Mercurial > repos > sanbi-uwc > ctb_report_datatypes

changeset 0:86807766529b draft

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planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 7b6b83e2ec95601a8af9c7d9e08159f08057d776
author sanbi-uwc
date Tue, 07 Jun 2016 10:05:14 -0400
parents
children 0921bdf0f5e1
files ctb_report.py datatypes_conf.xml
diffstat 2 files changed, 165 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ctb_report.py	Tue Jun 07 10:05:14 2016 -0400
@@ -0,0 +1,151 @@
+"""
+CtbReports Composite Dataset
+"""
+import logging
+import sys
+
+from galaxy.datatypes.data import Data
+from galaxy.datatypes.images import Html
+
+gal_Log = logging.getLogger(__name__)
+verbose = True
+
+
+class CtbReport(object):
+    """
+    base class to use for cbtreports datatypes
+    derived from html - composite datatype elements
+    stored in extra files path
+    """
+
+    def get_mime(self):
+        """Returns the mime type of the datatype"""
+        return 'text/html'
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        """Set the peek and blurb text"""
+        if not dataset.dataset.purged:
+            dataset.peek = 'CtbReports (multiple files)'
+            dataset.blurb = 'CtbReports (multiple files)'
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def display_peek(self, dataset):
+        """Create HTML content, used for displaying peek."""
+        try:
+            return dataset.peek
+        except Exception:
+            return "CtbReports (multiple files)"
+
+    def display_data(self, trans, data, preview=False, filename=None,
+                     to_ext=None, size=None, offset=None, **kwd):
+        """Documented as an old display method, but still gets called via tests etc
+        This allows us to format the data shown in the central pane via the "eye" icon.
+        """
+        if filename is not None and filename != "index":
+            # Change nothing - important for the unit tests to access child files:
+            return Data.display_data(self, trans, data, preview, filename,
+                                     to_ext, size, offset, **kwd)
+        if self.file_ext == "ctbreport":
+            title = "This is a CtbReports database"
+        msg = ""
+        try:
+            # Try to use any text recorded in the dummy index file:
+            handle = open(data.file_name, "rU")
+            msg = handle.read().strip()
+            handle.close()
+        except Exception:
+            pass
+        if not msg:
+            msg = title
+        # Galaxy assumes HTML for the display of composite datatypes,
+        return "<html><head><title>%s</title></head><body><pre>%s</pre></body></html>" % (title, msg)
+
+
+class CtbReportsNeo4j(CtbReport, Data):
+    """Class for neo4jDB database files."""
+    file_ext = 'ctbreportneo4j'
+    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.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)
+
+
+class CtbReportsJBrowse(CtbReport, Html):
+    """Class for ctb report jbrowse files."""
+    file_ext = 'ctbreportjbrowse'
+    composite_type = 'basic'
+    allow_datatype_change = False
+
+    def __init__(self, **kwd):
+        Html.__init__(self, **kwd)
+
+
+if __name__ == '__main__':
+    import doctest
+
+    doctest.testmod(sys.modules[__name__])
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml	Tue Jun 07 10:05:14 2016 -0400
@@ -0,0 +1,14 @@
+<?xml version="1.0"?>
+<datatypes>
+    <datatype_files>
+        <datatype_file name="ctb_report.py"/>
+    </datatype_files>
+    <registration>
+        <datatype extension="ctbreportneo4j" type="galaxy.datatypes.ctb_report:CtbReportsNeo4j" mimetype="text/html"  display_in_upload="false"/>
+        <datatype extension="ctbreportjbrowse" type="galaxy.datatypes.ctb_report:CtbReportsJBrowse" mimetype="text/html"  display_in_upload="false"/>
+    </registration>
+    <sniffers>
+        <sniffer type="galaxy.datatypes.ctb_report:CtbReportsNeo4j"/>
+        <sniffer type="galaxy.datatypes.ctb_report:CtbReportsJBrowse"/>
+    </sniffers>
+</datatypes>