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sb25/general_example_helpers.py

Created June 14, 2010 10:54
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general_example_helpers.py
#! /usr/bin/python
# Author:: Sébastien Briois (mailto:[email protected])
import httplib2 # http://httplib2.googlecode.com/files/httplib2-0.6.0.zip
import urllib
import base64
try:
import json # Python 2.6
except ImportError:
import simplejson as json # Python 2.4+ - http://pypi.python.org/pypi/simplejson/2.0.9
DOMAIN = 'localhost:3000'
USERNAME = 'htgt'
PASSWORD = 'htgt'
# Generic helper class for handling the web requests to the repository.
class UserAgent(object):
def __init__(self):
self.http = httplib2.Http()
self.http.add_credentials(USERNAME, PASSWORD)
self.base_url = BASE_URL
def uri_for(self, rel_url, params = None):
if params:
params = urllib.urlencode(params)
return urljoin( self.base_url, "%s?%s" % (rel_url, params) )
return urljoin( self.base_url, rel_url )
def request(self, method, rel_url, data = {}):
if method in ['GET', 'DELETE']:
uri = self.uri_for( rel_url, data )
resp, content = self.http.request( uri, method, headers = { 'Content-Type': 'application/json' } )
elif method in ['POST', 'PUT']:
uri = self.uri_for( rel_url )
data = json.dumps( data )
resp, content = self.http.request( uri, method, data, headers = { 'Content-Type': 'application/json' } )
else:
raise Exception( "Method %s unknown when requesting URL %s" % (method, rel_url) )
print "%s %s: %s" % (method, uri, resp['status'])
if resp['status'] in ['200', '201']:
# DELETE methods does not return any content
return method == 'DELETE' and True or json.loads( content )
raise Exception(content)
# Create a User Agent
ua = UserAgent()
def find( url, params ):
results = ua.request( 'GET', url, params )
if len(results) > 1:
raise "Your search returned more than one result."
if not results:
return None
return results[0]
#
# Allele specific methods
#
def create_allele( data ):
return ua.request( 'POST', 'alleles.json', { 'molecular_structure' : data } )
def update_allele( id, data ):
return ua.request( 'PUT', 'alleles/%s.json' % id, { 'molecular_structure' : data } )
def create_or_update_allele( data ):
allele_found = find('alleles.json', {
'mgi_accession_id' : data['mgi_accession_id'],
'project_design_id' : data['project_design_id'],
'loxp_start' : data['loxp_start'] or 'null',
'loxp_end' : data['loxp_end'] or 'null'
})
if not allele_found:
return create_allele( data )
else:
return update_allele( allele_found['id'], data )
def delete_allele( id ):
ua.request( 'DELETE', "alleles/%s.json" % id )
#
# Targeting Vector specific methods
#
def create_targeting_vector( data ):
return ua.request( 'POST', 'targeting_vectors.json', { 'targeting_vector' : data } )
def update_targeting_vector( id, data ):
return ua.request( 'PUT', 'targeting_vectors/%s.json' % id, { 'targeting_vector' : data } )
def create_or_update_vector( data ):
vector_found = find( "targeting_vectors.json", { 'name': data['name'] } )
if not vector_found:
return create_targeting_vector( data )
else:
return update_targeting_vector( vector_found['id'], data )
def delete_targeting_vector( id ):
ua.request( 'DELETE', "targeting_vectors/%s.json" % id )
#
# ES Cell specific methods
#
def create_es_cell( data ):
return ua.request( 'POST', 'es_cells.json', { 'es_cell' : data } )
def update_es_cell( id, data ):
return ua.request( 'POST', 'es_cells/%s.json' % id, { 'es_cell' : data } )
def create_or_update_es_cell( data ):
es_cell_found = find( "es_cells.json", { 'name': data['name'] } )
if not es_cell_found:
return create_es_cell( data )
else:
return update_es_cell( es_cell_found['id'], data )
def delete_es_cell( id ):
ua.request( 'DELETE', "es_cells/%s.json" % id )
Raw
general_example_main.py
##
## Main script scenario:
## - We create a data structure containing all the objects we want to create or update in the database
## - We loop over this data structure and follow this procedure:
## 1- Search the object
## 2- Object found ? Yes: Update; No: Create
##
# We will work with the data linked to the pipeline named "EUCOMM", let's find its ID
pipeline_list = ua.request( 'GET', 'pipelines.json' )
