# HG changeset patch
# User Matt Shirley <mdshw5@gmail.com>
# Date 1405006914 14400
# Node ID 33fa019735a48b09dcbaf0ccc276199a5605c131
# Parent  96103d66b7afc7b3fcf381f0824260b79f9a0b8f
Save extra files path as extra_files, not extra_data. Changed type of dataset for new primary datasets. db_key becomes dbkey. Added example json files.

diff -r 96103d66b7af -r 33fa019735a4 example.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/example.json	Thu Jul 10 11:41:54 2014 -0400
@@ -0,0 +1,20 @@
+[ {"url":"http://rafalab.jhsph.edu/CGI/model-based-cpg-islands-hg19.txt",
+   "name":"Rafa CpG islands (human)",
+   "extension":"bed",
+   "metadata":{"dbkey":"hg19"},
+   "extra_data":[{"url":"http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/refGene.txt.gz",
+      "path":"path/to/refGene.txt.gz"}]
+  },
+  {"url":"http://rafalab.jhsph.edu/CGI/model-based-cpg-islands-ce2.txt",
+     "name":"Rafa CpG islands (ce)",
+     "extension":"bed",
+     "metadata":{"dbkey":"ce2"}
+  },
+  {"url":"http://rafalab.jhsph.edu/CGI/model-based-cpg-islands-mm9.txt",
+     "name":"Rafa CpG islands (mouse)",
+     "extension":"bed",
+     "metadata":{"dbkey":"mm9"},
+     "extra_data":[{"url":"http://hgdownload.cse.ucsc.edu/goldenpath/mm9/database/refGene.txt.gz",
+        "path":"path/to/refGene.txt.gz"}]
+  }
+]
diff -r 96103d66b7af -r 33fa019735a4 example.line_sep.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/example.line_sep.json	Thu Jul 10 11:41:54 2014 -0400
@@ -0,0 +1,3 @@
+{"name": "Rafa CpG islands (human)", "filename": "/mnt/galaxy/files/000/dataset_125.dat", "ext": "bed", "dataset_id": 125, "extra_files": "/mnt/galaxy/files/000/dataset_125.dat_files", "type": "dataset", "metadata": {"dbkey": "hg19"}}
+{"name": "Rafa CpG islands (ce)", "base_dataset_id": 125, "filename": "primary_125_http---rafalab.jhsph.edu-CGI-model-based-cpg-islands-ce2.txt_visible_bed", "ext": "bed", "type": "dataset", "metadata": {"dbkey": "ce2"}}
+{"name": "Rafa CpG islands (mouse)", "base_dataset_id": 125, "filename": "primary_125_http---rafalab.jhsph.edu-CGI-model-based-cpg-islands-mm9.txt_visible_bed", "ext": "bed", "extra_files": "primary_125_http---rafalab.jhsph.edu-CGI-model-based-cpg-islands-mm9.txt_visible_bed_files", "type": "dataset", "metadata": {"dbkey": "mm9"}}
diff -r 96103d66b7af -r 33fa019735a4 json_data_source.py
--- a/json_data_source.py	Wed Jul 02 09:33:03 2014 -0400
+++ b/json_data_source.py	Thu Jul 10 11:41:54 2014 -0400
@@ -73,7 +73,7 @@
                       name = metadata.get( 'name' ),
                       metadata = metadata.get( 'metadata' ) )
     if metadata.get( 'extra_data', None ):
-        meta_dict[ 'extra_data' ] = '_'.join( [ filename, 'files' ] )
+        meta_dict[ 'extra_files' ] = '_'.join( [ filename, 'files' ] )
     if primary:
         meta_dict[ 'base_dataset_id' ] = dataset_id
     else:
@@ -96,14 +96,19 @@
         filename = ''.join( c in VALID_CHARS and c or '-' for c in filename )
         name = construct_multi_filename( hda_id, filename, extension )
         target_output_filename = os.path.normpath( '/'.join( [ output_base_path, name ] ) )
+        metadata_parameter_file.write( metadata_to_json( dataset_id, query_item,
+                                                         target_output_filename,
+                                                         ds_type='new_primary_dataset'
+                                                         primary=primary) )
     else:
         target_output_filename = output_filename
+        metadata_parameter_file.write( metadata_to_json( dataset_id, query_item,
+                                                         target_output_filename,
+                                                         ds_type='dataset'
+                                                         primary=primary) )
     download_from_query( query_item, target_output_filename )
     if extra_data:
         download_extra_data( extra_data, '_'.join( [ target_output_filename, 'files' ] ) )
-    metadata_parameter_file.write( metadata_to_json( dataset_id, query_item,
-                                                     target_output_filename,
-                                                     primary=primary) )
     return True