Version 1.2.8

flask-app/!!build__mtw-server-win-service.bat

@@ -16,8 +16,7 @@ echo rem call %targetDir%\%fileHandle%.exe stop
 echo.
 echo Building %srcFile% ...
 
-rem CALL c:\Python37\Scripts\pyinstaller.exe --log-level ERROR --onedir -y --hidden-import=_cffi_backend --distpath %targetDir% %srcFile% >> %logFile% 2>&1
-CALL c:\Python37\Scripts\pyinstaller.exe --log-level ERROR --onefile --hidden-import=_cffi_backend --distpath %targetDir% %srcFile% >> %logFile% 2>&1
+CALL c:\Python37\Scripts\pyinstaller.exe --log-level ERROR --onefile --hidden-import=_cffi_backend --add-data mtw_utils/pyuca/*.txt;pyuca --distpath %targetDir% %srcFile% >> %logFile% 2>&1
 
 echo  - Done!
 echo.

flask-app/!!build__mtw-server-win-worker.bat

@@ -15,8 +15,7 @@ echo rem call %targetDir%\%fileHandle%.exe stop
 echo.
 echo Building %srcFile% ...
 
-rem CALL c:\Python37\Scripts\pyinstaller.exe --log-level ERROR --onedir -y --distpath %targetDir% %srcFile% >> %logFile% 2>&1
-CALL c:\Python37\Scripts\pyinstaller.exe --log-level ERROR --onefile --distpath %targetDir% %srcFile% >> %logFile% 2>&1
+CALL c:\Python37\Scripts\pyinstaller.exe --log-level ERROR --onefile --add-data mtw_utils/pyuca/*.txt;pyuca --distpath %targetDir% %srcFile% >> %logFile% 2>&1
 
 echo  - Done!
 

flask-app/!!build__set-mtw-admin.bat

@@ -12,7 +12,6 @@ echo. > %logFile%
 echo.
 echo Building %srcFile% ...
 
-rem CALL c:\Python37\Scripts\pyinstaller.exe --log-level ERROR --onedir -y --hidden-import=_cffi_backend --distpath %targetDir% %srcFile% >> %logFile% 2>&1
 CALL c:\Python37\Scripts\pyinstaller.exe --log-level ERROR --onefile --hidden-import=_cffi_backend --distpath %targetDir% %srcFile% >> %logFile% 2>&1
 
 echo.

flask-app/instance/conf/mesh.ttl

@@ -7,9 +7,9 @@
 @prefix fuseki:  <http://jena.apache.org/fuseki#> .
 @prefix meshv:   <http://id.nlm.nih.gov/mesh/vocab#> .
 @prefix mesht:   <http://www.medvik.cz/schema/mesh/vocab/#> .
-@prefix meshcs:  <http://mesh.medvik.cz/link/> .
+@prefix meshx:   <http://mesh.medvik.cz/link/> .
 
-### Version 1.0.1
+### Version 1.0.2
 
 ## Initialize text query
 [] ja:loadClass       "org.apache.jena.query.text.TextQuery" .

flask-app/instance/conf/mtw.ini

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# *** Config version 0.1.5 ***
+# *** Config version 0.1.6 ***
 ### Important values are marked with !  ###
 ### ! This file MUST BE UTF-8 encoded ! ###
 ### ! Restart the App after modifying ! ###
@@ -105,9 +105,9 @@ TARGET_NS = http://mesh.medvik.cz/link/
 
 ### Default values:
 #SPARQL_HOST = http://localhost:3030/
+#SPARQL_DATASET = mesh
 
 ### DO NOT EDIT BELOW THIS LINE ###
-#SPARQL_DATASET = mesh
 
 ### MeSH RDF SPARQL Endpoint
 #MESH_RDF = http://id.nlm.nih.gov/mesh/sparql

flask-app/mtw-server-win-service.py

@@ -32,16 +32,16 @@ def run_server():
     ##asyncio.set_event_loop(asyncio.new_event_loop())
 
     http_server = HTTPServer(WSGIContainer(app))
-    http_server.listen(SERVER_PORT)
+    http_server.listen( int( os.environ.get('MTW_SERVER_PORT', SERVER_PORT) ) )
 
