Fix some datatype issues

- dmnd had a wrong class name
- biom1, cool and postgresql shouldn't have `subclass="true"`
- extension should be lowercase
- add missing file_ext attribute to various datatype classes

config/datatypes_conf.xml.sample

@@ -39,7 +39,7 @@
     <datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true">
       <converter file="len_to_linecount.xml" target_datatype="linecount" />
     </datatype>
-    <datatype extension="dmnd" type="galaxy.datatypes.binary:Binary:DMND" display_in_upload="false"/>
+    <datatype extension="dmnd" type="galaxy.datatypes.binary:DMND" display_in_upload="false"/>
     <datatype extension="bigbed" type="galaxy.datatypes.binary:BigBed" mimetype="application/octet-stream" display_in_upload="true">
       <display file="ucsc/bigbed.xml" />
       <display file="igb/bb.xml" />
@@ -146,7 +146,7 @@
     <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="true" />
     <datatype extension="h5" type="galaxy.datatypes.binary:H5" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="mz5" type="galaxy.datatypes.binary:H5" subclass="true" mimetype="application/octet-stream" display_in_upload="true"/>
-    <datatype extension="cool" type="galaxy.datatypes.binary:Cool" subclass="true" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="cool" type="galaxy.datatypes.binary:Cool" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="html" type="galaxy.datatypes.text:Html" mimetype="text/html"/>
     <datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true" description="File must start with definition line in the following format (columns may be in any order)." >
       <converter file="interval_to_bed_converter.xml" target_datatype="bed"/>
@@ -237,7 +237,7 @@
     <datatype extension="sf3" type="galaxy.datatypes.proteomics:Sf3" display_in_upload="true" />
     <datatype extension="cps" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="true" />
     <datatype extension="ct" type="galaxy.datatypes.tabular:ConnectivityTable" display_in_upload="true"/>
-    <datatype extension="postgresql" type="galaxy.datatypes.binary:PostgresqlArchive" subclass="True" display_in_upload="True"/>
+    <datatype extension="postgresql" type="galaxy.datatypes.binary:PostgresqlArchive" display_in_upload="True"/>
     <datatype extension="searchgui_archive" type="galaxy.datatypes.binary:SearchGuiArchive" display_in_upload="true"/>
     <datatype extension="fast5.tar" type="galaxy.datatypes.binary:Fast5Archive" display_in_upload="true"/>
     <datatype extension="fast5.tar.gz" type="galaxy.datatypes.binary:Fast5ArchiveGz" display_in_upload="true"/>
@@ -282,13 +282,13 @@
     <datatype extension="qualillumina" type="galaxy.datatypes.qualityscore:QualityScoreIllumina" display_in_upload="true"/>
     <datatype extension="qualsolid" type="galaxy.datatypes.qualityscore:QualityScoreSOLiD" display_in_upload="true"/>
     <datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/>
-    <datatype extension="Roadmaps" type="galaxy.datatypes.assembly:Roadmaps" display_in_upload="false"/>
+    <datatype extension="roadmaps" type="galaxy.datatypes.assembly:Roadmaps" display_in_upload="false"/>
     <datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true">
         <converter file="sam_to_bam.xml" target_datatype="bam"/>
         <converter file="sam_to_bigwig_converter.xml" target_datatype="bigwig"/>
     </datatype>
     <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true" description="A binary sequence file in 'scf' format with a '.scf' file extension.  You must manually select this 'File Format' when uploading the file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Scf"/>
-    <datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/>
+    <datatype extension="sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/>
     <datatype extension="snpeffdb" type="galaxy.datatypes.text:SnpEffDb" display_in_upload="true"/>
     <datatype extension="snpsiftdbnsfp" type="galaxy.datatypes.text:SnpSiftDbNSFP" display_in_upload="true"/>
     <datatype extension="dbnsfp.tabular" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true">
@@ -518,7 +518,7 @@
     <datatype extension="vtkascii" type="galaxy.datatypes.constructive_solid_geometry:VtkAscii" display_in_upload="true" />
     <datatype extension="vtkbinary" type="galaxy.datatypes.constructive_solid_geometry:VtkBinary" display_in_upload="true" />
     <!-- Metagenomic Datatypes -->
-    <datatype extension="biom1" type="galaxy.datatypes.text:Biom1" display_in_upload="true" subclass="true" mimetype="application/json">
+    <datatype extension="biom1" type="galaxy.datatypes.text:Biom1" display_in_upload="true" mimetype="application/json">
         <display file="biom/biom_simple.xml" />
         <converter file="biom1_to_biom2.xml" target_datatype="biom2"/>
     </datatype>

