Merge pull request #67 from filak/dev-1.6.7

Support for broaderQualifier

flask-app/application/modules/routes.py

@@ -836,11 +836,12 @@ def compare(dui):
 
     if dui:
         dui = dui.replace('?', '').strip()
-        dview_data = sparql.getSparqlData('descriptor_view', query=dui, output='tsv', key=dui + '_diff', cache=cache)
+        otype = getObjType(dui)
+        dview_data = sparql.getSparqlData('descriptor_view', query=dui, output='tsv', key=dui + '_diff', cache=cache, otype=otype)
         if dview_data:
             dview = mtu.cleanDescView(dview_data)
 
-        prev_data = sparql.getSparqlDataExt(dui, 'tsv', year=year, key=dui + '_prev_' + year, cache=cache)
+        prev_data = sparql.getSparqlDataExt(dui, 'tsv', year=year, key=dui + '_prev_' + year, cache=cache, otype=otype)
         if prev_data:
             prev = mtu.cleanDescView(prev_data)
 
@@ -1129,7 +1130,8 @@ def search(dui, action):
             tree = sparql.parseSparqlData(tree_data)
 
             started = timer()
-            dview = sparql.getSparqlData('descriptor_view_trx', query=dui, output='tsv', key=dui + '_dview', cache=cache)
+            otype = getObjType(dui)
+            dview = sparql.getSparqlData('descriptor_view_trx', query=dui, output='tsv', key=dui + '_dview', cache=cache, otype=otype)
             show_elapsed(t0, started=started, tag='dview_data')
 
             dview = mtu.cleanDescView(dview)
@@ -1702,6 +1704,13 @@ def logout():
 
 # Functions, context_processors, etc.
 
+def getObjType(dui):
+    otype = "Descriptor"
+    if dui.startswith('Q'):
+        otype = "Qualifier"
+    return otype
+
+
 def checkWorker(worker):
     try:
         with closing(requests.get(worker, timeout=10)) as r:

flask-app/application/modules/sparql.py

@@ -35,7 +35,7 @@ def show_elapsed(begin, tag=''):
     return elapsed
 
 
-def getSparqlData(template, query='', show='', status='', top='', tn='', concept='',
+def getSparqlData(template, query='', show='', status='', top='', tn='', concept='', otype='Descriptor',
                   output='json', slang=None, lang=None, scr=None, key=None, cache=None):
 
     t0 = timer()
@@ -58,7 +58,7 @@ def getSparqlData(template, query='', show='', status='', top='', tn='', concept
 
     lang_umls = mtu.getLangCodeUmls(lang)
 
-    sparql = render_template('sparql/' + template + '.sparql', query=cleanQuery(query),
+    sparql = render_template('sparql/' + template + '.sparql', query=cleanQuery(query), otype=otype,
                              show=show, status=status, top=top, tn=tn, toptn=toptn, concept=concept,
                              lang=lang, lang_umls=lang_umls, slang=slang, scr=scr)
 
@@ -92,15 +92,15 @@ def getSparqlData(template, query='', show='', status='', top='', tn='', concept
         app.logger.error('%s \n\n %s \n\n %s \n\n %s', endpoint, template, query, str(err))
 
 
-def getSparqlDataExt(dui, output, year='', key=None, cache=None):
+def getSparqlDataExt(dui, output, year='', key=None, cache=None, otype='Descriptor'):
 
     if key and cache:
         if cache.get(key):
             return cache.get(key)
 
     endpoint = app.config['MESH_RDF']
 
-    dview_ext_query = render_template('sparql/descriptor_view.sparql', query=dui, official=True, year=year)
+    dview_ext_query = render_template('sparql/descriptor_view.sparql', query=dui, official=True, year=year, otype=otype)
     # print(dview_ext_query)
 
     query = mtu.encodeMeshRdfQuery(dview_ext_query)
@@ -343,7 +343,7 @@ def parseDescriptor(descriptor):
             val = row['label']['value']
             qualifiers.append({'ui': ui, 'val': val})
 
-        elif p in ['broaderDescriptor', 'seeAlso', 'pharmacologicalAction', 'preferredTerm']:
+        elif p in ['broaderDescriptor', 'broaderQualifier', 'seeAlso', 'pharmacologicalAction', 'preferredTerm']:
             if p == 'preferredTerm':
                 result['labels']['prefTerm'] = row['o']['value'].replace(app.config['SOURCE_NS'], '')
             else:

flask-app/application/templates/sparql/descriptor_view.sparql

@@ -4,7 +4,7 @@
 {% include 'sparql/_namespaces.sparql' %}
 {% endif %}
 
-## Descriptor view query v1.0
+## Descriptor view query v1.1
 
 SELECT DISTINCT * {
 {SELECT ?p ?o
@@ -63,10 +63,10 @@ WHERE {
 }} UNION {
 SELECT ?p ?o
 WHERE {
-    BIND(meshv:narrowerDescriptor as ?p)
+    BIND(meshv:narrower{{ otype }} as ?p)
     ?id ?px mesh:{{ query }} .
     ?id rdfs:label ?val
-    FILTER(?px IN(meshv:broaderDescriptor))
+    FILTER(?px IN(meshv:broader{{ otype }}))
     FILTER(!isLiteral(?id))
     BIND(STR(?val) AS ?o)
 }} UNION {
@@ -89,3 +89,4 @@ WHERE {
 }}
 
 } ORDER BY ?p ?o
+

flask-app/application/templates/sparql/descriptor_view_trx.sparql

@@ -1,7 +1,7 @@
 {% include 'sparql/_namespaces.sparql' %}
 PREFIX a:  <http://aaa>
 
-## Descriptor trx view query v1.0
+## Descriptor trx view query v1.1
 
 SELECT DISTINCT * {
 {SELECT ?p ?o
@@ -61,8 +61,8 @@ WHERE {
 }} UNION {
 SELECT ?p ?o
 WHERE {
-    BIND(meshv:narrowerDescriptor as ?p)
-    ?id meshv:broaderDescriptor mesh:{{ query }} .
+    BIND(meshv:narrower{{ otype }} as ?p)
+    ?id meshv:broader{{ otype }} mesh:{{ query }} .
     ?id rdfs:label ?val
     FILTER(!isLiteral(?id))
     BIND(STR(?val) AS ?o)

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

@@ -1,4 +1,4 @@
-## Base export query v1.0
+## Base export query v1.1
 
 {% include 'sparql/_namespaces.sparql' %}
 
@@ -36,6 +36,14 @@ WHERE {
     ?ndx meshv:broaderDescriptor ?d .
     ?ndx meshv:identifier ?nd
   }
+  OPTIONAL {
+    ?d meshv:broaderQualifier ?bdx .
+    ?bdx meshv:identifier ?bd
+  }
+  OPTIONAL {
+    ?ndx meshv:broaderQualifier ?d .
+    ?ndx meshv:identifier ?nd
+  }
   OPTIONAL {
     ?d meshv:seeAlso ?rdx .
     ?rdx meshv:identifier ?rd
@@ -52,3 +60,4 @@ WHERE {
 }
 GROUP BY ?dui ?cui ?dtype ?den ?trx ?notrx ?active ?crt ?est ?nlm ?cas ?rn  
 ###LIMIT 100
+