removed sniffers, removed pinned, removed classes

config/datatypes_conf.xml.sample

@@ -524,8 +524,7 @@
     <datatype extension="xmfa" type="galaxy.datatypes.msa:MauveXmfa" display_in_upload="true" />
     <datatype extension="cel" type="galaxy.datatypes.binary:Cel" display_in_upload="true" />
     <datatype extension="rdata" type="galaxy.datatypes.binary:RData" display_in_upload="true" description="Stored data from an R session"/>
-    <datatype extension="rds" type="galaxy.datatypes.binary:RDS" display_in_upload="true" description="RDS serialised RData object"/>
-    <datatype extension="sce" type="galaxy.datatypes.binary:SingleCellExperiment" display_in_upload="true" description="Stored RDS from a SingleCellObject"/>
+    <datatype extension="sce" type="galaxy.datatypes.binary:RData" description="Stored RDS from a SingleCellObject" subclass="true" />
     <datatype extension="oxlicg" type="galaxy.datatypes.binary:OxliCountGraph" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="oxling" type="galaxy.datatypes.binary:OxliNodeGraph" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="oxlits" type="galaxy.datatypes.binary:OxliTagSet" mimetype="application/octet-stream" display_in_upload="true"/>
@@ -825,8 +824,6 @@
     <sniffer type="galaxy.datatypes.annotation:SnapHmm" />
     <sniffer type="galaxy.datatypes.binary:Cel" />
     <sniffer type="galaxy.datatypes.binary:RData" />
-    <sniffer type="galaxy.datatypes.binary:RDS" />
-    <sniffer type="galaxy.datatypes.binary:SingleCellExperiment" />
     <sniffer type="galaxy.datatypes.images:Jpg"/>
     <sniffer type="galaxy.datatypes.images:Png"/>
     <sniffer type="galaxy.datatypes.images:Tiff"/>

lib/galaxy/datatypes/binary.py

@@ -19,8 +19,6 @@ import h5py
 import pysam
 import pysam.bcftools
 from bx.seq.twobit import TWOBIT_MAGIC_NUMBER, TWOBIT_MAGIC_NUMBER_SWAP, TWOBIT_MAGIC_SIZE
-from rpy2.rinterface import RRuntimeError
-from rpy2.robjects.packages import importr
 
 from galaxy import util
 from galaxy.datatypes import metadata
@@ -1298,54 +1296,6 @@ class RData(Binary):
             return False
 
 
-class RDS(Binary):
-    """RDS object, compressed R object
-
-    >>> from galaxy.datatypes.sniff import get_test_fname
-    >>> fname = get_test_fname( 'test.sce' )
-    >>> RDS().sniff( fname )
-    True
-    >>> fname = get_test_fname( 'test.rds' )
-    >>> RDS().sniff( fname )
-    True
-    >>> fname = get_test_fname( 'oxli_countgraph.oxlicg' )
-    >>> RDS().sniff( fname )
-    False
-    >>> fname = get_test_fname( 'sequence.csfasta' )
-    >>> RDS().sniff( fname )
-    False
-    """
-    file_ext = "rds"
-    class_name = None
-
-    def sniff(self, filename):
-        base = importr('base')
-        try:
-            fdat = base.readRDS(filename)
-        except RRuntimeError:
-            return False
-
-        if self.class_name is None:
-            return True
-
-        return tuple(fdat.rclass)[0] == self.class_name
-
-
-class SingleCellExperiment(RDS):
-    """Specific class file for RDS, R data
-
-    >>> from galaxy.datatypes.sniff import get_test_fname
-    >>> fname = get_test_fname( 'test.sce' )
-    >>> SingleCellExperiment().sniff( fname )
-    True
-    >>> fname = get_test_fname( 'test.rds' )
-    >>> SingleCellExperiment().sniff( fname )
-    False
-    """
-    file_ext = "sce"
-    class_name = "SingleCellExperiment"
-
-
 class OxliBinary(Binary):
 
     @staticmethod

lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt

@@ -34,4 +34,3 @@ nose==1.3.7
 requests==2.18.4
 idna==2.6
 nodeenv==1.2.0
-rpy2==2.8.6