small changes and bugfixes (portal shows only cdms-data)

Former-commit-id: 99f7400

.gitignore

@@ -20,3 +20,6 @@ doc*/build/*
 *.json
 *.dat
 *.log
+*.save
+mysqldatabase/*
+settings.py

nodes/VamdcSpeciesDB/node/update_functions.py

@@ -54,6 +54,14 @@
 
 ##    return charge + num_protons
 
+def get_node_list():
+    """
+    Returns a list of all nodes which are stored in the speciesdatabase
+    """
+    nodes = VamdcMemberDatabases.objects.all()
+
+    return nodes
+
 def get_node(nodename):
     """
     Returns a node instance of the node specified by the short_name
@@ -87,8 +95,8 @@ def get_species(nodename):
     query = q.Query()
     request = r.Request()
 
-
-    query_string = "SELECT SPECIES" 
+    query_string = "SELECT SPECIES"
+    query_string = "SELECT SPECIES WHERE ((InchiKey!='UGFAIRIUMAVXCW'))" 
     request.setnode(node)
     request.setquery(query_string)
 
@@ -200,7 +208,10 @@ def process_species(nodename, checkonly = False):
         # Insert names for the specie
         # The element ChemicalName cannot be repeated in current XSAMS versions. A list
         # of names has to be separated by ', ' therefore.
-        names = molecule.ChemicalName.split(', ')
+        try:
+            names = molecule.ChemicalName.split(', ')
+        except AttributeError:
+            names = []
         for name in names:
             insert_species_name(id, name, checkonly = checkonly)
 
@@ -265,22 +276,25 @@ def insert_molecule(molecule, member_db_id = 0, checkonly = False):
         print "DETERMINED Formula: %s" % molecule.StoichiometricFormula
 
     try:
-        if molecular_weight != int(molecule.MolecularWeight):
-            print "MISMATCH mass: %d does not match %d" % (molecular_weight, int(molecule.MolecularWeight))
+        if molecular_weight != int(float(molecule.MolecularWeight)):
+           print "MISMATCH mass: %d does not match %d" % (molecular_weight, int(float(molecule.MolecularWeight)))
     except AttributeError:
         print "DETERMINED mass: %d" % molecular_weight 
 
     if checkonly == False:
         specie = VamdcSpecies()
+
+        type_2 = VamdcSpeciesTypes.objects.get(id = 2)
+        member_database = VamdcMemberDatabases.objects.get(id = member_db_id)
 
         specie.id = inchikey
         specie.inchi = inchi
         specie.inchikey = inchikey
         specie.inchikey_duplicate_counter = 1
         specie.stoichiometric_formula = stoichiometricformula
-        specie.species_type = 2
+        specie.species_type = type_2
         specie.created = datetime.now()
-        specie.member_database = member_db_id
+        specie.member_database = member_database
         specie.mass_number = molecular_weight
         specie.charge = charge
 
@@ -328,6 +342,9 @@ def insert_atom(atom, member_db_id = 0, checkonly = False):
     elif len(ids) > 1:
         return None
 
+    print "Insert Atom: %s" % atom.InChIKey
+    print ids
+
     try:
         inchi = atom.InChI
     except:
@@ -350,20 +367,26 @@ def insert_atom(atom, member_db_id = 0, checkonly = False):
         if massnumber != int(atom.MassNumber):
             print "MISMATCH mass: %d does not match %d" % (massnumber, int(atom.MassNumber))
     except AttributeError:
+        atom.MassNumber = massnumber
         print "DETERMINED mass: %d" % massnumber
 
     if checkonly == False:
+        type_1 = VamdcSpeciesTypes.objects.get(id = 1)
+        member_database = VamdcMemberDatabases.objects.get(id = member_db_id)
         specie = VamdcSpecies()
 
         specie.id = atom.InChIKey
-        specie.inchi = atom.InChI
+        if atom.InChI[:6] == 'InChI=':
+            specie.inchi = atom.InChI
+        else:
+            specie.inchi = 'InChI='+atom.InChI
         specie.inchikey = atom.InChIKey
         specie.inchikey_duplicate_counter = 1
         specie.stoichiometric_formula = stoichiometricformula
-        specie.species_type = 2
+        specie.species_type = type_1
         specie.created = datetime.now()
-        specie.member_database = member_db_id
-        specie.mass_number = atom.massnumber
+        specie.member_database = member_database
+        specie.mass_number = atom.MassNumber
         specie.charge = charge
 
