def getTrackData(user_name, root):
#start from root and recursively makeItems
#if they have a key, ie are queries/FeatureTracks turn only the relevant bits into a json string suitable for trackInfo.
#Make a big list of all these and print to the server
#important to read in SequenceTrack data (and other "default" tracks, like one with gene annotations or something) here
print "inside getTrackData"
trackData = []
#manually add the sequence trackdata
#TODO
#will have to add "seq/{assembly}/{refseq}" and change directory structure
#accordingly. Remember to modify the prepare-refseq script to not overwrite #hg18 that's already there. Also, have to give each donor genome a
# assembly field to be able to pass correctly to Christos's stuff
seqtrack = \
{"args" : {"chunkSize" : 20000}, \
"url" : "seq/{assembly}/{refseq}/", \
"type" : "SequenceTrack", \
"label" : "DNA", \
"key" : "DNA"}
trackData.append(seqtrack)
#TODO:
#there has to be a way to make this less gross
#generate all the query trackdata
for project in os.listdir(root):
project_path = "%s/%s" % (root, project)
if project.startswith( PROJECT_PREFIX ) and \
os.path.isdir( project_path ) :
for donor in os.listdir(project_path):
donor_path = "%s/%s" % (project_path, donor)
if donor.startswith( DONOR_PREFIX ) and \
os.path.isdir(donor_path) :
for query in os.listdir(donor_path):
query_path = "%s/%s" % (donor_path, query)
if query.startswith( QUERY_PREFIX ) and \
os.path.isdir(query_path) :
item = filestore_dojotree.makeItem(
user_name, query_path)
properties = ["url", "label", "key", "type"]
if len(item["sub_results"]) > 0:
for sr in item["sub_results"]:
entry = {}
for p in properties:
entry[p] = item[p]
entry["key"] = item["key"] + "/" + sr
entry["url"] = item["url"] % sr
trackData.append(entry)
else:
entry = {}
for p in properties:
entry[p] = item[p]
trackData.append(entry)
print entry
utils.printToServer(json.dumps(trackData))
def getTrackData( user_name, root ) :
#start from root and recursively makeItems
#if they have a key, ie are queries/FeatureTracks turn only the relevant bits into a json string suitable for trackInfo.
#Make a big list of all these and print to the server
#important to read in SequenceTrack data (and other "default" tracks, like one with gene annotations or something) here
print "inside getTrackData"
trackData = []
#manually add the sequence trackdata
#TODO
#will have to add "seq/{assembly}/{refseq}" and change directory structure
#accordingly. Remember to modify the prepare-refseq script to not overwrite #hg18 that's already there. Also, have to give each donor genome a
# assembly field to be able to pass correctly to Christos's stuff
seqtrack = \
{"args" : {"chunkSize" : 20000}, \
"url" : "seq/{assembly}/{refseq}/", \
"type" : "SequenceTrack", \
"label" : "DNA", \
"key" : "DNA"}
trackData.append( seqtrack )
#TODO:
#there has to be a way to make this less gross
#generate all the query trackdata
for project in os.listdir(root) :
project_path = "%s/%s" % (root,project)
if project.startswith( PROJECT_PREFIX ) and \
os.path.isdir( project_path ) :
for donor in os.listdir(project_path) :
donor_path = "%s/%s" % (project_path,donor)
if donor.startswith( DONOR_PREFIX ) and \
os.path.isdir(donor_path) :
for query in os.listdir( donor_path ) :
query_path = "%s/%s" % (donor_path, query)
if query.startswith( QUERY_PREFIX ) and \
os.path.isdir(query_path) :
item = filestore_dojotree.makeItem( user_name, query_path )