     IOLoop.instance().start()
 
 def stop_server():
     IOLoop.instance().stop()
 
 class Service(win32serviceutil.ServiceFramework):
-    _svc_name_ = SERVICE_NAME
-    _svc_display_name_ = SERVICE_DISPLAY_NAME
+    _svc_name_ = SERVICE_NAME + '-' + str( os.environ.get('MTW_SERVER_PORT', SERVER_PORT) )
+    _svc_display_name_ = SERVICE_DISPLAY_NAME + ' - port:' + str( os.environ.get('MTW_SERVER_PORT', SERVER_PORT) )
     _svc_description_ = SERVICE_DESCRIPTION
 
     def __init__(self, *args, **kwargs):

flask-app/mtw-server-win-worker.py

@@ -26,16 +26,16 @@ def run_server():
         app.template_folder = os.path.join(os.path.dirname(sys.executable), 'templates')
 
     http_server = HTTPServer(WSGIContainer(app))
-    http_server.listen(SERVER_PORT)
+    http_server.listen( int( os.environ.get('MTW_WORKER_PORT', SERVER_PORT) ) )
 
     IOLoop.instance().start()
 
 def stop_server():
     IOLoop.instance().stop()
 
 class Service(win32serviceutil.ServiceFramework):
-    _svc_name_ = SERVICE_NAME
-    _svc_display_name_ = SERVICE_DISPLAY_NAME
+    _svc_name_ = SERVICE_NAME + '-' + str( os.environ.get('MTW_WORKER_PORT', SERVER_PORT) )
+    _svc_display_name_ = SERVICE_DISPLAY_NAME + ' - port:' + str( os.environ.get('MTW_WORKER_PORT', SERVER_PORT) )
     _svc_description_ = SERVICE_DESCRIPTION
 
     def __init__(self, *args, **kwargs):

flask-app/mtw/flask.py

@@ -46,7 +46,7 @@ def __call__(self, environ, start_response):
 
 app.config.update(dict(
     APP_NAME = 'MTW',
-    APP_VER = '1.2.7',
+    APP_VER = '1.2.8',
     API_VER = '1.0.0',
     APP_URL = '/mtw',
     DEFAULT_THEME = 'slate',
@@ -1244,8 +1244,8 @@ def manage(action):
     ### YYYY_lookups.json.gz
     exports['lookups'] = mtu.getStatsFpath('lookups', ext='json.gz')
 
-    ### YYYY_lookups_notes.json.gz
-    exports['lookups_notes'] = mtu.getStatsFpath('lookups_notes', ext='json.gz')
+    ### YYYY_lookups_rest.json.gz
+    exports['lookups_rest'] = mtu.getStatsFpath('lookups_rest', ext='json.gz')
 
     ### YYYY_js_all.json.gz
     exports['js_all'] = mtu.getStatsFpath('js_all', ext='json.gz')
@@ -1284,8 +1284,8 @@ def manage(action):
         show_lookups_exports = True
 
     show_marc_exports = False
-    lookups_notes = mtu.getTempFpath('lookups_notes')
-    if lookups_notes.is_file():
+    lookups_rest = mtu.getTempFpath('lookups_rest')
+    if lookups_rest.is_file():
         show_marc_exports = True
 
     lpath = mtu.getLockFpath('stats')
@@ -1328,7 +1328,7 @@ def update_stats(stat):
         flash(msg, 'warning')
         return render_template('errors/error_page.html', errcode=403, error=msg), 403
 
-    if stat not in ('initial','actual','umls','lookups','lookups_notes','js_all','js_elastic','xml_desc','xml_qualif','marc'):
+    if stat not in ('initial','actual','umls','lookups','lookups_rest','js_all','js_elastic','xml_desc','xml_qualif','marc'):
         msg = 'Unknown params for update_stats'
         flash(msg, 'danger')
         return render_template('errors/error_page.html', errcode=404, error=msg), 404

flask-app/mtw/templates/manage.html

@@ -98,7 +98,7 @@ <h5>Initial stats </h5>
 
     <ul class="list-inline mb-2">
       <li class="list-inline-item mt-2">
-        <h4>Exports <small class="text-warning">Always do Checks before exports!</small></h4>
+        <h4>Exports <small class="text-warning">Always do Checks before!</small></h4>
       </li>
       <li class="list-inline-item float-right">
       </li>
@@ -154,10 +154,10 @@ <h5>UMLS TSV</h5>
 
     <div class="row mb-4">
       <div class="col">
-        <h5>Base &amp; Notes<small class="text-success"> [generate to enable more exports]</small></h5>
+        <h5>Base Exports<small class="text-success"> [generate to enable more exports]</small></h5>
           <form action="{{ url_for('update_stats', stat='lookups') }}" method="post">
             <input type="hidden" name="_csrf_token" value="{{ csrf_token() }}">
-            <button class="btn btn-sm btn-success mb-2" type="submit" title="Create export Base file (JSON)" {{ export_disabled }}>
+            <button class="btn btn-sm btn-success mb-2" type="submit" title="Create Base-export file (JSON)" {{ export_disabled }}>
               Generate Base
                 </button>
 
@@ -173,14 +173,14 @@ <h5>Base &amp; Notes<small class="text-success"> [generate to enable more export
 
