Mercurial > repos > sanbi-uwc > neo4j_datatypes

changeset 17:969c57578047 draft

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planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
author sanbi-uwc
date Wed, 18 May 2016 10:11:25 -0400
parents de002a093129
children 3472a853df10
files neo4j.py
diffstat 1 files changed, 80 insertions(+), 62 deletions(-) [+]
line wrap: on
line diff
--- a/neo4j.py	Wed May 18 10:03:02 2016 -0400
+++ b/neo4j.py	Wed May 18 10:11:25 2016 -0400
@@ -7,8 +7,7 @@
 
 from galaxy.datatypes.images import Html
 from galaxy.datatypes.data import Data, Text
-
-# from galaxy.datatypes.metadata import MetadataElement
+#from galaxy.datatypes.metadata import MetadataElement
 
 gal_Log = logging.getLogger(__name__)
 verbose = True
@@ -20,6 +19,54 @@
     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'
+    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"""
@@ -72,73 +119,44 @@
     composite_type = 'basic'
     allow_datatype_change = False
 
+
     def __init__(self, **kwd):
         Data.__init__(self, **kwd)
         self.add_composite_file('neostore', substitute_name_with_metadata='neostore', is_binary=True)
         self.add_composite_file('neostore.id', substitute_name_with_metadata='neostore', is_binary=True)
-        self.add_composite_file('neostore.counts.db.a', substitute_name_with_metadata='neostore_count_file',
-                                is_binary=True)
-        self.add_composite_file('neostore.counts.db.b', substitute_name_with_metadata='neostore_count_file',
-                                is_binary=True)
-        self.add_composite_file('neostore.labeltokenstore.db',
-                                substitute_name_with_metadata='neostore_labeltokenstore_db_file', is_binary=True)
-        self.add_composite_file('neostore.labeltokenstore.db.id',
-                                substitute_name_with_metadata='neostore_labeltokenstore_db_file', is_binary=True)
-        self.add_composite_file('neostore.labeltokenstore.db.names',
-                                substitute_name_with_metadata='neostore_labeltokenstore_db_file', is_binary=True)
-        self.add_composite_file('neostore.labeltokenstore.db.names.id',
-                                substitute_name_with_metadata='neostore_labeltokenstore_db_file', is_binary=True)
-        self.add_composite_file('neostore.nodestore.db', substitute_name_with_metadata='neostore_nodestore_file',
-                                is_binary=True)
-        self.add_composite_file('neostore.nodestore.db.id', substitute_name_with_metadata='neostore_nodestore_file',
-                                is_binary=True)
-        self.add_composite_file('neostore.nodestore.db.labels', substitute_name_with_metadata='neostore_nodestore_file',
-                                is_binary=True)
-        self.add_composite_file('neostore.nodestore.db.labels.id',
-                                substitute_name_with_metadata='neostore_nodestore_file', is_binary=True)
+        self.add_composite_file('neostore.counts.db.a', substitute_name_with_metadata='neostore_count_file', is_binary=True)
+        self.add_composite_file('neostore.counts.db.b', substitute_name_with_metadata='neostore_count_file', is_binary=True)
+        self.add_composite_file('neostore.labeltokenstore.db', substitute_name_with_metadata='neostore_labeltokenstore_db_file', is_binary=True)
+        self.add_composite_file('neostore.labeltokenstore.db.id', substitute_name_with_metadata='neostore_labeltokenstore_db_file', is_binary=True)
+        self.add_composite_file('neostore.labeltokenstore.db.names', substitute_name_with_metadata='neostore_labeltokenstore_db_file', is_binary=True)
+        self.add_composite_file('neostore.labeltokenstore.db.names.id', substitute_name_with_metadata='neostore_labeltokenstore_db_file', is_binary=True)
+        self.add_composite_file('neostore.nodestore.db', substitute_name_with_metadata='neostore_nodestore_file', is_binary=True)
+        self.add_composite_file('neostore.nodestore.db.id', substitute_name_with_metadata='neostore_nodestore_file', is_binary=True)
+        self.add_composite_file('neostore.nodestore.db.labels', substitute_name_with_metadata='neostore_nodestore_file', is_binary=True)
+        self.add_composite_file('neostore.nodestore.db.labels.id', substitute_name_with_metadata='neostore_nodestore_file', is_binary=True)
 
