Add RDF comparator and remove use of "name" col from "biomarkers" table

setup.cfg

@@ -15,9 +15,9 @@ namespace_packages = edrn
 package_dir =
     = src
 packages = find:
-python_requires = >= 3.9, <3.11
+python_requires = >= 3.9, <3.12
 install_requires =
-    rdflib ~= 6.1.0
+    rdflib ~= 7.0.0
     pymysql ~= 1.0.2
     pyramid ~= 2.0
 
@@ -49,5 +49,4 @@ console_scripts =
     report52            = edrn.bmdb.report52:main
     zombie              = edrn.bmdb.maureen_zombie_report:main
     kristen             = edrn.bmdb.kristen_report:main
-
-
+    rdfcompare          = edrn.bmdb.compare:main

src/edrn/bmdb/rdf.py

@@ -52,14 +52,14 @@ def publications(connection, graph, public):
 
 def biomarkers(connection, graph, public):
     bioType, bsdType = rdflib.URIRef(_bmdb.Biomarker), rdflib.URIRef(_bmdb.BiomarkerStudyData)
-    query = 'SELECT id, name, shortName, description, qastate, phase, security, type, isPanel, panelID, curatorNotes FROM biomarkers'
+    query = 'SELECT id, shortName, description, qastate, phase, security, type, isPanel, panelID, curatorNotes FROM biomarkers'
     if public:
         query += " WHERE qastate != 'Under Review'"
     biocursor = connection.cursor()
     biocursor.execute("SET CHARACTER_SET_RESULTS='latin1'")
     biocursor.execute(query)
     # TODO: get created & modified datetimes?
-    for dbid, name, shortName, desc, qaState, phase, security, btype, isPanel, panelID, curatorNotes in biocursor.fetchall():
+    for dbid, shortName, desc, qaState, phase, security, btype, isPanel, panelID, curatorNotes in biocursor.fetchall():
         isPublicBiomaker = qaState == 'Accepted'
 
         subject   = rdflib.URIRef('{}biomarkers/view/{}'.format(_biomarkerBase, dbid))

src/edrn/bmdb/server.py

@@ -62,7 +62,9 @@ def __init__(self, request):
 
     def includePrivate(self):
         '''Return true if the request for this view wants *all* entities or False if just the public ones'''
-        return self.request.params.get('all') == os.getenv('TOKEN')
+        supplied, expected = self.request.params.get('all'), os.getenv('TOKEN')
+        rc = supplied == expected
+        return rc
 
     def serialize(self, graph):
         '''Serialize the given RDF ``graph`` into an HTTP response'''