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Commit 92971d67 authored by barillac's avatar barillac
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small fix 

SVN: 35357
parent ad3c6fd2
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plasmid/source/core-plugins/weismigration/1/dss/drop-boxes/add_plasmid_parents/add_plasmid_parents.py
+ 28
− 65
View file @ 92971d67
......@@ -32,11 +32,9 @@ def update_sample_with_parents(tr, sample_dict):
parents_code_list=re.split(" ", parents_code)
plasmid_list=[]
plasmid_parent_code = sample_dict['Parent plasmid']
plasmid_parent_code_split = re.split("/|\+|-|\?|\(|\)", plasmid_parent_code)
plasmid_parent_code_split = re.split("/|\+|-|\?|\(|\)|\ and |", plasmid_parent_code)
print sample_code, plasmid_parent_code_split
sample_id = "/%(space_code)s/%(sample_code)s" % vars()
......@@ -48,54 +46,45 @@ def update_sample_with_parents(tr, sample_dict):
if not sample_id =="/MATERIALS/PKW581" and not sample_id == "/MATERIALS/PKW3386" and not sample_id == "/MATERIALS/PKW3158":
if re.search ("pKW ", name):
plasmid_parent_id = "/MATERIALS/"+name.replace("pKW ","PKW").strip()
print "P1 : ", plasmid_parent_id
print "PARENT: ", plasmid_parent_id
if not parents_code_list ==['']:
parents_code_list.append(plasmid_parent_id)
print "P1 : ", parents_code_list
sample_for_update.setParentSampleIdentifiers(parents_code_list)
else:
plasmid_list.append(plasmid_parent_id)
print "P1 : ", plasmid_list
sample_for_update.setParentSampleIdentifiers(plasmid_list)
elif re.search ("pKW467 pRS CRM1", name):
plasmid_parent_id = "/MATERIALS/"+name.replace("pKW467 pRS CRM1","PKW467").strip()
print "P2 : ", plasmid_parent_id
print "PARENT: ", plasmid_parent_id
if not parents_code_list ==['']:
parents_code_list.append(plasmid_parent_id)
print "P2 : ", parents_code_list
sample_for_update.setParentSampleIdentifiers(parents_code_list)
else:
plasmid_list.append(plasmid_parent_id)
print "P2 : ", plasmid_list
sample_for_update.setParentSampleIdentifiers(plasmid_list)
elif re.search ("pKW468 pRS CRM1", name):
plasmid_parent_id = "/MATERIALS/"+name.replace("pKW468 pRS CRM1","PKW468").strip()
print "P2 : ", plasmid_parent_id
print "PARENT: ", plasmid_parent_id
if not parents_code_list ==['']:
parents_code_list.append(plasmid_parent_id)
print "P2 : ", parents_code_list
sample_for_update.setParentSampleIdentifiers(parents_code_list)
else:
plasmid_list.append(plasmid_parent_id)
print "P2 : ", plasmid_list
sample_for_update.setParentSampleIdentifiers(plasmid_list)
elif re.search ("HA pKW2682", name):
plasmid_parent_id = "/MATERIALS/"+name.replace("HA pKW2682","PKW2682").strip()
print "P2 : ", plasmid_parent_id
print "PARENT: ", plasmid_parent_id
if not parents_code_list ==['']:
parents_code_list.append(plasmid_parent_id)
print "P2 : ", parents_code_list
sample_for_update.setParentSampleIdentifiers(parents_code_list)
else:
plasmid_list.append(plasmid_parent_id)
print "P2 : ", plasmid_list
sample_for_update.setParentSampleIdentifiers(plasmid_list)
elif re.search ("pKW639 pCFP", name):
plasmid_parent_id = "/MATERIALS/"+name.replace("pKW639 pCFP","PKW639").strip()
print "P2 : ", plasmid_parent_id
print "PARENT: ", plasmid_parent_id
if not parents_code_list ==['']:
parents_code_list.append(plasmid_parent_id)
print "P2 : ", parents_code_list
sample_for_update.setParentSampleIdentifiers(parents_code_list)
else:
plasmid_list.append(plasmid_parent_id)
......@@ -105,79 +94,53 @@ def update_sample_with_parents(tr, sample_dict):
plasmid_parent_id = "/MATERIALS/"+name.replace("pKW001","PKW1").strip()
if not parents_code_list ==['']:
parents_code_list.append(plasmid_parent_id)
print "P3 : ", parents_code_list
sample_for_update.setParentSampleIdentifiers(parents_code_list)
else:
plasmid_list.append(plasmid_parent_id)
sample_for_update.setParentSampleIdentifiers(plasmid_list)
elif re.search ("PKW001", name):
