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changeset 5:ef086bb44e6c

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Uploaded
author jorrit
date Tue, 12 Feb 2013 14:48:56 -0500
parents d455c48f74fa
children ebf2b433a239
files annotation.py datatypes_conf.xml ontology.py repository_dependencies.xml termenrichment.py
diffstat 5 files changed, 4 insertions(+), 199 deletions(-) [+]
line wrap: on
line diff
--- a/annotation.py	Tue Feb 12 14:13:23 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,42 +0,0 @@
-"""
-Annotation datatypes
-
-"""
-import pkg_resources
-pkg_resources.require( "bx-python" )
-
-import logging, os, sys, time, tempfile, shutil
-import data
-from galaxy import util
-from galaxy.datatypes.sniff import *
-from galaxy.web import url_for
-from cgi import escape
-import urllib
-from bx.intervals.io import *
-from galaxy.datatypes import metadata
-from galaxy.datatypes.metadata import MetadataElement
-from galaxy.datatypes.tabular import Tabular
-import math
-
-log = logging.getLogger(__name__)
-
-class Gaf( Tabular ):
-    """Tab delimited data in Gene Ontology Association File (GAF) format"""
-    file_ext = "gaf"
-
-    def init_meta( self, dataset, copy_from=None ):
-        data.Text.init_meta( self, dataset, copy_from=copy_from )
-    def sniff( self, filename ):
-        """
-        Determines whether the file is in GAF format
-        """
-        headers = get_headers( filename, '\t' )
-        try:
-            for hdr in headers:
-                if hdr and hdr[0].startswith( '!gaf-version:' ) :
-                    return True
-            return False
-        except:
-            return False
-
-
--- a/datatypes_conf.xml	Tue Feb 12 14:13:23 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-<?xml version="1.0"?>
-<!-- see http://wiki.galaxyproject.org/ToolShedDatatypesFeatures for more info -->
-<datatypes>
-    <datatype_files>
-        <datatype_file name="annotation.py"/>
-        <datatype_file name="ontology.py"/>
-        <datatype_file name="termenrichment.py"/>
-    </datatype_files>
-    <registration> 
-        <datatype extension="ontology" type="galaxy.datatypes.ontology:Ontology" display_in_upload="true"/>
-        <datatype extension="obo" type="galaxy.datatypes.ontology:Obo" display_in_upload="true"/>
-        <datatype extension="owl" type="galaxy.datatypes.ontology:Owl" display_in_upload="true"/>
-        <datatype extension="gaf" type="galaxy.datatypes.annotation:Gaf" display_in_upload="true"/>
-        <datatype extension="terf" type="galaxy.datatypes.termenrichment:TerfTab" display_in_upload="true"/>
-    </registration>
-</datatypes>
--- a/ontology.py	Tue Feb 12 14:13:23 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,90 +0,0 @@
-"""
-Ontology datatypes
-
-"""
-import pkg_resources
-pkg_resources.require( "bx-python" )
-
-import logging, os, sys, time, tempfile, shutil
-import data
-from galaxy import util
-from galaxy.datatypes.sniff import *
-from galaxy.web import url_for
-from cgi import escape
-import urllib
-from bx.intervals.io import *
-from galaxy.datatypes import metadata
-from galaxy.datatypes.metadata import MetadataElement
-from galaxy.datatypes.tabular import Tabular
-import math
-
-log = logging.getLogger(__name__)
-
-class Ontology( data.Text ):
-    """Any ontology Format"""
-    file_ext = "ontology"
-
-    def init_meta( self, dataset, copy_from=None ):
-        data.Text.init_meta( self, dataset, copy_from=copy_from )
-
-
-class Obo( Ontology ):
-    """OBO Format"""
-    file_ext = "obo"
-
-    def init_meta( self, dataset, copy_from=None ):
-        data.Text.init_meta( self, dataset, copy_from=copy_from )
-    def sniff( self, filename ):
-        """
-        Determines whether the file is in OBO format
-        """
-        headers = get_headers( filename, '\n' )
-        try:
-            for hdr in headers:
-                if hdr and hdr[0].startswith( 'format-version:' ) :
-                    return True
-            return False
-        except:
-            return False
-
-class Owl( Ontology ):
-    """OWL"""
-    file_ext = "owl"
-
-    def init_meta( self, dataset, copy_from=None ):
-        data.Text.init_meta( self, dataset, copy_from=copy_from )
-    def sniff( self, filename ):
-        """
-        Determines whether the file is in OWL RDF-XML format
-        """
-        headers = get_headers( filename, '\n' )
-        try:
-            for hdr in headers:
-                if hdr and hdr[0].find( '<owl' ) > -1 :
-                    return True
-                if hdr and hdr[0].find( 'http://www.w3.org/2002/07/owl' ) > -1 :
-                    return True
-            return False
-        except:
-            return False
-
-
-class OwlRdfXML( Owl ):
-    """OWL RDF/XML"""
-
-    def init_meta( self, dataset, copy_from=None ):
-        data.Text.init_meta( self, dataset, copy_from=copy_from )
-    def sniff( self, filename ):
-        """
-        Determines whether the file is in OWL RDF-XML format
-        """
-        headers = get_headers( filename, '\n' )
-        try:
-            for hdr in headers:
-                if hdr and hdr[0].find( '<owl:Ontology' ) > -1 :
-                    return True
-            return False
-        except:
-            return False
-
-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Tue Feb 12 14:48:56 2013 -0500
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories description="Obo tools requires the Galaxy applicable data formats used by Obo tools.">
+	<repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="obo_datatypes" owner="jorrit" changeset_revision="b4db4eaf8fff" />
+</repositories>
--- a/termenrichment.py	Tue Feb 12 14:13:23 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,51 +0,0 @@
-"""
-Term enrichment datatypes
-
-"""
-import pkg_resources
-pkg_resources.require( "bx-python" )
-
-import logging, os, sys, time, tempfile, shutil
-import data
-from galaxy import util
-from galaxy.datatypes.sniff import *
-from galaxy.web import url_for
-from cgi import escape
-import urllib
-from bx.intervals.io import *
-from galaxy.datatypes import metadata
-from galaxy.datatypes.metadata import MetadataElement
-from galaxy.datatypes.tabular import Tabular
-import math
-
-log = logging.getLogger(__name__)
-
-class TermEnrichmentResult( data.Text ):
-    """Any term enrichment format"""
-    file_ext = "enrichment"
-
-    def init_meta( self, dataset, copy_from=None ):
-        data.Text.init_meta( self, dataset, copy_from=copy_from )
-
-
-class TerfTab( TermEnrichmentResult ):
-    """TERF TSV Format"""
-    file_ext = "terf"
-
-    def init_meta( self, dataset, copy_from=None ):
-        data.Text.init_meta( self, dataset, copy_from=copy_from )
-    def sniff( self, filename ):
-        """
-        Determines whether the file is in TERF format
-        """
-        headers = get_headers( filename, '\n' )
-        try:
-            for hdr in headers:
-                if hdr and hdr[0].startswith( '##terf-version' ) :
-                    return True
-            return False
-        except:
-            return False
-
-
-