def getPathwayAs(pathway_db, species_code, mod):
begin_time = time.time()
try:
export.deleteFolder(
'BuildDBs/WPs') ### clear any remaining pathway files
except Exception:
null = []
for wpid in pathway_db:
file_type = 'gpml'
wp_id_data = client.service.getPathwayAs(fileType=file_type,
pwId=wpid,
revision=0)
wp_id_data = base64.b64decode(wp_id_data)
gpml_path = filepath('BuildDBs/WPs/' + wpid + '.gpml')
outfile = export.ExportFile(gpml_path)
outfile.write(wp_id_data)
outfile.close()
gene_system_list = string.split(wp_id_data, '\n')
parent_path = export.findParentDir(gpml_path)
pathway_db = gene_associations.getGPMLGraphData(
parent_path, species_code, mod) ### get GPML data back
os.remove(gpml_path) ### Only store the file temporarily
end_time = time.time()
time_diff = float(end_time - begin_time)
"""
try: print "WikiPathways data imported in %d seconds" % time_diff
except Exception: null=None ### Occurs when transitioning back from the Official Database download window (not sure why) -- TclError: can't invoke "update" command
"""
return pathway_db
def getPathwayAs(pathway_db,species_code,mod):
begin_time = time.time()
for wpid in pathway_db:
#print [wpid],'pathway_db',len(pathway_db)
file_type = 'gpml'
#file_type = 'application/gpml+xml'
processor_time = str(time.clock())
#try: export.deleteFolder('BuildDBs/WPs') ### clear any remaining pathway files
#except Exception: pass
#wp_id_data = client.service.getPathwayAs(fileType = file_type,pwId = wpid, revision = 0)
kwargs = {
'identifier': 'WP2062',
'version': 0,
'file_format': 'application/gpml+xml'}
#wp_id_data = wikipathways_api_client_instance.get_pathway_as(**kwargs)
wp_id_data = wikipathways_api_client_instance.get_pathway_as(file_format = file_type,identifier = wpid, version = 0)
#wp_id_data = base64.b64decode(wp_id_data)
gpml_path = filepath('BuildDBs/WPs/'+processor_time+'/'+wpid+'.gpml')
#print gpml_path
outfile = export.ExportFile(gpml_path)
outfile.write(wp_id_data); outfile.close()
gene_system_list = string.split(wp_id_data,'\n')
parent_path = export.findParentDir(gpml_path)
pathway_db = gene_associations.getGPMLGraphData(parent_path,species_code,mod) ### get GPML data back
#os.remove(gpml_path) ### Only store the file temporarily
try: export.deleteFolder('BuildDBs/WPs/'+processor_time) ### clear any remaining pathway files
except Exception: pass
end_time = time.time(); time_diff = float(end_time-begin_time)
"""
try: print "WikiPathways data imported in %d seconds" % time_diff
except Exception: null=None ### Occurs when transitioning back from the Official Database download window (not sure why) -- TclError: can't invoke "update" command
"""
return pathway_db
def getPathwayAs(pathway_db, species_code, mod):
begin_time = time.time()
for wpid in pathway_db:
#print [wpid],'pathway_db',len(pathway_db)
file_type = 'gpml'
#file_type = 'application/gpml+xml'
processor_time = str(time.clock())
#try: export.deleteFolder('BuildDBs/WPs') ### clear any remaining pathway files
#except Exception: pass
#wp_id_data = client.service.getPathwayAs(fileType = file_type,pwId = wpid, revision = 0)
kwargs = {
'identifier': 'WP2062',
'version': 0,
'file_format': 'application/gpml+xml'
}
#wp_id_data = wikipathways_api_client_instance.get_pathway_as(**kwargs)
wp_id_data = wikipathways_api_client_instance.get_pathway_as(
file_format=file_type, identifier=wpid, version=0)
#wp_id_data = base64.b64decode(wp_id_data)
gpml_path = filepath('BuildDBs/WPs/' + processor_time + '/' + wpid +
'.gpml')
#print gpml_path
outfile = export.ExportFile(gpml_path)
outfile.write(wp_id_data)
outfile.close()
gene_system_list = string.split(wp_id_data, '\n')
parent_path = export.findParentDir(gpml_path)
pathway_db = gene_associations.getGPMLGraphData(
parent_path, species_code, mod) ### get GPML data back
#os.remove(gpml_path) ### Only store the file temporarily
try:
export.deleteFolder(
'BuildDBs/WPs/' +
processor_time) ### clear any remaining pathway files
except Exception:
pass
end_time = time.time()
time_diff = float(end_time - begin_time)
"""
try: print "WikiPathways data imported in %d seconds" % time_diff
except Exception: null=None ### Occurs when transitioning back from the Official Database download window (not sure why) -- TclError: can't invoke "update" command
"""
return pathway_db