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Commit 773c162a authored by barillac's avatar barillac
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modified to account for missing labels in xml import file 

SVN: 30346
parent 6694b670
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plasmid/source/drop-boxes/ylab-buffers-dropbox/xml_import-Buffers-dropbox-v2.py
+ 153
− 115
View file @ 773c162a
......@@ -67,112 +67,147 @@ def process(transaction):
for path in [ './Identifier']:
node = tree.find(path)
if node.text != "":
sample_name = node.text
sample_name = node.text
else:
node.text = ""
node.text = ""
for path in [ './Experiment']:
node = tree.find(path)
if node.text != "":
if node.text != "":
experiment_name = node.text
else:
node.text = ""
node.text = ""
def Chemicals():
for path in [ './Chemicals']:
node = tree.find(path)
if node.text is not None:
chemicals = node.text
tokens = chemicals.split(',')
for token in tokens:
if re.search(":", token):
token = token.split(':')
chemical_name = token[0]
chemical_concentration=token[1]
chemicals_list.append(chemical_name)
concentration_list.append(chemical_concentration)
else:
chemical_name=token
chemical_concentration = "n.a."
chemicals_list.append(chemical_name)
concentration_list.append(chemical_concentration)
else:
node.text = "n.a."
print "CHEM", chemicals_list, concentration_list
return chemicals_list, concentration_list
Chemicals()
def Buffers():
for path in [ './Solutions_Buffers']:
node = tree.find(path)
if node.text is not None:
buffers = node.text
tokens = buffers.split(',')
for token in tokens:
if re.search(":", token):
token = token.split(':')
buffer_name = token[0]
buffer_concentration=token[1]
buffers_list.append(buffer_name)
buffers_concentration_list.append(buffer_concentration)
else:
buffer_name=token
buffer_concentration = "n.a."
buffers_list.append(buffer_name)
buffers_concentration_list.append(buffer_concentration)
else:
node.text = "n.a."
print "BUFF", buffers_list, buffers_concentration_list
return buffers_list, buffers_concentration_list
Buffers()
def Medias():
for path in [ './Media']:
node = tree.find(path)
if node.text is not None:
medias = node.text
tokens = medias.split(',')
for token in tokens:
if re.search(":", token):
token = token.split(':')
media_name = token[0]
media_concentration=token[1]
medias_list.append(media_name)
medias_concentration_list.append(media_concentration)
chemicals_found = False
for child in root.getchildren():
if child.tag == 'Chemicals':
chemicals_found = True
def Chemicals():
for path in [ './Chemicals']:
node = tree.find(path)
if node.text is not None:
chemicals = node.text
tokens = chemicals.split(',')
for token in tokens:
if re.search(":", token):
token = token.split(':')
chemical_name = token[0]
chemical_concentration=token[1]
chemicals_list.append(chemical_name)
concentration_list.append(chemical_concentration)
else:
chemical_name=token
chemical_concentration = "n.a."
chemicals_list.append(chemical_name)
concentration_list.append(chemical_concentration)
else:
node.text = "n.a."
return chemicals_list, concentration_list
Chemicals()
if not chemicals_found:
chemicals= None
chemical_name = None
chemical_concentration = None
chemicals_list = None
concentration_list = None
buffers_found = False
for child in root.getchildren():
if child.tag == 'Solutions_Buffers':
buffers_found = True
def Buffers():
for path in [ './Solutions_Buffers']:
node = tree.find(path)
if node.text is not None:
buffers = node.text
tokens = buffers.split(',')
for token in tokens:
if re.search(":", token):
token = token.split(':')
buffer_name = token[0]
buffer_concentration=token[1]
buffers_list.append(buffer_name)
buffers_concentration_list.append(buffer_concentration)
else:
buffer_name=token
buffer_concentration = "n.a."
buffers_list.append(buffer_name)
buffers_concentration_list.append(buffer_concentration)
else:
node.text = "n.a."
return buffers_list, buffers_concentration_list
Buffers()
if not chemicals_found:
buffers= None
buffer_name = None
buffer_concentration = None
buffers_list = None
buffers_concentration_list = None
medias_found = False
for child in root.getchildren():
if child.tag == 'Media':
medias_found = True
def Medias():
for path in [ './Media']:
node = tree.find(path)
if node.text is not None:
medias = node.text
tokens = medias.split(',')
for token in tokens:
if re.search(":", token):
token = token.split(':')
media_name = token[0]
media_concentration=token[1]
medias_list.append(media_name)
medias_concentration_list.append(media_concentration)
else:
media_name=token
media_concentration = "n.a."