properties = ["url","label","key","type"]
if len(item["sub_results"]) > 0 :
for sr in item["sub_results"] :
entry = {}
for p in properties :
entry[p] = item[p]
entry["key"] = item["key"]+"/"+sr
entry["url"] = item["url"] % sr
trackData.append(entry)
else :
entry = {}
for p in properties :
entry[p] = item[p]
trackData.append(entry)
print entry
utils.printToServer( json.dumps(trackData) );
def handleQuery( user_name, path ) :
print "handleQuery,", path
total = 0
items = []
things = os.listdir( path )
things = sorted( things, key=utils.chromKeyer )
for thing in things :
total += 1
fullpath = "%s/%s" % (path,thing)
item = makeItem( user_name, fullpath )
if item :
items.append( item )
jresponse = {'total' : total, 'items' : items}
response = json.dumps( jresponse )
print response
utils.printToServer( response )
def handleQuery(user_name, path):
print "handleQuery,", path
total = 0
items = []
things = os.listdir(path)
things = sorted(things, key=utils.chromKeyer)
for thing in things:
total += 1
fullpath = "%s/%s" % (path, thing)
item = makeItem(user_name, fullpath)
if item:
items.append(item)
jresponse = {'total': total, 'items': items}
response = json.dumps(jresponse)
print response
utils.printToServer(response)
importre = re.compile(r'\s*import\s+(.*)\s*;')
debugging = False
def moveIfExists( source, dest ) :
if os.path.exists( source ) :
shutil.move( source, dest )
return True
else :
print "\n%s doesn't exist!\n" % source
return False
def validateGenomes( query, perms ) :
pass
utils.printToServer( 'Content-type: text/json\n\n' )
#utils.printToServer( utils.textarea_opener )
if debugging :
query_name = 'debug'
query = '''use parsed_tables
genome NA18507;
import READS;
import genes;
H1=select interval_creation() from READS using intervals(location,
mate_loc, both_mates) where location>=0 and mate_loc>=0 and
((mate_loc-location>1000 and mate_loc-location<2000000) or
(location-mate_loc>1000 and location-mate_loc<2000000))
select * from H1 where interval_coverage>5'''
import utils
import time
import hashlib
from subprocess import Popen, PIPE
err_filename = "%s/login_error.txt" % (GlobalConfig.DEBUG_DIR)
sys.stderr = open(err_filename, 'w')
out_filename = "%s/login_output.txt" % (GlobalConfig.DEBUG_DIR)
sys.stdout = open(out_filename, 'w')
fields = cgi.FieldStorage()
user_name = fields.getvalue("user_name")
passwd = fields.getvalue("passwd")
is_registering = fields.getvalue("is_registering")
utils.printToServer('Content-type: text/json\n\n')
status, message = "ok", "ok"
print fields
if is_registering == 'true':
#add permissions
passwd_file = "../lib/passwds.json"
perm_file = "../lib/permissions.json"
jperms = utils.fileToJson(perm_file)
jpasswds = utils.fileToJson(passwd_file)
if user_name in jpasswds:
status, message = "bad", "A user by the name '%s' already exists" % user_name
else:
m = hashlib.md5()
m.update(passwd)
import sys
sys.path.append("../lib")
import GlobalConfig
import utils
import time
import re
from subprocess import Popen, PIPE
err_filename = "%s/delete_table_error.txt" % (GlobalConfig.DEBUG_DIR)
sys.stderr = open( err_filename,'w')
out_filename = "%s/delete_table_output.txt" % (GlobalConfig.DEBUG_DIR)
sys.stdout = open( out_filename,'w')
fields = cgi.FieldStorage()
utils.printToServer( 'Content-type: text/html\n\n' )
def validateSchema( first_line, filename ) :
#name check
m = rename.match( first_line )
linename = m.group(1)
name_check = linename.lower() == filename.lower()
#TODO:
#column type checking?
if name_check :
return (True,"good to go")
else :
return (False, "%s != %s" % (linename, filename))
def moveIfExists(source, dest):
if os.path.exists(source):
shutil.move(source, dest)
return True
else:
print "\n%s doesn't exist!\n" % source
return False
def validateGenomes(query, perms):
pass
utils.printToServer('Content-type: text/json\n\n')
#utils.printToServer( utils.textarea_opener )
if debugging:
query_name = 'debug'
query = '''use parsed_tables
genome NA18507;
import READS;
import genes;
H1=select interval_creation() from READS using intervals(location,
mate_loc, both_mates) where location>=0 and mate_loc>=0 and
((mate_loc-location>1000 and mate_loc-location<2000000) or
(location-mate_loc>1000 and location-mate_loc<2000000))
select * from H1 where interval_coverage>5'''
os.mkdir("%s/%s" % (user_upload_root, refinfo_name))
fout = open(
"%s/%s/%s" % (user_upload_root, refinfo_name, refinfo_file.filename),
'w')
handle = refinfo_file.file
lines = handle.read()
fout.write(lines)
fout.close()
refinfo = refinfo_name
else:
refinfo = fields.getvalue("refinfo")
#project_names = fields.getvalue("project_names")
#project_names = project_names.split(",")
utils.printToServer('Content-type: text/html\n\n')
status, messages = "notcool", []
upload_dir = "/home/uploader/%s/%s" % (user_name, donor_name)
#if not os.path.exists( upload_dir ) :
#messages.append( "No folder named: %s exists" % upload_dir )
#else :
root = "%s/%s/%s" % (user_upload_root, refinfo, donor_name)
#shutil.move( upload_dir, root )
#TODO
#index this using the ref file (maybe not all chroms are there, or are named differently)
#also, run_biosql will need to be changed
#run script to index
for chrom in range(1, 23) + ['X', 'Y']:
import sys
sys.path.append("../lib")
import GlobalConfig
import utils
import time
import re
from subprocess import Popen, PIPE
err_filename = "%s/upload_error.txt" % (GlobalConfig.DEBUG_DIR)
sys.stderr = open( err_filename,'w')
out_filename = "%s/upload_output.txt" % (GlobalConfig.DEBUG_DIR)
sys.stdout = open( out_filename,'w')
fields = cgi.FieldStorage()
print fields
utils.printToServer( 'Content-type: text/html\n\n' )
#TODO: ownership and permission for inteval files
rename = re.compile(r'#?table\s+(\w+)\s+(.*);', re.I)
def validateSchema( first_line, filename ) :
#name check
m = rename.match( first_line )
linename = m.group(1)
name_check = linename.lower() == filename.lower()
#TODO:
#column type checking?
if name_check :
return (True,"good to go")
def handlePath(user_name, path):
print "handlePath,", path
item = makeItem(user_name, path)
utils.printToServer(json.dumps(item))
def handlePath( user_name, path ) :
print "handlePath,", path
item = makeItem( user_name, path )
utils.printToServer( json.dumps( item ) )
if ext == "txt" :
item["txts"].append( thing )
if len(item['sub_results']) > 0 :
item['url'] = "%s/%%s/trackData.json" % tt
else :
item['url'] = "%s/trackData.json" % tt
if is_dir :
item["children"] = getChildren( user_name, path )
return item
if __name__ == '__main__' :
utils.printToServer( "Content-type: text/json\n\n" )
projects_root = "%s/data/tracks" % ROOT_DIR
sys.stderr = open("%s/filestore_err.txt" % DEBUG_DIR,'w')
sys.stdout = open("%s/filestore_out.txt" % DEBUG_DIR,'w')
user_name = "generic"
print os.environ["HTTP_COOKIE"]
for kvpair in os.environ["HTTP_COOKIE"].split(";") :
[k,v] = kvpair.split("=",1)
if k.endswith("user_name") :
user_name = v
elif k.endswith("passwd") :
passwd = v
if len(item["sub_results"]) > 0:
for sr in item["sub_results"]:
entry = {}
for p in properties:
