diff tools/data_source/microbial_import_code.py @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/data_source/microbial_import_code.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,154 @@
+
+def load_microbial_data( GALAXY_DATA_INDEX_DIR, sep='\t' ):
+    # FIXME: this function is duplicated in the DynamicOptions class.  It is used here only to
+    # set data.name in exec_after_process(). 
+    microbe_info= {}
+    orgs = {}
+    
+    filename = "%s/microbial_data.loc" % GALAXY_DATA_INDEX_DIR
+    for i, line in enumerate( open( filename ) ):
+        line = line.rstrip( '\r\n' )
+        if line and not line.startswith( '#' ):
+            fields = line.split( sep )
+            #read each line, if not enough fields, go to next line
+            try:
+                info_type = fields.pop(0)
+                if info_type.upper() == "ORG":
+                    #ORG     12521   Clostridium perfringens SM101   bacteria        Firmicutes      CP000312,CP000313,CP000314,CP000315     http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=12521
+                    org_num = fields.pop(0)
+                    name = fields.pop(0)
+                    kingdom = fields.pop(0)
+                    group = fields.pop(0)
+                    chromosomes = fields.pop(0)
+                    info_url = fields.pop(0)
+                    link_site = fields.pop(0)
+                    if org_num not in orgs:
+                        orgs[ org_num ] = {}
+                        orgs[ org_num ][ 'chrs' ] = {}
+                    orgs[ org_num ][ 'name' ] = name
+                    orgs[ org_num ][ 'kingdom' ] = kingdom
+                    orgs[ org_num ][ 'group' ] = group
+                    orgs[ org_num ][ 'chromosomes' ] = chromosomes
+                    orgs[ org_num ][ 'info_url' ] = info_url
+                    orgs[ org_num ][ 'link_site' ] = link_site
+                elif info_type.upper() == "CHR":
+                    #CHR     12521   CP000315        Clostridium perfringens phage phiSM101, complete genome 38092   110684521       CP000315.1
+                    org_num = fields.pop(0)
+                    chr_acc = fields.pop(0)
+                    name = fields.pop(0)
+                    length = fields.pop(0)
+                    gi = fields.pop(0)
+                    gb = fields.pop(0)
+                    info_url = fields.pop(0)
+                    chr = {}
+                    chr[ 'name' ] = name
+                    chr[ 'length' ] = length
+                    chr[ 'gi' ] = gi
+                    chr[ 'gb' ] = gb
+                    chr[ 'info_url' ] = info_url
+                    if org_num not in orgs:
+                        orgs[ org_num ] = {}
+                        orgs[ org_num ][ 'chrs' ] = {}
+                    orgs[ org_num ][ 'chrs' ][ chr_acc ] = chr
+                elif info_type.upper() == "DATA":
+                    #DATA    12521_12521_CDS 12521   CP000315        CDS     bed     /home/djb396/alignments/playground/bacteria/12521/CP000315.CDS.bed
+                    uid = fields.pop(0)
+                    org_num = fields.pop(0)
+                    chr_acc = fields.pop(0)
+                    feature = fields.pop(0)
+                    filetype = fields.pop(0)
+                    path = fields.pop(0)
+                    data = {}
+                    data[ 'filetype' ] = filetype
+                    data[ 'path' ] = path
+                    data[ 'feature' ] = feature
+
+                    if org_num not in orgs:
+                        orgs[ org_num ] = {}
+                        orgs[ org_num ][ 'chrs' ] = {}
+                    if 'data' not in orgs[ org_num ][ 'chrs' ][ chr_acc ]:
+                        orgs[ org_num ][ 'chrs' ][ chr_acc ][ 'data' ] = {}
+                    orgs[ org_num ][ 'chrs' ][ chr_acc ][ 'data' ][ uid ] = data
+                else: continue
+            except: continue
+    for org_num in orgs:
+        org = orgs[ org_num ]
+        if org[ 'kingdom' ] not in microbe_info:
+            microbe_info[ org[ 'kingdom' ] ] = {}
+        if org_num not in microbe_info[ org[ 'kingdom' ] ]:
+            microbe_info[ org[ 'kingdom' ] ][org_num] = org
+    return microbe_info
+
+#post processing, set build for data and add additional data to history
+from galaxy import datatypes, config, jobs, tools
+from shutil import copyfile
+
+def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
+    base_dataset = out_data.items()[0][1]
+    history = base_dataset.history
+    if history == None:
+        print "unknown history!"
+        return
+    kingdom = param_dict.get( 'kingdom', None )
+    #group = param_dict.get( 'group', None )
+    org = param_dict.get( 'org', None )
+    
+    #if not (kingdom or group or org):
+    if not (kingdom or org):
+        print "Parameters are not available."
+    #workflow passes galaxy.tools.parameters.basic.UnvalidatedValue instead of values
+    if isinstance( kingdom, tools.parameters.basic.UnvalidatedValue ):
+        kingdom = kingdom.value
+    if isinstance( org, tools.parameters.basic.UnvalidatedValue ):
+        org = org.value
+    
+    GALAXY_DATA_INDEX_DIR = app.config.tool_data_path
+    microbe_info = load_microbial_data( GALAXY_DATA_INDEX_DIR, sep='\t' )
+    new_stdout = ""
+    split_stdout = stdout.split("\n")
+    basic_name = ""
+    for line in split_stdout:
+        fields = line.split("\t")
+        if fields[0] == "#File1":
+            description = fields[1]
+            chr = fields[2]
+            dbkey = fields[3]
+            file_type = fields[4]
+            name, data = out_data.items()[0]
+            data.set_size()
+            basic_name = data.name
+            data.name = data.name + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] +" for " + microbe_info[kingdom][org]['name'] + ":" + chr + ")"
+            data.dbkey = dbkey
+            data.info = data.name
+            data = app.datatypes_registry.change_datatype( data, file_type )
+            data.init_meta()
+            data.set_peek()
+            app.model.context.add( data )
+            app.model.context.flush()
+        elif fields[0] == "#NewFile":
+            description = fields[1]
+            chr = fields[2]
+            dbkey = fields[3]
+            filepath = fields[4]
+            file_type = fields[5]
+            newdata = app.model.HistoryDatasetAssociation( create_dataset = True, sa_session = app.model.context ) #This import should become a library
+            newdata.set_size()
+            newdata.extension = file_type
+            newdata.name = basic_name + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] +" for "+microbe_info[kingdom][org]['name']+":"+chr + ")"
+            app.model.context.add( newdata )
+            app.model.context.flush()
+            app.security_agent.copy_dataset_permissions( base_dataset.dataset, newdata.dataset )
+            history.add_dataset( newdata )
+            app.model.context.add( history )
+            app.model.context.flush()
+            try:
+                copyfile(filepath,newdata.file_name)
+                newdata.info = newdata.name
+                newdata.state = jobs.JOB_OK
+            except:
+                newdata.info = "The requested file is missing from the system."
+                newdata.state = jobs.JOB_ERROR
+            newdata.dbkey = dbkey
+            newdata.init_meta()
+            newdata.set_peek()
+            app.model.context.flush()