medias_list.append(media_name)
medias_concentration_list.append(media_concentration)
else:
node.text = "n.a."
return medias_list, medias_concentration_list
Medias()
if not medias_found:
medias= None
media_name = None
media_concentration = None
medias_list = None
medias_concentration_list = None
xmlcomments_found = False
for child in root.getchildren():
if child.tag == 'XMLCOMMENTS':
xmlcomments_found = True
for path in [ './XMLCOMMENTS']:
node = tree.find(path)
if node.text is not None:
comment_text_list= node.text
else:
media_name=token
media_concentration = "n.a."
medias_list.append(media_name)
medias_concentration_list.append(media_concentration)
else:
node.text = "n.a."
print "MEDIA", medias_list, medias_concentration_list
return medias_list, medias_concentration_list
Medias()
for path in [ './XMLCOMMENTS']:
node = tree.find(path)
if node.text is not None:
comment_text_list= node.text
else:
comment_text_list = None
comment_text_list = None
if not xmlcomments_found:
comment_text_list = None
elementFactory = ElementFactory()
propertyConverter = XmlStructuredPropertyConverter(elementFactory);
###IMPORT CHEMICALS####################################################################
......@@ -203,7 +238,7 @@ def process(transaction):
return sampleLink
"""
Example input:
......@@ -252,7 +287,7 @@ def process(transaction):
return sampleLink
"""
Example input:
......@@ -300,7 +335,7 @@ def process(transaction):
return sampleLink
"""
Example input:
......@@ -327,7 +362,7 @@ def process(transaction):
def _createCommentsSampleLink(comment_text_list):
#if comment_text_list is not None:
commentEntry = elementFactory.createElement(COMMENT_ENTRY_ELEMENT_LABEL)
user = transaction.getUserId()
commentEntry.addAttribute(PERSON_ATTRIBUTE, user)
commentEntry.addAttribute(DATE_ATTRIBUTE,str(create_openbis_timestamp()))
......@@ -357,25 +392,28 @@ def process(transaction):
exp = transaction.getExperiment(experiment_name)
newSample.setExperiment(exp)
""" Set medias, chemicals, buffers as parents for the sample"""
""" Set medias, chemicals, buffers as parents for the sample"""
mediaId_list =[]
for media in medias_list:
mediaIdentifier = "/YEAST_LAB/" + media.strip()
mediaId_list.append(mediaIdentifier)
chemicalId_list =[]
for chemical in chemicals_list:
chemicalIdentifier = "/YEAST_LAB/" + chemical.strip()
chemicalId_list.append(chemicalIdentifier)
bufferId_list =[]
for buffer in buffers_list:
bufferIdentifier = "/YEAST_LAB/" + buffer.strip()
bufferId_list.append(bufferIdentifier)
parents_list = mediaId_list + chemicalId_list + bufferId_list
newSample.setParentSampleIdentifiers(parents_list)
if medias_list != None:
for media in medias_list:
mediaIdentifier = "/YEAST_LAB/" + media.strip()
mediaId_list.append(mediaIdentifier)
chemicalId_list =[]
if chemicals_list != None:
for chemical in chemicals_list:
chemicalIdentifier = "/YEAST_LAB/" + chemical.strip()
chemicalId_list.append(chemicalIdentifier)
bufferId_list =[]
if buffers_list !=None:
for buffer in buffers_list:
bufferIdentifier = "/YEAST_LAB/" + buffer.strip()
bufferId_list.append(bufferIdentifier)
parents_list = mediaId_list + chemicalId_list + bufferId_list
newSample.setParentSampleIdentifiers(parents_list)
for child in root:
if child.tag == "Chemicals":
......@@ -384,11 +422,11 @@ def process(transaction):
newSample.setPropertyValue("SOLUTIONS_BUFFERS",updateBuffersFromBatchInput(buffers_list,buffers_concentration_list))
if child.tag == "Media":
newSample.setPropertyValue("Media",updateMediasFromBatchInput(medias_list,medias_concentration_list))
if child.tag == "XMLCOMMENTS":
newSample.setPropertyValue("XMLCOMMENTS", updateCommentsFromBatchInput(comment_text_list))
if child.tag == "XMLCOMMENTS":
newSample.setPropertyValue("XMLCOMMENTS", updateCommentsFromBatchInput(comment_text_list))
if child.tag != "Identifier" and child.tag !="Experiment" and child.tag != "Chemicals" and child.tag != "XMLCOMMENTS" and child.tag != "Solutions_Buffers" and child.tag != "Media":
if child.text != None:
newSample.setPropertyValue(child.tag, child.text)
else:
else:
child.text= ""
newSample.setPropertyValue(child.tag, child.text)
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