_parent_id = "/MATERIALS/"+name.replace("KWy","KWY").strip()
sample_for_update.setParentSampleIdentifiers([yeast_parent_id])
if not sample_id=="/MATERIALS/KWY5055" and not sample_id=="/MATERIALS/KWY5542" and not sample_id=="/MATERIALS/KWY4260":
sample = tr.getSample(sample_id)
sample_for_update = tr.makeSampleMutable(sample)
if not re.search("Roy Parker", name) and not re.search("ku",name):
if re.search ("kwy ", name):
yeast_parent_id = "/MATERIALS/"+name.replace("kwy ","KWY").strip()
parents_code_list.append(yeast_parent_id)
print "PARENTS: ", parents_code_list
sample_for_update.setParentSampleIdentifiers(parents_code_list)
elif re.search ("KWY ", name):
yeast_parent_id = "/MATERIALS/"+name.replace("KWY ","KWY").strip()
parents_code_list.append(yeast_parent_id)
print "PARENTS: ", parents_code_list
sample_for_update.setParentSampleIdentifiers(parents_code_list)
elif re.search ("pKW", name):
yeast_parent_id = "/MATERIALS/"+name.replace("pKW","PKW").strip()
parents_code_list.append(yeast_parent_id)
print "PARENTS: ", parents_code_list
sample_for_update.setParentSampleIdentifiers(parents_code_list)
elif re.search ("PKW", name):
yeast_parent_id = "/MATERIALS/"+name
parents_code_list.append(yeast_parent_id)
print "PARENTS: ", parents_code_list
sample_for_update.setParentSampleIdentifiers(parents_code_list)
elif re.search ("kwy", name):
yeast_parent_id = "/MATERIALS/"+name.replace("kwy","KWY").strip()
parents_code_list.append(yeast_parent_id)
print "PARENTS: ", parents_code_list
sample_for_update.setParentSampleIdentifiers(parents_code_list)
elif re.match ("KW\d+", name):
yeast_parent_id = "/MATERIALS/"+name.replace("KW","KWY").strip()
parents_code_list.append(yeast_parent_id)
print "PARENTS: ", parents_code_list
sample_for_update.setParentSampleIdentifiers(parents_code_list)
# elif re.search ("k", name):
# yeast_parent_id = "/MATERIALS/"+name.replace("k","KWY").strip()
# parents_code_list.append(yeast_parent_id)
sample_for_update.setParentSampleIdentifiers(parents_code_list)
elif re.search ("KWYY", name):
yeast_parent_id = "/MATERIALS/"+name.replace("KWYY","KWY").strip()
parents_code_list.append(yeast_parent_id)
print "PARENTS: ", parents_code_list
sample_for_update.setParentSampleIdentifiers(parents_code_list)
elif re.search ("KWy", name):
yeast_parent_id = "/MATERIALS/"+name.replace("KWy","KWY").strip()
parents_code_list.append(yeast_parent_id)
print "PARENTS: ", parents_code_list
sample_for_update.setParentSampleIdentifiers(parents_code_list)
elif re.search ("KWY", name):
yeast_parent_id = "/MATERIALS/"+name.strip()
if not yeast_parent_id =="/MATERIALS/KWY":
parents_code_list.append(yeast_parent_id)
print "PARENTS: ", parents_code_list
sample_for_update.setParentSampleIdentifiers(parents_code_list)
......
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