           </form>
 
-          <form action="{{ url_for('update_stats', stat='lookups_notes') }}" method="post">
+          <form action="{{ url_for('update_stats', stat='lookups_rest') }}" method="post">
             <input type="hidden" name="_csrf_token" value="{{ csrf_token() }}">
-            <button class="btn btn-sm btn-success mb-2" type="submit" title="Create export Notes file (JSON)" {{ export_disabled }}>
-              Generate Notes
+            <button class="btn btn-sm btn-success mb-2" type="submit" title="Create Base-rest file (JSON)" {{ export_disabled }}>
+              Generate Rest
                 </button>
 
-          {% if exports['lookups_notes'] %}
-            {% set file = exports['lookups_notes'] %}
+          {% if exports['lookups_rest'] %}
+            {% set file = exports['lookups_rest'] %}
             <p class="mb-1">
               [{{ file['fdate'] }}]
               <a href="{{ url_for('download', fname=file['fname']) }}" title="Download file" target="_blank">
@@ -241,11 +241,11 @@ <h5>Settings</h5>
             <div class="form-group mb-2">
               <div class="custom-control custom-radio custom-control-inline">
                 <input type="radio" id="radioMarcTreeDef" name="tree_style" value="def" class="custom-control-input" {{ def_checked }}>
-                <label class="custom-control-label" for="radioMarcTreeDef">Default tree (field 072)</label>
+                <label class="custom-control-label" for="radioMarcTreeDef">Default tree (fld 072)</label>
               </div>
               <div class="custom-control custom-radio custom-control-inline">
                 <input type="radio" id="radioMarcTreeCustom" name="tree_style" value="daw" class="custom-control-input" {{ daw_checked }}>
-                <label class="custom-control-label" for="radioMarcTreeCustom">Custom tree (field 686)</label>
+                <label class="custom-control-label" for="radioMarcTreeCustom">Custom tree (fld 686)</label>
               </div>
             </div>
 
@@ -342,6 +342,8 @@ <h5>JSON <small class="text-info">for Javascript</small></h5>
     <div class="row mb-4">
       <div class="col">
         <h5>JSON <small class="text-info">for Elastic</small></h5>
+
+        {% if show_marc %}
           <form action="{{ url_for('update_stats', stat='js_elastic') }}" method="post">
             <input type="hidden" name="_csrf_token" value="{{ csrf_token() }}">
 
@@ -364,6 +366,7 @@ <h5>JSON <small class="text-info">for Elastic</small></h5>
           {% endif %}
 
           </form>
+        {% endif %}
       </div>
     </div>
 

flask-app/mtw/templates/modals/edit-concept.html

@@ -249,11 +249,10 @@ <h4 class="modal-title">
 
             <button type="button" class="btn btn-link ml-3" data-dismiss="modal">Close</button>
 
-         {% if item['active'] == 'false' %}
-            <!-- set submit_inactive = 'disabled' -->
+         {% if item['active'] == 'false' and item['lang'] == config.TARGET_LANG and item['lang'] != 'en' %}
+            {% set submit_inactive = 'disabled' %}
          {% endif %}
 
-
         {% if session.ugroup in ('admin','manager','editor','contributor') and not isDbLocked() %}
           {% if descriptor.get('lockedBy','') %}
             {% if getLockedBy(session.userid, session.uname) == descriptor.get('lockedBy','') %}

flask-app/mtw/templates/sparql/concepts_terms.sparql

@@ -1,5 +1,4 @@
 ## Descriptor query v1.0
-## endpoint: http://localhost:3030/mesh/query
 