entry[p] = item[p]
entry["key"] = item["key"] + "/" + sr
entry["url"] = item["url"] % sr
trackData.append(entry)
else:
entry = {}
for p in properties:
entry[p] = item[p]
trackData.append(entry)
print entry
utils.printToServer(json.dumps(trackData))
if __name__ == '__main__':
utils.printToServer("Content-type: text/json\n\n")
project_root = "%s/data/tracks" % ROOT_DIR
sys.stderr = open("%s/trackdata_err.txt" % DEBUG_DIR, 'w')
sys.stdout = open("%s/trackdata_out.txt" % DEBUG_DIR, 'w')
dparams = cgi.parse()
print dparams
getTrackData(dparams["user_name"], project_root)
import GlobalConfig
import utils
import time
err_filename = "%s/create_new_project_error.txt" % (GlobalConfig.DEBUG_DIR)
sys.stderr = open(err_filename, 'w')
out_filename = "%s/create_new_project_output.txt" % (GlobalConfig.DEBUG_DIR)
sys.stdout = open(out_filename, 'w')
fields = cgi.FieldStorage()
user_name = fields.getvalue("user_name")
project_name = fields.getvalue("project_name")
assembly = fields.getvalue("assembly")
#fileitem = field['reference_file']
utils.printToServer('Content-type: text/json\n\n')
print fields
project_dir = "%s/data/tracks/%s%s" % \
(GlobalConfig.ROOT_DIR,
GlobalConfig.PROJECT_PREFIX,
project_name)
src_table_dir = "%s/%s" % (GlobalConfig.SRC_TABLE_DIR, project_name)
#setup directory for the explorer tree to find
if os.path.exists(project_dir) or os.path.exists(src_table_dir):
print "project_dir", project_dir
#TODO:
#name comflicts between users?
status, message = "bad", "The project name '%s' is already taken" % project_name
print status, message
#if len(retained_tracks) == len(json_tracks) :
#raise Exception("No tracks were removed. Check to make sure the supplied track names are correct")
#
#tifile = open( filename, 'w')
#tifile.write( "%s = \n%s" % (js_var_name, json.dumps( retained_tracks, indent=4 )))
#tifile.close()
if __name__ == '__main__' :
root_dir = GlobalConfig.ROOT_DIR
sys.stderr = open("%s/delete_error.txt" % GlobalConfig.DEBUG_DIR,'w')
sys.stdout = open("%s/delete_output.txt" % GlobalConfig.DEBUG_DIR,'w')
fields = cgi.FieldStorage()
utils.printToServer( 'Content-type: text/json\n\n' )
print 'fields: ', fields
if not fields :
donor = sys.argv[1]
query_name = sys.argv[2]
removeQuery( donor, query_name, delete=True )
else :
fields = cgi.parse()
#utils.printToServer('<html><body><textarea>')
#try :
(status, message) = removeQuery( fields["project"][0], fields["donor"][0], fields["query_name"][0], delete=True )
utils.printToServer( '{"status":"%s", "message":"%s"}' % (status,message) )
#except Exception :
#utils.printToServer( '{"status":"error", "message":"Something went wrong, check the logs"}' )
import sys
sys.path.append("../lib")
import GlobalConfig
import utils
import time
from subprocess import Popen, PIPE
err_filename = "%s/list_project_donors_error.txt" % (GlobalConfig.DEBUG_DIR)
sys.stderr = open( err_filename,'w')
out_filename = "%s/list_project_donors_output.txt" % (GlobalConfig.DEBUG_DIR)
sys.stdout = open( out_filename,'w')
fields = cgi.FieldStorage()
project_name = fields.getvalue("project_name")
utils.printToServer( 'Content-type: text/json\n\n' )
project_dir = "%s/data/tracks/%s%s/" \
% (GlobalConfig.ROOT_DIR, GlobalConfig.PROJECT_PREFIX, project_name)
donors = []
for donor in os.listdir( project_dir ) :
if donor.startswith( GlobalConfig.DONOR_PREFIX ) :
if donor.find( GlobalConfig.DONOR_PREFIX ) == 0 :
donors.append( donor[len(GlobalConfig.DONOR_PREFIX):] )
if len(donors) == 0 :
status = "empty"
message = "\"No genomes associated with this project\""
else :
status = "ok"
