def hasPermission( user, path, name ) :
if user == 'su' : return True
else :
if name.startswith(PROJECT_PREFIX) :
try :
return perms[user][utils.unprefix(name)]
except KeyError :
return False
else :
return True
def hasPermission(user, path, name):
if user == 'su': return True
else:
if name.startswith(PROJECT_PREFIX):
try:
return perms[user][utils.unprefix(name)]
except KeyError:
return False
else:
return True
def makeItem( user_name, path ) :
print "path: %s" % path
(head,gparent_name,parent_name,name) = path.rsplit('/',3)
gparent = "%s/%s" % (head, gparent_name)
parent= "%s/%s" % (gparent, parent_name)
#is_dir = os.path.isdir(path)
prefix = getPrefix( path, name )
is_dir = prefix == DONOR_PREFIX or prefix == PROJECT_PREFIX
item = {}
if show( user_name, path, name) :
name = utils.unprefix(name)
parent_prefix = getPrefix( parent, parent_name )
gparent_prefix = getPrefix( gparent, gparent_name )
gparent_name = utils.extractName(gparent_prefix, path)
parent_name = utils.extractName(parent_prefix, path)
item = {'name' : name, \
'parentDir' : parent, \
'directory' : is_dir, \
'path' : path,
'prefix' : prefix}
if prefix == PROJECT_PREFIX :
if name in dassembly :
item['assembly'] = dassembly[name]
else :
item['assembly'] = "n/a"
if prefix == QUERY_PREFIX :
print "QUERY_PREFIX"
assert parent_prefix == DONOR_PREFIX
item['project'] = gparent_name
item['donor'] = parent_name
#project/query_name
item['key'] = "%s/%s" % (gparent_name,name)
tt = TRACK_TEMPLATE % \
(gparent_name, parent_name, name, UNBOUND_CHROM)
item['label'] = name
item['type'] = 'FeatureTrack'
if item['project'] in dassembly :
item['assembly'] = dassembly[item['project']]
else :
item['assembly'] = "n/a"
#Associate these three keys with each query menuitem
#It will tell the browser how many of each filetype we
#have in the chrom folders.
#(Remember: Using the counts for chr1)
#dkey_ext = {"bam_ixs" : ".bam", \
#"interval_ixs" : ".interval", \
#"txt_ixs" : ".txt" }
#for key in dkey_ext :
#item[key] = []
item["bams"] = []
item["txts"] = []
item["sub_results"] = []
item["sub_exts"] = []
#pick the first available chrom folder and inspect its contents
#use them to build up the list of bams, txts, sub_results, ....
chrom_folder = ""
for listing in os.listdir( path ) :
folder = path + '/' + listing
if os.path.isdir( folder ) :
chrom_folder = folder
break
print "folder", chrom_folder
if not chrom_folder :
pass
else :
#folder = "%s/data/%s" % (ROOT_DIR, tt.replace( UNBOUND_CHROM, 'chr1' ) )
print "canonical chrom folder is %s" % chrom_folder
#TODO
#more specific than just looking for a .txt file?
for thing in sorted( os.listdir( chrom_folder ) ) :
if os.path.isdir( chrom_folder+"/"+thing ) and thing != ".svn" :
print "listdir:", thing
item["sub_results"].append( thing )
for subthing in sorted(os.listdir( chrom_folder+"/"+thing )) :
head,ext = subthing.rsplit(".",1)
if ext == "short" or ext == "interval" :
if ext == "short" :
item["sub_exts"].append( "bam.short" )
else :
item["sub_exts"].append( ext )
else :
head,ext = thing.rsplit(".",1)
if ext == "bam" :
item["bams"].append( thing )
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
def makeItem(user_name, path):
print "path: %s" % path
(head, gparent_name, parent_name, name) = path.rsplit('/', 3)
gparent = "%s/%s" % (head, gparent_name)
parent = "%s/%s" % (gparent, parent_name)
#is_dir = os.path.isdir(path)
prefix = getPrefix(path, name)
is_dir = prefix == DONOR_PREFIX or prefix == PROJECT_PREFIX
item = {}
if show(user_name, path, name):
name = utils.unprefix(name)
parent_prefix = getPrefix(parent, parent_name)
gparent_prefix = getPrefix(gparent, gparent_name)
gparent_name = utils.extractName(gparent_prefix, path)
parent_name = utils.extractName(parent_prefix, path)
item = {'name' : name, \
'parentDir' : parent, \
'directory' : is_dir, \
'path' : path,
'prefix' : prefix}
if prefix == PROJECT_PREFIX:
if name in dassembly:
item['assembly'] = dassembly[name]
else:
item['assembly'] = "n/a"
if prefix == QUERY_PREFIX:
print "QUERY_PREFIX"
assert parent_prefix == DONOR_PREFIX
item['project'] = gparent_name
item['donor'] = parent_name
#project/query_name
item['key'] = "%s/%s" % (gparent_name, name)
tt = TRACK_TEMPLATE % \
(gparent_name, parent_name, name, UNBOUND_CHROM)
item['label'] = name
item['type'] = 'FeatureTrack'
if item['project'] in dassembly:
item['assembly'] = dassembly[item['project']]
else:
item['assembly'] = "n/a"
#Associate these three keys with each query menuitem
#It will tell the browser how many of each filetype we
#have in the chrom folders.
#(Remember: Using the counts for chr1)
#dkey_ext = {"bam_ixs" : ".bam", \
#"interval_ixs" : ".interval", \
#"txt_ixs" : ".txt" }
#for key in dkey_ext :
#item[key] = []
item["bams"] = []
item["txts"] = []
item["sub_results"] = []
item["sub_exts"] = []
#pick the first available chrom folder and inspect its contents
#use them to build up the list of bams, txts, sub_results, ....
chrom_folder = ""
for listing in os.listdir(path):
folder = path + '/' + listing
if os.path.isdir(folder):
chrom_folder = folder
break
print "folder", chrom_folder
if not chrom_folder:
pass
else:
#folder = "%s/data/%s" % (ROOT_DIR, tt.replace( UNBOUND_CHROM, 'chr1' ) )
print "canonical chrom folder is %s" % chrom_folder
#TODO
#more specific than just looking for a .txt file?
for thing in sorted(os.listdir(chrom_folder)):
if os.path.isdir(chrom_folder + "/" +
thing) and thing != ".svn":
print "listdir:", thing
item["sub_results"].append(thing)
for subthing in sorted(
os.listdir(chrom_folder + "/" + thing)):
head, ext = subthing.rsplit(".", 1)
if ext == "short" or ext == "interval":
if ext == "short":
item["sub_exts"].append("bam.short")
else:
item["sub_exts"].append(ext)
else:
head, ext = thing.rsplit(".", 1)
if ext == "bam":
item["bams"].append(thing)
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