 {% include 'sparql/_namespaces.sparql' %}
 

flask-app/mtw/templates/sparql/exports/lookups_base.sparql

@@ -8,8 +8,6 @@ SELECT ?dui ?cui ?dtype ?den ?trx ?notrx ?active ?crt ?nlm ?rn ?cas
       (GROUP_CONCAT(DISTINCT ?bd ; separator='~') AS ?btd)
       (GROUP_CONCAT(DISTINCT ?nd ; separator='~') AS ?ntd)
       (GROUP_CONCAT(DISTINCT ?rd ; separator='~') AS ?rtd)
-      (GROUP_CONCAT(DISTINCT ?term ; separator='~') AS ?terms)
-      (GROUP_CONCAT(DISTINCT ?xterm ; separator='~') AS ?xterms)
 WHERE {
   ?d rdf:type ?dtype .
   FILTER(?dtype IN(meshv:TopicalDescriptor,meshv:GeographicalDescriptor,meshv:PublicationType,meshv:CheckTag,meshv:Qualifier))
@@ -18,29 +16,17 @@ WHERE {
   ?d meshv:dateCreated ?crt .
   OPTIONAL {
     ?d meshv:treeNumber ?tree .
-    ?tree rdfs:label ?trns .
+    ?tree meshv:active ?activetrn .
+    FILTER(?activetrn)
+    ?tree rdfs:label ?trns
   }
   ?d meshv:preferredConcept ?c .
   ?c meshv:identifier ?cui .
   ?c meshv:preferredTerm ?t .
   ?t meshv:prefLabel ?den .
   OPTIONAL {
     ?c mesht:preferredTerm ?tp .
-    ?tp mesht:prefLabel ?trx .
-  }
-  OPTIONAL {
-    ?c meshv:term|mesht:term ?ptt .
-    ?ptt meshv:prefLabel|mesht:prefLabel ?term .
-  }
-  OPTIONAL {
-    ?d meshv:concept ?ct .
-    ?ct meshv:preferredTerm|meshv:term ?tt .
-    ?tt meshv:prefLabel ?xterm .
-  }
-  OPTIONAL {
-    ?d mesht:concept ?ctt .
-    ?ctt mesht:preferredTerm|mesht:term ?ttt .
-    ?ttt mesht:prefLabel ?xterm .
+    ?tp mesht:prefLabel ?trx
   }
   OPTIONAL {
     ?d meshv:broaderDescriptor ?bdx .

flask-app/mtw/templates/sparql/exports/lookups_qualifs.sparql

@@ -1,4 +1,4 @@
-## Base export query v1.0
+## Base allowed qualifs export query v1.0
 
 {% include 'sparql/_namespaces.sparql' %}
 
@@ -7,8 +7,12 @@ SELECT ?dui
 WHERE {
   ?d rdf:type ?dtype .
   FILTER(?dtype IN(meshv:TopicalDescriptor,meshv:GeographicalDescriptor,meshv:PublicationType,meshv:CheckTag))
+  ?d meshv:active ?actived .
+  FILTER(?actived)
   ?d meshv:identifier ?dui .
   ?d meshv:allowableQualifier ?q .
+  ?q meshv:active ?activeq .
+  FILTER(?activeq)
   ?q meshv:identifier ?qui
 }
 GROUP BY ?dui

flask-app/mtw/templates/sparql/exports/umls.sparql

@@ -1,5 +1,4 @@
 ## UMLS export query v1.0
-## endpoint: http://localhost:3030/mesh/query
 
 {% include 'sparql/_namespaces.sparql' %}
 

flask-app/mtw/templates/sparql/tree-browse.sparql

@@ -1,5 +1,4 @@
 ## Browse query v1.0 - always with a treeNumber prefix !
-## endpoint: http://localhost:3030/mesh/query
 
 ## Preferred concepts AKA descriptors
 

flask-app/mtw/templates/sparql/tree.sparql

@@ -1,5 +1,4 @@
 ## Tree display query v1.0
-## endpoint: http://localhost:3030/mesh/query
 
 {% include 'sparql/_namespaces.sparql' ignore missing %}
 

flask-app/mtw/worker.py

@@ -64,7 +64,7 @@ def hello_world():
 @app.route('/refresh_stats/get:<stat>', methods=['GET','POST'])
 def refresh_stats(stat):
 
-    if stat in ('initial','actual','all','duplicates','lookups','lookups_notes'):
+    if stat in ('initial','actual','all','duplicates','lookups','lookups_rest'):
 
         app.logger.info('Stats gen started  ...')
         mtu.refreshStats(stat)

flask-app/mtw_requirements.txt

@@ -5,6 +5,7 @@ Flask==1.0.2
 Flask_SeaSurf==0.2.2
 flask_talisman==0.6.0
 Jinja2==2.10
+pyuca==1.2
 requests==2.20.0
 requests_futures==0.9.8
 bcrypt==3.1.4 # NOT python-bcrypt !!!

flask-app/mtw_sparql/mtw_sparql.py

@@ -44,7 +44,7 @@ def getSparqlData(template, query='', show='', status='', top='', tn='', concept
     out = {}
 
     try:
-        with closing(requests.post(endpoint, headers=headers, data=sparql.encode('utf-8'), timeout=300) ) as r:
+        with closing(requests.post(endpoint, headers=headers, data=sparql.encode('utf-8'), timeout=600) ) as r:
             if r.status_code == 200:
                 if output == 'json':
                     return r.json()
@@ -219,7 +219,7 @@ def parseSparqlStats(data, template):
 
         metadata['hits_cnt'] = hits_cnt
 
-    elif template in ('lookups_base','lookups_notes','lookups_qualifs'):
+    elif template in ('lookups_base','lookups_terms','lookups_notes','lookups_qualifs'):
         metadata['data'] = []
         items = data['head']['vars']
         for row in data['results']['bindings']: