Detect pdf files on upload [Brad Chapman]. Resolves #357

datatypes_conf.xml.sample

@@ -79,7 +79,7 @@
         <datatype extension="mafcustomtrack" type="galaxy.datatypes.sequence:MafCustomTrack">
             <display file="ucsc/maf_customtrack.xml" />
         </datatype>
-        <datatype extension="pdf" type="galaxy.datatypes.images:Image" mimetype="application/pdf"/>
+        <datatype extension="pdf" type="galaxy.datatypes.images:Pdf" mimetype="application/pdf"/>
         <datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true" />
         <datatype extension="png" type="galaxy.datatypes.images:Image" mimetype="image/png"/>
         <datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" />
@@ -260,6 +260,7 @@
         <sniffer type="galaxy.datatypes.sequence:Fastq"/>
         <sniffer type="galaxy.datatypes.interval:Wiggle"/>
         <sniffer type="galaxy.datatypes.images:Html"/>
+        <sniffer type="galaxy.datatypes.images:Pdf"/>
         <sniffer type="galaxy.datatypes.sequence:Axt"/>
         <sniffer type="galaxy.datatypes.interval:Bed"/>
         <sniffer type="galaxy.datatypes.interval:CustomTrack"/>

lib/galaxy/datatypes/images.py

@@ -23,6 +23,19 @@ class Image( data.Data ):
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
 
+class Pdf( Image ):
+    def sniff(self, filename):
+        """Determine if the file is in pdf format.
+        """
+        headers = get_headers(filename, None, 1)
+        try:
+            if headers[0][0].startswith("%PDF"):
+                return True
+            else:
+                return False
+        except IndexError:
+            return False
+
 def create_applet_tag_peek( class_name, archive, params ):
     text = """
 <!--[if !IE]>-->

tools/data_source/upload.py

@@ -10,6 +10,7 @@ from galaxy import eggs
 import galaxy.model
 from galaxy.datatypes import sniff
 from galaxy.datatypes.binary import *
+from galaxy.datatypes.images import Pdf
 from galaxy.datatypes.registry import Registry
 from galaxy import util
 from galaxy.util.json import *
@@ -85,6 +86,8 @@ def check_bam( temp_name ):
     return Bam().sniff( temp_name )
 def check_sff( temp_name ):
     return Sff().sniff( temp_name )
+def check_pdf( temp_name ):
+    return Pdf().sniff( temp_name )
 def check_gzip( temp_name ):
     # This method returns a tuple of booleans representing ( is_gzipped, is_valid )
     # Make sure we have a gzipped file
@@ -160,6 +163,9 @@ def add_file( dataset, json_file, output_path ):
     elif check_sff( dataset.path ):
         ext = 'sff'
         data_type = 'sff'
+    elif check_pdf( dataset.path ):
+        ext = 'pdf'
+        data_type = 'pdf'
     else:
         # See if we have a gzipped file, which, if it passes our restrictions, we'll uncompress
         is_gzipped, is_valid = check_gzip( dataset.path )
@@ -215,7 +221,7 @@ def add_file( dataset, json_file, output_path ):
                         return
         if not data_type:
             if check_binary( dataset.path ):
-                # We have a binary dataset, but it is not Bam or Sff
+                # We have a binary dataset, but it is not Bam, Sff or Pdf
                 data_type = 'binary'
                 #binary_ok = False
                 parts = dataset.name.split( "." )