         #    charge = m.Charge
@@ -401,11 +424,13 @@ def insert_structural_formula(id, formula, checkonly = False):
             search_priority = 1
 
         if checkonly == False:
+            specie = VamdcSpecies.objects.get(id = id)
+            m_type_1 = VamdcMarkupTypes.objects.get(id = 1)
             structformula = VamdcSpeciesStructFormulae()
-            structformula.species = id
+            structformula.species = specie
             structformula.formula = formula
             # Currently only pure text markup-type can be retrieved via XSAMS
-            structformula.markup_type = 1
+            structformula.markup_type = m_type_1
             structformula.search_priority = search_priority
             structformula.created = datetime.now()
 
@@ -421,23 +446,26 @@ def insert_species_name(id, name, checkonly = False):
     # Check if it is already in the species-database
     names = VamdcSpeciesNames.objects.filter(species = id, name = name)
 
+    m_type_1 = VamdcMarkupTypes.objects.get(id = 1)
+
     # Insert name into the species-database if not found
     if len(names) == 0:
 
         # determine the search-priority. There is no automatic way to determine it, so new entries
         # will be added with the highest priority
         search_priorities = VamdcSpeciesNames.objects.filter(species = id).values_list("search_priority", flat = True)
         if len(search_priorities)>0:
-            search_priority = max(search_priorities)
+            search_priority = max(search_priorities)+1
         else:
             search_priority = 1
 
         if checkonly == False:
+            specie = VamdcSpecies.objects.get(id = id)
             speciesname = VamdcSpeciesNames()
-            speciesname.species = id
+            speciesname.species = specie
             speciesname.name = name
             # Currently only pure text markup-type can be retrieved via XSAMS
-            speciesname.markup_type = 1
+            speciesname.markup_type = m_type_1 
             speciesname.search_priority = search_priority
             speciesname.created = datetime.now()
 
@@ -449,17 +477,25 @@ def insert_member_db_speciesid(id, member_db_id, speciesid, checkonly = False):
     """
     Inserts the Species-ID available at a specific database node into
     the species-database. 
+
+    id = VamdcSpeciesID (Inchikey)
+    member_db_id = id of the database node
+    speciesid = id of the specie in the database node
+    checkonly = Boolean (False if the data is inserted in the database, otherwise it is only printed)
     """
     # Check if it is already in the species-database
     dbidentifier = VamdcMemberDatabaseIdentifiers.objects.filter(species = id, member_database = member_db_id, database_species_id = speciesid)
-
-    # Insert database-species-id into the species-database if not found
+    print "%20s %2d %20s" % (id, member_db_id, speciesid)
+   # Insert database-species-id into the species-database if not found
     if len(dbidentifier) == 0:
 
         if checkonly == False:
+            specie = VamdcSpecies.objects.get(id = id)
+            member_database = VamdcMemberDatabases.objects.get(id = member_db_id)
+
             dbidentifier = VamdcMemberDatabaseIdentifiers()
-            dbidentifier.species = id
-            dbidentifier.member_database = member_db_id
+            dbidentifier.species = specie
+            dbidentifier.member_database = member_database
             dbidentifier.database_species_id = speciesid
 
             dbidentifier.save()

nodes/cdms/node/queryfunc.py

@@ -365,7 +365,7 @@ def setupResults(sql):
 
     # this header info is used in xsams-header-info (html-request)
     headerinfo={\
-        'Truncated':"100", # CDMS will not truncate data (at least for now)
+        'Truncated':"0", # CDMS will not truncate data (at least for now)
         'count-sources':nsources, 
         'count-species':nspecies,
         'count-molecules':nmolecules,
@@ -437,7 +437,7 @@ def returnResults(tap, LIMIT=None):
     # use tap.parsedSQL.columns instead of tap.requestables
     # because only the selected columns should be returned and no additional ones
     col = tap.parsedSQL.columns #.asList()
-    transs = RadiativeTransitions.objects.filter(q,specie__archiveflag=0,dataset__archiveflag=0,energylower__gt=0) 
+    transs = RadiativeTransitions.objects.filter(q,specie__archiveflag=0,dataset__archiveflag=0) #,energylower__gt=0) 
     ntrans = transs.count()
 
     if LIMIT is not None and ntrans > LIMIT:

nodes/cdms/templates/cdmsportal/contact.html

@@ -13,26 +13,22 @@
 
     <div style="margin: 20px 0 -10px 0;padding:15px;text-align:center;font-size:13px;background:#fff;-webkit-border-radius: 4px;-moz-border-radius: 4px;border-radius: 4px;-webkit-box-shadow: 0 1px 3px rgba(0, 0, 0, 0.2);-moz-box-shadow: 0 1px 3px rgba(0, 0, 0, 0.2);box-shadow: 0 1px 3px rgba(0, 0, 0, 0.2);">
 