plasmid_parent_id = "/MATERIALS/"+name.replace("PKW001","PKW1").strip()
print "P3 : ", plasmid_parent_id
print "PARENT: ", plasmid_parent_id
if not parents_code_list ==['']:
parents_code_list.append(plasmid_parent_id)
print "P3 : ", parents_code_list
sample_for_update.setParentSampleIdentifiers(parents_code_list)
else:
plasmid_list.append(plasmid_parent_id)
print "P3 : ", plasmid_list
sample_for_update.setParentSampleIdentifiers(plasmid_list)
elif re.search ("pkw", name):
plasmid_parent_id = "/MATERIALS/"+name.replace("pkw","PKW").strip()
print "PARENT: ", plasmid_parent_id
if not parents_code_list ==['']:
parents_code_list.append(plasmid_parent_id)
sample_for_update.setParentSampleIdentifiers(parents_code_list)
else:
plasmid_list.append(plasmid_parent_id)
sample_for_update.setParentSampleIdentifiers(plasmid_list)
elif re.search ("pKW", name):
plasmid_parent_id = "/MATERIALS/"+name.replace("pKW","PKW").strip()
print "P2 : ", plasmid_parent_id
print "PARENT: ", plasmid_parent_id
if not parents_code_list ==['']:
parents_code_list.append(plasmid_parent_id)
print "P2 : ", parents_code_list
sample_for_update.setParentSampleIdentifiers(parents_code_list)
else:
plasmid_list.append(plasmid_parent_id)
print "P2 : ", plasmid_list
sample_for_update.setParentSampleIdentifiers(plasmid_list)
elif re.search ("pkw", name):
plasmid_parent_id = "/MATERIALS/"+name.replace("pkw","PKW").strip()
print "P2 : ", plasmid_parent_id
sample_for_update.setParentSampleIdentifiers(plasmid_list)
elif re.search ("pKw", name):
plasmid_parent_id = "/MATERIALS/"+name.replace("pKw","PKW").strip()
print "PARENT: ", plasmid_parent_id
if not parents_code_list ==['']:
parents_code_list.append(plasmid_parent_id)
print "P2 : ", parents_code_list
sample_for_update.setParentSampleIdentifiers(parents_code_list)
else:
plasmid_list.append(plasmid_parent_id)
print "P2 : ", plasmid_list
sample_for_update.setParentSampleIdentifiers(plasmid_list)
sample_for_update.setParentSampleIdentifiers(plasmid_list)
elif re.search ("PKW", name):
plasmid_parent_id = "/MATERIALS/"+name.strip()
plasmid_list.append(plasmid_parent_id)
print "PARENT : ", plasmid_list
sample_for_update.setParentSampleIdentifiers(plasmid_list)
#=================================================================================================
# for name in plasmid_parent_code_split:
# sample = tr.getSample(sample_id)
# sample_for_update = tr.makeSampleMutable(sample)
# if not sample_id =="/MATERIALS/PKW581":
# if re.search ("pKW ", name):
# plasmid_parent_id = "/MATERIALS/"+name.replace("pKW ","PKW").strip()
# if not parents_code_list ==['']:
# parents_code_list.append(plasmid_parent_id)
# print "P1.1", parents_code_list
# sample_for_update.setParentSampleIdentifiers(parents_code_list)
# else:
# print "P1.2", plasmid_parent_id
# sample_for_update.setParentSampleIdentifiers([plasmid_parent_id])
# elif re.search ("pKW", name):
# plasmid_parent_id = "/MATERIALS/"+name.replace("pKW","PKW").strip()
# if not parents_code_list ==['']:
# parents_code_list.append(plasmid_parent_id)
# print "P2.1", parents_code_list
# sample_for_update.setParentSampleIdentifiers(parents_code_list)
# else:
# print "P2.2", plasmid_parent_id
# sample_for_update.setParentSampleIdentifiers([plasmid_parent_id])
# elif re.search ("pKW001", name):
# plasmid_parent_id = "/MATERIALS/"+name.replace("pKW001","PKW1").strip()
# if not parents_code_list ==['']:
# parents_code_list.append(plasmid_parent_id)
# print "P3.1", parents_code_list
# sample_for_update.setParentSampleIdentifiers(parents_code_list)
# else:
# print "P3.2", plasmid_parent_id
# sample_for_update.setParentSampleIdentifiers([plasmid_parent_id])
#
#=================================================================================================
def register_samples_in_openbis(tr, data_rows):
for sample_dict in data_rows:
......
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