Mercurial > repos > sanbi-uwc > neo4j_datatypes

changeset 10:ce5df18856ee draft

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planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 31097469911a6200b265a1a8dcea285b3a65b6a9
author sanbi-uwc
date Wed, 18 May 2016 09:17:11 -0400
parents f4714c838f27
children 6a177f046b73
files datatypes_conf.xml neo4j.py
diffstat 2 files changed, 8 insertions(+), 56 deletions(-) [+]
line wrap: on
line diff
--- a/datatypes_conf.xml	Wed May 18 09:10:51 2016 -0400
+++ b/datatypes_conf.xml	Wed May 18 09:17:11 2016 -0400
@@ -4,8 +4,8 @@
         <datatype_file name="neo4j.py"/>
     </datatype_files>
     <registration>
-        <datatype extension="neo4j" type="galaxy.datatypes.neo4j:Neo4j" mimetype="text/html"  display_in_upload="false"/>
-        <datatype extension="neostore" type="galaxy.datatypes.neo4j:Neo4jDB" mimetype="text/html"  display_in_upload="false"/>
+        <datatype extension="neo4j" type="galaxy.datatypes.neo4j:Neo4j"  display_in_upload="false"/>
+        <datatype extension="neostore" type="galaxy.datatypes.neo4j:Neo4jDB"   display_in_upload="false"/>
     </registration>
     <sniffers>
         <sniffer type="galaxy.datatypes.neo4j:Neo4j"/>
--- a/neo4j.py	Wed May 18 09:10:51 2016 -0400
+++ b/neo4j.py	Wed May 18 09:17:11 2016 -0400
@@ -5,68 +5,20 @@
 import sys
 import os
 
-from galaxy.datatypes.images import Html
+#from galaxy.datatypes.images import Html
 from galaxy.datatypes.data import Data, Text, Html
-from galaxy.datatypes.metadata import MetadataElement
+#from galaxy.datatypes.metadata import MetadataElement
 
 gal_Log = logging.getLogger(__name__)
 verbose = True
 
 
-class Neo4j(Html):
+class Neo4j(object):
     """
     base class to use for neostore datatypes
     derived from html - composite datatype elements
     stored in extra files path
     """
-    MetadataElement( name='neostore', default=None, desc='Neo4j NeoStore File', readonly=True, visible=True, set_in_upload=True, no_value=None )
-    MetadataElement( name='neostore_count_file', default=None, desc='Neo4j Count File', readonly=True, visible=True, set_in_upload=True, no_value=None )
-    MetadataElement( name="neostore_labeltokenstore_db_file", default=None, desc="Neostore LabelTokenStore File", readonly=True, visible=True, no_value=None )
-    MetadataElement( name="neostore_nodestore_file", default=None, desc="Neostore NodeStore File", readonly=True, visible=True, no_value=None)
-    MetadataElement( name="neostore_propertystore_file", default=None, desc="Neostore Property Store File", readonly=True, visible=True, no_value=None)
-    MetadataElement( name="neostore_relationship_group_file", default=None, desc="Neostore Relationship Group File", readonly=True, visible=True, no_value=None)
-    MetadataElement( name="neostore_relationship_file", default=None, desc="Neostore Relationship File", readonly=True, visible=True, no_value=None)
-    MetadataElement( name="neostore_relationship_type_file", default=None, desc="Neostore Relationship Type File", readonly=True, visible=True, no_value=None)
-    MetadataElement( name="neostore_schema_store_file", default=None, desc="Neostore Schema Store File", readonly=True, visible=True, no_value=None)
-    MetadataElement( name="neostore_transaction_db_file", default=None, desc="Neostore Transaction File", readonly=True, visible=True, no_value=None)
-
-    composite_type = 'auto_primary_file'
-    #composite_type = 'basic'
-    allow_datatype_change = False
-    file_ext = 'neo4j'
-
-    def generate_primary_file( self, dataset=None ):
-        rval = ['<html><head><title>Neo4j Galaxy Composite Dataset </title></head><p/>']
-        rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
-        for composite_name, composite_file in self.get_composite_files( dataset=dataset ).iteritems():
-            fn = composite_name
-            opt_text = ''
-            if composite_file.optional:
-                opt_text = ' (optional)'
-            if composite_file.get('description'):
-                rval.append( '<li><a href="%s" type="application/binary">%s (%s)</a>%s</li>' % ( fn, fn, composite_file.get('description'), opt_text ) )
-            else:
-                rval.append( '<li><a href="%s" type="application/binary">%s</a>%s</li>' % ( fn, fn, opt_text ) )
-        rval.append( '</ul></div></html>' )
-        return "\n".join( rval )
-
-    def regenerate_primary_file(self, dataset):
-        """
-        cannot do this until we are setting metadata
-        """
-        efp = dataset.extra_files_path
-        flist = os.listdir(efp)
-        rval = ['<html><head><title>Files for Composite Dataset %s</title></head><body><p/>Composite %s contains:<p/><ul>' % (dataset.name, dataset.name)]
-        for i, fname in enumerate(flist):
-            sfname = os.path.split(fname)[-1]
-            f, e = os.path.splitext(fname)
-            rval.append( '<li><a href="%s">%s</a></li>' % ( sfname, sfname) )
-        rval.append( '</ul></body></html>' )
-        f = file(dataset.file_name, 'w')
-        f.write("\n".join( rval ))
-        f.write('\n')
-        f.close()
-
     def get_mime(self):
         """Returns the mime type of the datatype"""
         return 'text/html'
@@ -115,6 +67,8 @@
 class Neo4jDB(Neo4j, Data):
     """Class for neo4jDB database files."""
     file_ext = 'neostore'
+    allow_datatype_change = False
+    composite_type = 'basic'
 
     def __init__(self, **kwd):
         Data.__init__(self, **kwd)
@@ -155,6 +109,4 @@
 
 if __name__ == '__main__':
     import doctest
-
-
-    doctest.testmod(sys.modules[__name__])
+    doctest.testmod(sys.modules[__name__])
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