# HG changeset patch
# User bgruening
# Date 1423399591 18000
# Node ID 98de3779045a584f0ac32f8b98964f24f0db3faf
# Parent  dbd491c28590b27fd8e8015cb57071cc9ebeda70
Uploaded

diff -r dbd491c28590 -r 98de3779045a data_manager/data_manager_diamond_database_builder.py
--- a/data_manager/data_manager_diamond_database_builder.py	Sun Feb 08 07:28:34 2015 -0500
+++ b/data_manager/data_manager_diamond_database_builder.py	Sun Feb 08 07:46:31 2015 -0500
@@ -5,7 +5,6 @@
 import shutil
 import optparse
 import urllib2
-#import uuid
 import subprocess
 from ftplib import FTP
 import tarfile
@@ -66,19 +65,19 @@
 
     path_contents = _get_files_in_ftp_path( ftp, NCBI_DOWNLOAD_PATH )
 
-    ucsc_file_name = None
+    ncbi_file_name = None
     get_stream_reader = None
     ext = None
     for ext, get_stream_reader in COMPRESSED_EXTENSIONS:
         if "%s%s" % ( ncbi_identifier, ext ) in path_contents:
-            ucsc_file_name = "%s%s%s" % ( NCBI_DOWNLOAD_PATH, ncbi_identifier, ext )
+            ncbi_file_name = "%s%s%s" % ( NCBI_DOWNLOAD_PATH, ncbi_identifier, ext )
             break
 
-    if not ucsc_file_name:
-        raise Exception( 'Unable to determine filename for UCSC Genome for %s: %s' % ( ncbi_identifier, path_contents ) )
+    if not ncbi_file_name:
+        raise Exception( 'Unable to determine filename for NCBI database for %s: %s' % ( ncbi_identifier, path_contents ) )
 
-    tmp_dir = tempfile.mkdtemp( prefix='tmp-data-manager-ucsc-' )
-    ucsc_fasta_filename = os.path.join( tmp_dir, "%s%s" % ( ncbi_identifier, ext ) )
+    tmp_dir = tempfile.mkdtemp( prefix='tmp-data-manager-ncbi-' )
+    ncbi_fasta_filename = os.path.join( tmp_dir, "%s%s" % ( ncbi_identifier, ext ) )
     
     fasta_base_filename = "%s.fa" % database_id
     fasta_filename = os.path.join( target_directory, fasta_base_filename )
@@ -87,9 +86,9 @@
     tmp_extract_dir = os.path.join ( tmp_dir, 'extracted_fasta' )
     os.mkdir( tmp_extract_dir )
     
-    tmp_fasta = open( ucsc_fasta_filename, 'wb+' )
+    tmp_fasta = open( ncbi_fasta_filename, 'wb+' )
     
-    ftp.retrbinary( 'RETR %s' % ucsc_file_name, tmp_fasta.write )
+    ftp.retrbinary( 'RETR %s' % ncbi_file_name, tmp_fasta.write )
     
     tmp_fasta.flush()
     tmp_fasta.seek( 0 )
diff -r dbd491c28590 -r 98de3779045a data_manager/data_manager_diamond_database_builder.xml
--- a/data_manager/data_manager_diamond_database_builder.xml	Sun Feb 08 07:28:34 2015 -0500
+++ b/data_manager/data_manager_diamond_database_builder.xml	Sun Feb 08 07:46:31 2015 -0500
@@ -1,5 +1,5 @@
-<tool id="diamond_database_builder" name="Diamond Database" tool_type="manage_data" version="0.0.1">
-    <description>builder</description>
+<tool id="diamond_database_builder" name="Diamond" tool_type="manage_data" version="0.0.1">
+    <description> Database builder</description>
     <requirements>
         <requirement type="package" version="0.6.13">diamond</requirement>
     </requirements>
@@ -9,7 +9,7 @@
     <inputs>
         <param type="text" name="database_name" value="" label="Database name or description"
             help="This will be shown to the user in the databse selectbox."/>
-        <param type="text" name="database_id" value="" label="Database ID" help="This needs to be unique." />
+        <param type="text" name="database_id" value="" label="Database ID" help="This needs to be unique. No whitespaces allowed. Use underscores." />
         <conditional name="reference_source">
           <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
             <option value="ncbi">NCBI</option>