# HG changeset patch
# User ieguinoa
# Date 1531234547 14400
# Node ID c57bd7f3fb466142cc03eadc3289e3ce9eab8c99
# Parent  955a8d483fa356ab2c3e3c6f99beb09e8d689923
Uploaded

diff -r 955a8d483fa3 -r c57bd7f3fb46 data_manager/data_manager_fetch_gff.py
--- a/data_manager/data_manager_fetch_gff.py	Tue Jul 10 05:30:23 2018 -0400
+++ b/data_manager/data_manager_fetch_gff.py	Tue Jul 10 10:55:47 2018 -0400
@@ -39,19 +39,20 @@
 
 
 def get_dbkey_dbname_id_name( params, dbkey_description=None ):
-    dbkey = params['param_dict']['dbkey_source']['dbkey']
+#    dbkey = params['param_dict']['dbkey_source']['dbkey']
     #TODO: ensure sequence_id is unique and does not already appear in location file
     sequence_id = params['param_dict']['sequence_id']
     if not sequence_id:
         sequence_id = dbkey #uuid.uuid4() generate and use an uuid instead?
     
-    if params['param_dict']['dbkey_source']['dbkey_source_selector'] == 'new':
-        dbkey_name = params['param_dict']['dbkey_source']['dbkey_name']
-        if not dbkey_name:
-            dbkey_name = dbkey
-    else:
-        dbkey_name = None
-    
+#    if params['param_dict']['dbkey_source']['dbkey_source_selector'] == 'new':
+#        dbkey_name = params['param_dict']['dbkey_source']['dbkey_name']
+#        if not dbkey_name:
+#            dbkey_name = dbkey
+#    else:
+#        dbkey_name = None
+    dbkey = params['param_dict']['dbkey'] 
+    dbkey_name = dbkey_description
     sequence_name = params['param_dict']['sequence_name']
     if not sequence_name:
         sequence_name = dbkey_description
@@ -360,14 +361,8 @@
 
     #sort_fasta( fasta_filename, params['param_dict']['sorting']['sort_selector'], params )
     
-    dbkey_dict = None
-    if dbkey_name:
-        #do len calc here
-        #len_base_name = "%s.len" % ( dbkey )
-        #compute_fasta_length( fasta_filename, os.path.join( target_directory, len_base_name ), keep_first_word=True )
-        dbkey_dict = dict( value=dbkey, name=dbkey_name, len_path='' )
     
-    return [ ( '__dbkeys__', dbkey_dict ), ( DATA_TABLE_NAME, dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ]
+    return [ ( DATA_TABLE_NAME, dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ]
 
 
 def compute_fasta_length( fasta_file, out_file, keep_first_word=False ):
@@ -407,15 +402,7 @@
     fasta_base_filename = "%s.fa" % sequence_id
     fasta_filename = os.path.join( target_directory, fasta_base_filename )
     os.symlink( input_filename, fasta_filename )
-    
-    dbkey_dict = None
-    if dbkey_name:
-        #do len calc here
-        len_base_name = "%s.len" % ( dbkey )
-        compute_fasta_length( fasta_filename, os.path.join( target_directory, len_base_name ), keep_first_word=True )
-        dbkey_dict = dict( value=dbkey, name=dbkey_name, len_path=len_base_name )
-    
-    return [ ( '__dbkeys__', dbkey_dict ), ( DATA_TABLE_NAME, dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ]
+    return [  ( DATA_TABLE_NAME, dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ]
 
 
 REFERENCE_SOURCE_TO_DOWNLOAD = dict( ucsc=download_from_ucsc, ncbi=download_from_ncbi, url=download_from_url, history=download_from_history, directory=copy_from_directory )
diff -r 955a8d483fa3 -r c57bd7f3fb46 data_manager/data_manager_fetch_gff.xml
--- a/data_manager/data_manager_fetch_gff.xml	Tue Jul 10 05:30:23 2018 -0400
+++ b/data_manager/data_manager_fetch_gff.xml	Tue Jul 10 10:55:47 2018 -0400
@@ -3,11 +3,7 @@
     <command><![CDATA[
        python "$__tool_directory__"/data_manager_fetch_gff.py "${out_file}"
        --type $file_type
-       #if str( $dbkey_source.dbkey_source_selector ) == 'existing':
-       --dbkey_description ${ dbkey_source.dbkey.get_display_text() }
-       #else
-       --dbkey_description "${ dbkey_source.dbkey_name or $dbkey_source.dbkey }"
-       #end if
+       --dbkey_description ${ dbkey.get_display_text() }
         
     ]]></command>
     <inputs>
@@ -16,19 +12,7 @@
                 <option value="full">GFF with complete features</option>
             </param>
  
-        <conditional name="dbkey_source">
-            <param name="dbkey_source_selector" type="select" label="Use existing dbkey or create a new one.">
-                <option value="existing" selected="True">Existing</option>
-                <option value="new">New</option>
-            </param>
-            <when value="existing">
-                <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
-            </when>
-            <when value="new">
-                <param type="text" name="dbkey" value="" label="dbkey" optional="False" />
-                <param type="text" name="dbkey_name" value="" label="Display name for dbkey" />
-            </when>
-        </conditional>
+        <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
         <param type="text" name="sequence_name" value="" label="Name of sequence" />
         <param type="text" name="sequence_id" value="" label="ID for sequence" />
         <conditional name="reference_source">
diff -r 955a8d483fa3 -r c57bd7f3fb46 data_manager_conf.xml
--- a/data_manager_conf.xml	Tue Jul 10 05:30:23 2018 -0400
+++ b/data_manager_conf.xml	Tue Jul 10 10:55:47 2018 -0400
@@ -31,20 +31,5 @@
                 </column>
             </output>
         </data_table>
-
-      <data_table name="__dbkeys__">
-            <output>
-                <column name="value" />
-                <column name="name" />
-                <column name="len_path" output_ref="out_file">
-                    <move type="file">
-                        <source>${len_path}</source>
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${value}/len/${len_path}</target>
-                    </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${value}/len/${len_path}</value_translation>
-                    <value_translation type="function">abspath</value_translation>
-                </column>
-            </output>
-        </data_table>
     </data_manager>
 </data_managers>
diff -r 955a8d483fa3 -r c57bd7f3fb46 tool-data/all_gff.loc.sample
--- a/tool-data/all_gff.loc.sample	Tue Jul 10 05:30:23 2018 -0400
+++ b/tool-data/all_gff.loc.sample	Tue Jul 10 10:55:47 2018 -0400
@@ -1,3 +1,3 @@
 #The all_gff.loc file has this format:
 #
-#<id> <dbkey> <name>  <path_to_gff_file>
+#<unique_build_id>	<dbkey>	<display_name>	<path_to_gff_file>
diff -r 955a8d483fa3 -r c57bd7f3fb46 tool-data/representative_gff.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/representative_gff.loc.sample	Tue Jul 10 10:55:47 2018 -0400
@@ -0,0 +1,3 @@
+#The representative_gff.loc file has this format:
+#
+#<unique_build_id>	<dbkey>	<display_name>	<path_to_gff_file>