Merge branch '0.27'

Author: dbrnz

mapserver/server/__init__.py

@@ -65,12 +65,6 @@ def initialise(app: Litestar):
     if settings['MAP_VIEWER']:
         if not os.path.exists(settings['FLATMAP_VIEWER']):
             exit(f'Missing {settings["FLATMAP_VIEWER"]} directory -- set FLATMAP_VIEWER environment variable to the full path')
-        try:
-            with open(Path(settings['FLATMAP_VIEWER']) / 'package.json') as fp:
-                package_json = json.load(fp)
-        except:
-            exit(f'Cannot read `package.json` in of standalone viewer in {settings["FLATMAP_VIEWER"]}')
-        settings['VIEWER_VERSION'] = package_json['version']
 
     settings['LOGGER'] = logger = logging.getLogger('litestar')
     logger.info(f'Starting flatmap server version {__version__}')
@@ -104,10 +98,15 @@ async def version() -> list[dict]:
     versions = [
         {'id': 'server', 'version': __version__},
     ]
-    if (viewer_version := settings.get('VIEWER_VERSION')) is not None:
-        versions.append(
-            {'id': 'viewer', 'version': viewer_version},
-        )
+    if settings['MAP_VIEWER']:
+        try:
+            with open(Path(settings['FLATMAP_VIEWER']) / 'package.json') as fp:
+                package_json = json.load(fp)
+            versions.append(
+                {'id': 'viewer', 'version': package_json['version']},
+            )
+        except:
+            settings['LOGGER'].error(f'Cannot read `package.json` in of standalone viewer in {settings["FLATMAP_VIEWER"]}')
     return versions
 
 #===============================================================================

tools/pmr_knowledge.py

@@ -92,7 +92,8 @@ def main():
     if args.knowledge is not None:
         if not os.path.isdir(args.knowledge) or not os.path.exists(args.knowledge):
             exit(f'Missing flatmap root directory: {args.knowledge}')
-        knowledge_store = KnowledgeStore(args.knowledge, create=False, read_only=False)
+        knowledge_store = KnowledgeStore(args.knowledge, create=False, read_only=False,
+                                         use_sckan=False, verbose=False)
         db = knowledge_store.db
         if db is None:
             exit('Unable to get knowledge database connection')
@@ -111,10 +112,11 @@ def main():
         term_index = json.load(open(args.index))
         for sckan_models in term_index:
             term = sckan_models['sckan_term']
+            db.execute('delete from pmr_models where term=?', (term, ))
             for model in sckan_models['cellmls']:
-                db.execute('delete from pmr_models where term=?', (term, ))
                 db.execute('insert into pmr_models (term, model, workspace, exposure, score) values (?, ?, ?, ?, ?)',
-                                                   (term, model['cellml'], model['workspace'], model.get('exposure'), model['score']))
+                                                   (term, model.get('cellml'), model.get('workspace'),
+                                                          model['exposure'], model.get('score', 1.0)))
     if args.exposures is not None:
         if (args.clean):
             db.execute('delete from pmr_metadata')
@@ -152,6 +154,21 @@ def main():
 
 #===============================================================================
 
+"""
+# APS PMR knowledge
+$ python tools/pmr_knowledge.py  \
+           --clean  \
+           --knowledge flatmaps  \
+           --exposures pmr/lung_exposure.json  \
+           --index pmr/lung2pmr.json
+$ python tools/pmr_knowledge.py  \
+           --knowledge flatmaps  \
+           --exposures aps/pmr-exposures.json \
+           --index aps/models/BloodVolumeControl.map2pmr.json
+"""
+
+#===============================================================================
+
 """
 
 [