lib/galaxy/datatypes/assembly.py

@@ -71,6 +71,7 @@ class Amos(data.Text):
 class Sequences(sequence.Fasta):
     """Class describing the Sequences file generated by velveth """
     edam_data = "data_0925"
+    file_ext = 'sequences'
 
     def sniff(self, filename):
         """
@@ -110,6 +111,7 @@ class Sequences(sequence.Fasta):
 class Roadmaps(data.Text):
     """Class describing the Sequences file generated by velveth """
     edam_format = "format_2561"
+    file_ext = 'roadmaps'
 
     def sniff(self, filename):
         """

lib/galaxy/datatypes/binary.py

@@ -673,7 +673,6 @@ Binary.register_sniffable_binary_format('cram', 'cram', CRAM)
 class BaseBcf(Binary):
     edam_format = "format_3020"
     edam_data = "data_3498"
-    file_ext = "bcf"
 
 
 class Bcf(BaseBcf):
@@ -688,6 +687,7 @@ class Bcf(BaseBcf):
     >>> Bcf().sniff(fname)
     False
     """
+    file_ext = "bcf"
 
     MetadataElement(name="bcf_index", desc="BCF Index File", param=metadata.FileParameter, file_ext="csi", readonly=True, no_value=None, visible=False, optional=True)
 
@@ -1014,6 +1014,7 @@ class BigWig(Binary):
     """
     edam_format = "format_3006"
     edam_data = "data_3002"
+    file_ext = "bigwig"
     track_type = "LineTrack"
     data_sources = {"data_standalone": "bigwig"}
 
@@ -1054,6 +1055,7 @@ class BigBed(BigWig):
     """BigBed support from UCSC."""
     edam_format = "format_3004"
     edam_data = "data_3002"
+    file_ext = "bigbed"
     data_sources = {"data_standalone": "bigbed"}
 
     def __init__(self, **kwd):
@@ -1472,6 +1474,7 @@ class OxliCountGraph(OxliBinary):
     >>> OxliCountGraph().sniff( fname )
     True
     """
+    file_ext = 'oxlicg'
 
     def sniff(self, filename):
         return OxliBinary._sniff(filename, b"01")
@@ -1500,6 +1503,7 @@ class OxliNodeGraph(OxliBinary):
     >>> OxliNodeGraph().sniff( fname )
     True
     """
+    file_ext = 'oxling'
 
     def sniff(self, filename):
         return OxliBinary._sniff(filename, b"02")
@@ -1529,6 +1533,7 @@ class OxliTagSet(OxliBinary):
     >>> OxliTagSet().sniff( fname )
     True
     """
+    file_ext = 'oxlits'
 
     def sniff(self, filename):
         return OxliBinary._sniff(filename, b"03")
@@ -1552,6 +1557,7 @@ class OxliStopTags(OxliBinary):
     >>> OxliStopTags().sniff( fname )
     True
     """
+    file_ext = 'oxlist'
 
     def sniff(self, filename):
         return OxliBinary._sniff(filename, b"04")
@@ -1581,6 +1587,7 @@ class OxliSubset(OxliBinary):
     >>> OxliSubset().sniff( fname )
     True
     """
+    file_ext = 'oxliss'
 
     def sniff(self, filename):
         return OxliBinary._sniff(filename, b"05")
@@ -1610,6 +1617,7 @@ class OxliGraphLabels(OxliBinary):
     >>> OxliGraphLabels().sniff( fname )
     True
     """
+    file_ext = 'oxligl'
 
     def sniff(self, filename):
         return OxliBinary._sniff(filename, b"06")