Merge pull request #2706 from lecorguille/add_netcdf_datatype

add a netcdf datatype for metabolomics spectre data

config/datatypes_conf.xml.sample

@@ -187,6 +187,7 @@
     <datatype extension="searchgui_archive" type="galaxy.datatypes.binary:SearchGuiArchive" display_in_upload="True"/>
     <datatype extension="peptideshaker_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/>
     <!-- End Proteomics Datatypes -->
+    <datatype extension="netcdf" type="galaxy.datatypes.binary:NetCDF" mimetype="application/octet-stream" display_in_upload="true" description="Format used by netCDF software library for writing and reading chromatography-MS data files." />
     <datatype extension="eps" type="galaxy.datatypes.images:Eps" mimetype="image/eps"/>
     <datatype extension="rast" type="galaxy.datatypes.images:Rast" mimetype="image/rast"/>
     <datatype extension="laj" type="galaxy.datatypes.images:Laj"/>
@@ -575,6 +576,7 @@
     <sniffer type="galaxy.datatypes.binary:CRAM"/>
     <sniffer type="galaxy.datatypes.binary:Sff"/>
     <sniffer type="galaxy.datatypes.binary:Sra"/>
+    <sniffer type="galaxy.datatypes.binary:NetCDF"/>
     <sniffer type="galaxy.datatypes.triples:Rdf"/>
     <sniffer type="galaxy.datatypes.xml:Phyloxml"/>
     <sniffer type="galaxy.datatypes.xml:Owl"/>

lib/galaxy/datatypes/binary.py

@@ -1331,3 +1331,36 @@ def display_peek( self, dataset ):
             return "SearchGUI Archive, version %s" % ( dataset.metadata.searchgui_version or 'unknown' )
 
 Binary.register_sniffable_binary_format("searchgui_archive", "searchgui_archive", SearchGuiArchive)
+
+
+class NetCDF( Binary ):
+    """Binary data in netCDF format"""
+    file_ext = "netcdf"
+    edam_format = "format_3650"
+    edam_data = "data_0943"
+
+    def set_peek( self, dataset, is_multi_byte=False ):
+        if not dataset.dataset.purged:
+            dataset.peek = "Binary netCDF file"
+            dataset.blurb = nice_size( dataset.get_size() )
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def display_peek( self, dataset ):
+        try:
+            return dataset.peek
+        except:
+            return "Binary netCDF file (%s)" % ( nice_size( dataset.get_size() ) )
+
+    def sniff( self, filename ):
+        try:
+            with open( filename, 'r' ) as f:
+                header = f.read(3)
+            if binascii.b2a_hex( header ) == binascii.hexlify( 'CDF' ):
+                return True
+            return False
+        except:
+            return False
+
+Binary.register_sniffable_binary_format("netcdf", "netcdf", NetCDF)