Mercurial > repos > iuc > data_manager_meme_motif_database_downloader

changeset 5:7563ad02ce6a draft

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Uploaded
author iuc
date Thu, 15 Mar 2018 09:25:11 -0400
parents 6d6b69ad6bdc
children c7019708aac8
files data_manager/data_manager_meme_motif_databases_downloader.py data_manager/data_manager_meme_motif_databases_downloader.xml data_manager_conf.xml tool-data/meme_motif_databases.loc.sample
diffstat 4 files changed, 20 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager_meme_motif_databases_downloader.py	Tue Mar 13 08:58:05 2018 -0400
+++ b/data_manager/data_manager_meme_motif_databases_downloader.py	Thu Mar 15 09:25:11 2018 -0400
@@ -78,8 +78,8 @@
 
 
 def download(target_directory, web_url, name, description, data_table_names=DEFAULT_DATA_TABLE_NAMES):
+    motif_databases_directory = os.path.join(target_directory, 'motif_databases')
     data_manager_dict = {}
-    data_table_entry = {}
     # Download the databases.
     work_directory = os.path.abspath(os.path.join(os.getcwd(), 'meme_motif_databases'))
     make_directory(work_directory)
@@ -89,17 +89,20 @@
     # Move the database files into the defined output directory.
     move_files(work_directory, target_directory)
     remove_directory(work_directory)
-    # Populate the data_manager_dict with the database data entry.
-    for file_path in os.listdir(target_directory):
-        full_path = os.path.abspath(os.path.join(target_directory, file_path))
-        entry_name = "%s" % os.path.basename(file_path)
-        data_table_entry['value'] = name
-        data_table_entry['name'] = name
-        data_table_entry['path'] = full_path
-        data_table_entry['description'] = description
-        # Populate the data_manager_dict.
-        for data_table_name in data_table_names:
-            data_manager_dict = add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
+    # Populate the data_manager_dict with the database data entries.
+    for file_name in os.listdir(motif_databases_directory):
+        data_table_entry = {}
+        full_path = os.path.abspath(os.path.join(motif_databases_directory, file_name))
+        # Eliminate anything that is not a directory.
+        if os.path.isdir(full_path):
+            entry_name = "%s" % os.path.basename(full_path)
+            data_table_entry['value'] = entry_name
+            data_table_entry['name'] = entry_name
+            data_table_entry['path'] = full_path
+            data_table_entry['description'] = description
+            # Populate the data_manager_dict.
+            for data_table_name in data_table_names:
+                data_manager_dict = add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
     return data_manager_dict
 
 params = json.loads(open(args.out_file).read())
--- a/data_manager/data_manager_meme_motif_databases_downloader.xml	Tue Mar 13 08:58:05 2018 -0400
+++ b/data_manager/data_manager_meme_motif_databases_downloader.xml	Thu Mar 15 09:25:11 2018 -0400
@@ -36,3 +36,4 @@
     </citations>
     </citations>
 </tool>
+
--- a/data_manager_conf.xml	Tue Mar 13 08:58:05 2018 -0400
+++ b/data_manager_conf.xml	Thu Mar 15 09:25:11 2018 -0400
@@ -3,14 +3,14 @@
     <data_manager tool_file="data_manager/data_manager_meme_motif_databases_downloader.xml" id="data_manager_meme_motif_databases_download" >
         <data_table name="meme_motif_databases">
             <output>
-                <column name="value" />
+                <column name="value"/>
                 <column name="name"/>
                 <column name="path" output_ref="out_file">
                     <move type="file">
                         <source>${path}</source>
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">meme_motif_databases/${value}</target>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">meme_motif_databases/${name}</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/meme_motif_databases/${value}</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/meme_motif_databases/${name}</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
                 <column name="description" />
--- a/tool-data/meme_motif_databases.loc.sample	Tue Mar 13 08:58:05 2018 -0400
+++ b/tool-data/meme_motif_databases.loc.sample	Thu Mar 15 09:25:11 2018 -0400
@@ -1,3 +1,3 @@
 ## MEME Motif Databases
 #Value	Name	Path	Description
-#2017_12	2017_12	/meme_motif_databases/2017_12	December 2017
+#ARABD	ARABD	/meme_motif_databases/2017_12	December 2017