-        self.add_composite_file('neostore.propertystore.db',
-                                substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
-        self.add_composite_file('neostore.propertystore.db.id',
-                                substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
-        self.add_composite_file('neostore.propertystore.db.arrays',
-                                substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
-        self.add_composite_file('neostore.propertystore.db.arrays.id',
-                                substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
-        self.add_composite_file('neostore.propertystore.db.index',
-                                substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
-        self.add_composite_file('neostore.propertystore.db.index.id',
-                                substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
-        self.add_composite_file('neostore.propertystore.db.index.keys',
-                                substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
-        self.add_composite_file('neostore.propertystore.db.index.keys.id',
-                                substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
-        self.add_composite_file('neostore.propertystore.db.strings',
-                                substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
-        self.add_composite_file('neostore.propertystore.db.strings.id',
-                                substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
+        self.add_composite_file('neostore.propertystore.db', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
+        self.add_composite_file('neostore.propertystore.db.id', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
+        self.add_composite_file('neostore.propertystore.db.arrays', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
+        self.add_composite_file('neostore.propertystore.db.arrays.id', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
+        self.add_composite_file('neostore.propertystore.db.index', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
+        self.add_composite_file('neostore.propertystore.db.index.id', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
+        self.add_composite_file('neostore.propertystore.db.index.keys', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
+        self.add_composite_file('neostore.propertystore.db.index.keys.id', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
+        self.add_composite_file('neostore.propertystore.db.strings', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
+        self.add_composite_file('neostore.propertystore.db.strings.id', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
 
-        self.add_composite_file('neostore.relationshipgroupstore.db',
-                                substitute_name_with_metadata='neostore_relationship_group_file', is_binary=True)
-        self.add_composite_file('neostore.relationshipgroupstore.db.id',
-                                substitute_name_with_metadata='neostore_relationship_group_file', is_binary=True)
-        self.add_composite_file('neostore.relationshipstore.db',
-                                substitute_name_with_metadata='neostore_relationship_file', is_binary=True)
-        self.add_composite_file('neostore.relationshipstore.db.id',
-                                substitute_name_with_metadata='neostore_relationship_file', is_binary=True)
-        self.add_composite_file('neostore.relationshiptypestore.db.names',
-                                substitute_name_with_metadata='neostore_relationship_type_file', is_binary=True)
-        self.add_composite_file('neostore.relationshiptypestore.db.names.id',
-                                substitute_name_with_metadata='neostore_relationship_type_file', is_binary=True)
-        self.add_composite_file('neostore.schemastore.db', substitute_name_with_metadata='neostore_schema_store_file',
-                                is_binary=True)
-        self.add_composite_file('neostore.schemastore.db.id',
-                                substitute_name_with_metadata='neostore_schema_store_file', is_binary=True)
-        self.add_composite_file('neostore.transaction.db.0', substitute_name_with_metadata='neostore_count_file',
-                                is_binary=True)
+        self.add_composite_file('neostore.relationshipgroupstore.db', substitute_name_with_metadata='neostore_relationship_group_file', is_binary=True)
+        self.add_composite_file('neostore.relationshipgroupstore.db.id', substitute_name_with_metadata='neostore_relationship_group_file', is_binary=True)
+        self.add_composite_file('neostore.relationshipstore.db', substitute_name_with_metadata='neostore_relationship_file', is_binary=True)
+        self.add_composite_file('neostore.relationshipstore.db.id', substitute_name_with_metadata='neostore_relationship_file', is_binary=True)
+        self.add_composite_file('neostore.relationshiptypestore.db.names', substitute_name_with_metadata='neostore_relationship_type_file', is_binary=True)
+        self.add_composite_file('neostore.relationshiptypestore.db.names.id', substitute_name_with_metadata='neostore_relationship_type_file', is_binary=True)
+        self.add_composite_file('neostore.schemastore.db', substitute_name_with_metadata='neostore_schema_store_file', is_binary=True)
+        self.add_composite_file('neostore.schemastore.db.id', substitute_name_with_metadata='neostore_schema_store_file', is_binary=True)
+        self.add_composite_file('neostore.transaction.db.0', substitute_name_with_metadata='neostore_count_file', is_binary=True)
 
 
 if __name__ == '__main__':
     import doctest
-
-    doctest.testmod(sys.modules[__name__])
+    doctest.testmod(sys.modules[__name__])
\ No newline at end of file