-      <ul>
+        <ul>
+            <li>
+            Support 
+            <a href="mailto:[email protected]">endres(At)ph1(Dot)uni-koeln(Dot)de</a>
+            </li>
         <li>
           <a href="http://www.ph1.uni-koeln.de/~hspm" target="_top">Dr. Holger S. P. M&uuml;ller </a> 
           <a href="mailto:[email protected]">hspm(At)ph1(Dot)uni-koeln(Dot)de</a>
         </li>
-        <li>
-          <a href="http://www.ph1.uni-koeln.de/~stutzki" target="_top">Prof. Dr. J&uuml;rgen Stutzki</a> 
-          <a href="mailto:[email protected]">stutzki(At)ph1(Dot)uni-koeln(Dot)de</a>
-        </li>
-        <li>
-          <a href="http://www.ph1.uni-koeln.de/~schlemmer" target="_top">Prof. Dr. Stephan Schlemmer</a> 
-          <a href="mailto:[email protected]">schlemmer(At)ph1(Dot)uni-koeln(Dot)de</a>
-        </li>
-        <li>Prof. Dr. Thomas Giesen 
-          <a href="mailto:[email protected]">giesen(At)ph1(Dot)uni-koeln(Dot)de</a>
+        <li>Dr. Christian Endres 
+          <a href="mailto:[email protected]">endres(At)ph1(Dot)uni-koeln(Dot)de</a>
         </li>
       </ul>
 
     </div>
   </div>
 </div>
 
-{% endblock %}
+{% endblock %}

nodes/cdms/templates/cdmsportal/queryForm.html

@@ -164,7 +164,9 @@ <h6 class="vlist"> REFINEMENTS </h6>
       <INPUT TYPE="HIDDEN" NAME="col_speciesid" id="col_speciesid" VALUE="">
 
       <div class="type-button float_right radexsubmit">
-        <INPUT id="button1" TYPE="button" NAME="T_SEARCH" onclick='$("#control").hide();ajaxQuery("ajaxQuery","http://cdms.ph1.uni-koeln.de/cdms/tap/sync?REQUEST=doQuery&LANG=VSS2&FORMAT=XSAMS&QUERY=SELECT+ALL+WHERE+%28+InchiKey+=+%27UGFAIRIUMAVXCW-UHFFFAOYSA-N%27+%29&ORDERBY=frequency","http://cdms.ph1.uni-koeln.de/cdms/tap/");$("#result").show();docShowSubpage("queryresult");' VALUE="QUERY" >
+          <INPUT id="button2" TYPE="button" NAME="T_SEARCH" onclick='ajaxDownload("ajaxQuery","http://cdms.ph1.uni-koeln.de/cdms/tap/sync?REQUEST=doQuery&LANG=VSS2&FORMAT=XSAMS&QUERY=SELECT+ALL+WHERE+%28+InchiKey+=+%27UGFAIRIUMAVXCW-UHFFFAOYSA-N%27+%29&ORDERBY=frequency","http://cdms.ph1.uni-koeln.de/cdms/tap/");' VALUE="Download" >
+
+          <INPUT id="button1" TYPE="button" NAME="T_SEARCH" onclick='$("#control").hide();ajaxQuery("ajaxQuery","http://cdms.ph1.uni-koeln.de/cdms/tap/sync?REQUEST=doQuery&LANG=VSS2&FORMAT=XSAMS&QUERY=SELECT+ALL+WHERE+%28+InchiKey+=+%27UGFAIRIUMAVXCW-UHFFFAOYSA-N%27+%29&ORDERBY=frequency","http://cdms.ph1.uni-koeln.de/cdms/tap/");$("#result").show();docShowSubpage("queryresult");' VALUE="QUERY" >
       </div>
    </fieldset>
 

nodes/cdms/templates/cdmsportal/selectSpeciesAjax.html

@@ -65,7 +65,7 @@ <h6 class="vlist"> FILTER SPECIES LIST</h6>
 		isotopologs = [{% for inchikey in inchikey_list %}'{{inchikey}}',{% endfor %}] 
 		molecules = [{% for molecule in stoichio_list %}'{{molecule}}',{% endfor %}] 
                 $(document).ready(function() {
-                    ajaxGetSpeciesList(-5);
+                    ajaxGetSpeciesList(5);
                 });
 </script>
 

nodes/jpl/node/queryfunc.py

@@ -365,7 +365,7 @@ def setupResults(sql):
 
     # this header info is used in xsams-header-info (html-request)
     headerinfo={\
-        'Truncated':"100", # CDMS will not truncate data (at least for now)
+        'Truncated':"0", # CDMS will not truncate data (at least for now)
         'count-sources':nsources, 
         'count-species':nspecies,
         'count-molecules':nmolecules,