Add HTML and PDF file types. Add workaround for downloading of HTML r…

…eports as zip archives from Galaxy.
yvanlebras · Apr 22, 2014 · e866ca1 · e866ca1
1 parent 3a5dab9
commit e866ca1
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Showing 3 changed files with 17 additions and 7 deletions.
diff --git a/refinery/analysis_manager/tasks.py b/refinery/analysis_manager/tasks.py
@@ -694,23 +694,26 @@ def download_history_files(analysis) :
 
             if curr_file_id in dl_dict:
                 curr_dl_dict = dl_dict[curr_file_id]
-
                 result_name = curr_dl_dict['filename'] + '.' + file_type
-
                 # size of file defined by galaxy
                 file_size = results['file_size']
 
                 # Determing tag if galaxy results should be download through http or copying files directly
                 local_download = analysis.workflow.workflow_engine.instance.local_download
 
-                # URL to download
-                if local_download:
+                # to retrieve HTML files as zip archives via dataset URL
+                if local_download and file_type != 'html':
                     download_url = results['file_name']
                 else:
                     download_url = connection.make_url(
                         str(results['dataset_id']), is_data=True, key=False)
 
-                # getting file_store_uuid, 
+                # workaround to set the correct file type for zip archives of
+                # reports produced by FASTQC
+                if file_type == 'html':
+                    file_type = 'zip'
+
+                # getting file_store_uuid,
                 # TODO: when changing permanent=True, fix update of % download of file 
                 filestore_uuid = create(
                     source=download_url,

diff --git a/refinery/file_store/models.py b/refinery/file_store/models.py
@@ -91,13 +91,15 @@ def _mkdir(path):
 GFF = 'gff'
 GTF = 'gtf'
 GZ = 'gz'
+HTML = 'html'
 IDF = 'idf'
 FASTA = 'fasta'
 FASTQ = 'fastq'
 FASTQCSANGER = 'fastqcsanger'
 FASTQILLUMINA = 'fastqillumina'
 FASTQSANGER = 'fastqsanger'
 FASTQSOLEXA = 'fastqsolexa'
+PDF = 'pdf'
 SAM = 'sam'
 SEG = 'seg'
 TABULAR = 'tabular'
@@ -124,13 +126,15 @@ def _mkdir(path):
     (GFF, 'GFF file'),
     (GTF, 'GTF file'),
     (GZ, 'Gzip compressed archive'),
+    (HTML, 'Hypertext Markup Language'),
     (IDF, 'IDF file'),
     (FASTA, 'FASTA file'),
     (FASTQ, 'FASTQ file'),
     (FASTQCSANGER, 'FASTQC Sanger'),
     (FASTQILLUMINA, 'FASTQ Illumina'),
     (FASTQSANGER, 'FASTQ Sanger'),
     (FASTQSOLEXA, 'FASTQ Solexa'),
+    (PDF, 'Portable Document Format'),
     (SAM, 'Sequence Alignment/Map'),
     (SEG, 'Segmented Data File'), # http://broadinstitute.org/software/igv/SEG
     (TABULAR, 'Tabular file'),
@@ -165,6 +169,8 @@ def _mkdir(path):
     'fastqillumina': FASTQILLUMINA,
     'fastqsanger': FASTQSANGER,
     'fastqsolexa': FASTQSOLEXA,
+    'html': HTML,
+    'pdf': PDF,
     'sam': SAM,
     'tabular': TABULAR,
     'tdf': TDF, 'igv.tdf': TDF,

diff --git a/refinery/galaxy_connector/connection.py b/refinery/galaxy_connector/connection.py
@@ -41,7 +41,7 @@ def __init__(self, base_url, data_url, api_url, api_key ):
 
     # =========================================================================================================
 
-    def make_url( self, command, args=None, is_data=False, key=True ):
+    def make_url(self, command, args=None, is_data=False, key=True):
         # Adds the API Key to the URL if it's not already there.
         if args is None:
             args = []
@@ -51,7 +51,8 @@ def make_url( self, command, args=None, is_data=False, key=True ):
             if key:
                 return self.base_url + '/' + self.data_url + '/' + command + argsep + '&'.join( [ '='.join( t ) for t in args ] )
             else:
-                return self.base_url + '/' + self.data_url + '/' + command  + argsep + "to_ext=txt"
+                # to download HTML files and linked resources as zip archives
+                return self.base_url + '/' + self.data_url + '/' + command + '/display' + argsep + "to_ext=txt"
         else:
             return self.base_url + '/' + self.api_url + '/' + command + argsep + '&'.join( [ '='.join( t ) for t in args ] )