for pipeline in pipeline_list:
if pipeline['name'] == 'EUCOMM':
break
# Create our data structure
alleles = [
# First allele
{
'pipeline_id' : pipeline['id'],
'mgi_accession_id' : "MGI:123",
'project_design_id' : 23640,
'cassette' : "L1L2_gt2",
'backbone' : "L3L4_pZero_kan",
'assembly' : "NCBIM37",
'chromosome' : "1",
'strand' : "+",
'design_type' : "Knock Out",
'design_subtype' : "Frameshift",
'homology_arm_start' : 10,
'homology_arm_end' : 10000,
'cassette_start' : 50,
'cassette_end' : 500,
'loxp_start' : 1000,
'loxp_end' : 1500,
# Targeting vectors for the first allele
'targeting_vectors' : [
{
'name' : 'PRPGD001',
'intermediate_vector' : 'PGS001',
'ikmc_project_id' : 9801
},
{
'name' : 'PRPGD002',
'intermediate_vector' : 'PGS001',
'ikmc_project_id' : 9801
}
],
# ES Cells for the first allele
'es_cells' : [
{ 'name' : 'EPD001', 'allele_symbol_superscript' : 'tm1a', 'targeting_vector' : 'PRPGD001' },
{ 'name' : 'EPD002', 'allele_symbol_superscript' : 'tm1a', 'targeting_vector' : 'PRPGD001' },
{ 'name' : 'EPD003', 'allele_symbol_superscript' : 'tm1a', 'targeting_vector' : 'PRPGD001' },
{ 'name' : 'EPD004', 'allele_symbol_superscript' : 'tm1a', 'targeting_vector' : 'PRPGD002' },
{ 'name' : 'EPD005', 'allele_symbol_superscript' : 'tm1a', 'targeting_vector' : 'PRPGD002' },
{ 'name' : 'EPD006', 'allele_symbol_superscript' : 'tm1a', 'targeting_vector' : 'PRPGD002' }
],
# Genbank File for the first allele
'genbank_file' : {
'escell_clone' : "A GENBANK FILE IN PLAIN TEXT",
'targeting_vector' : "A GENBANK FILE IN PLAIN TEXT"
}
},
# Second allele
{
'pipeline_id' : pipeline['id'],
'mgi_accession_id' : "MGI:456",
'project_design_id' : 29871,
'cassette' : "L1L2_gt2",
'backbone' : "L3L4_pZero_kan",
'assembly' : "NCBIM37",
'chromosome' : "1",
'strand' : "+",
'design_type' : "Knock Out",
'design_subtype' : "Frameshift",
'homology_arm_start' : 10,
'homology_arm_end' : 10000,
'cassette_start' : 50,
'cassette_end' : 500,
'loxp_start' : 1000,
'loxp_end' : 1500,
# Targeting vectors for the second allele
'targeting_vectors' : [
{
'name' : 'PRPGD003',
'intermediate_vector' : 'PGS002',
'ikmc_project_id' : 6809480
},
{
'name' : 'PRPGD004',
'intermediate_vector' : 'PGS002',
'ikmc_project_id' : 6809480
}
],
# ES Cells for the second allele
'es_cells' : [
{ 'name' : 'EPD007', 'allele_symbol_superscript' : 'tm1a', 'targeting_vector' : 'PRPGD003' },
{ 'name' : 'EPD008', 'allele_symbol_superscript' : 'tm1a', 'targeting_vector' : 'PRPGD003' },
{ 'name' : 'EPD009', 'allele_symbol_superscript' : 'tm1a', 'targeting_vector' : 'PRPGD003' },
{ 'name' : 'EPD010', 'allele_symbol_superscript' : 'tm1a', 'targeting_vector' : 'PRPGD004' },
{ 'name' : 'EPD011', 'allele_symbol_superscript' : 'tm1a', 'targeting_vector' : 'PRPGD004' },
{ 'name' : 'EPD012', 'allele_symbol_superscript' : 'tm1a', 'targeting_vector' : 'PRPGD004' }
]
}
]
# Create or Update Alleles
for allele_hash in alleles:
# allele_hash should not contain unknown fields
targeting_vectors = allele_hash.pop( 'targeting_vectors' )
es_cells = allele_hash.pop( 'es_cells' )
allele = create_or_update_allele( allele_hash )
allele_hash['id'] = allele['id']
# Create or Update Targeting Vectors
for vector_hash in targeting_vectors:
vector_hash['molecular_structure_id'] = allele['id']
vector = create_or_update_vector( vector_hash )
vector_hash['id'] = vector['id']
# Find, Create or Update ES Cells
for es_cell_hash in es_cells:
es_cell_hash['molecular_structure_id'] = allele['id']
# Find targeting vector ID from its name or set it to nil
# if ES Cell is not linked to a targeting vector
if 'targeting_vector' in es_cell_hash:
targ_vec_name = es_cell_hash.pop('targeting_vector')
for vector in targeting_vectors:
if vector['name'] == targ_vec_name:
break
es_cell_hash['targeting_vector_id'] = vector['id']
else:
es_cell_hash['targeting_vector_id'] = None
es_cell = create_or_update_es_cell( es_cell_hash )
es_cell_hash['id'] = es_cell['id']
# DELETE All ES Cells
for es_cell in es_cells: delete_es_cell( es_cell['id'] )
for vector in targeting_vectors: delete_targeting_vector( vector['id'] )
for allele in alleles: delete_allele( allele['id'] )
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