update html, add inScheme property on Chromista

tools/navocab/__init__.py

@@ -9,6 +9,7 @@
 import rdflib
 import rdflib.namespace
 import rdflib.plugins.sparql
+
 import sqlalchemy
 import logging
 import logging.config

tools/runVocabTools.py

@@ -63,15 +63,26 @@ def main(command, path):
 
     # do function of original Makefile here
 
-    for inputf in inputttl:
-        result = load_cachedb(sourcevocabdir + "/" + inputf + ".ttl", cachepath)
+    # for inputf in inputttl:
+    #     result = load_cachedb(sourcevocabdir + "/" + inputf + ".ttl", cachepath)
+    #     if (result == 0):
+    #         print(f"load_cachedb call successful for: {inputf}")
+    #     else:
+    #         print(f"load_cachedb had problem processing: {inputf}")
+
+            # ***********************
+    index = 0
+    while index < len(inputttl):
+        # for inputf in inputttl:
+        result = load_cachedb(sourcevocabdir + "/" + inputttl[index] + ".ttl", inputvocaburi[index], cachepath)
         if (result == 0):
-            print(f"load_cachedb call successful for: {inputf}")
+            print(f"load_cachedb call successful for: {inputttl[index]}")
         else:
-            print(f"load_cachedb had problem processing: {inputf}")
-
+            print(f"load_cachedb had problem processing: {inputttl[index]}")
+        index += 1
         # ***********************
 
+
     #  essfrole_earthenv_sampled_feature_role  spec_earthenv_specimen_type
     if command == "uijson":
         print("Generating uijson for inclusion in webUI build")
@@ -95,10 +106,10 @@ def main(command, path):
 # def _run_make_in_container(target: str):
 #    subprocess.run(["/usr/bin/make", "-C", "/app", "-f", "/app/Makefile", target])
 
-def load_cachedb(inputf, cachepath):
+def load_cachedb(inputf, inputuri, cachepath):
     # tools/vocab.py --verbosity ERROR -s $(CACHE) load $(SRC)/$@
     print(f"cachdb file to load: {inputf}")
-    load_args = ["--verbosity", "ERROR", "-s", cachepath, "load", inputf]
+    load_args = ["--verbosity", "ERROR", "-s", cachepath, "load", inputf, inputuri]
     result = _run_python_in_container("vocab.py", load_args, f="")
     if (result == 0):
         print(f"vocab.py call successful for {inputf}")

tools/vocab.py

@@ -93,7 +93,7 @@ def main(ctx, store, verbosity) -> int:
     ctx.ensure_object(dict)
     store_uri = f"sqlite:///{store}"
     L.debug("Using store at: %s", store_uri)
-    ctx.obj["store"] = navocab.VocabularyStore(storage_uri=store_uri)
+    ctx.obj["store"] = navocab.VocabularyStore(storage_uri=store_uri, purge_existing=False)
     return 0
 
 @main.command("purgeStore")

vocabulary/biology_sampledfeature_extension.ttl

@@ -155,6 +155,7 @@ bioe:chromista
   skos:broader bioe:eukaryote ;
   skos:definition "Chromists are unified by a shared common ancestral body plan with (1) a skeleton comprising cortical alveoli with subpellicular microtubules and a microtubule bypassing band distinct from the three major microtubule centriolar roots inherited from excavate protozoa, and (2) chloroplasts of red algal origin inside the endomembrane system with unique membrane topology and derlin-based periplastid protein import machinery.  Chromists are distinguished from Plantae because of more complex chloroplast-associated membrane topology and rigid tubular multipartite ciliary hairs.  The kingdom includes highly divergent cytoskeletons and trophic modes. Chromista comprise eight distinctive phyla (Cavalier-Smith, 2018) and includes a majority of marine algae and of heterotrophic protists,  various human disease agents such as malaria parasites, and agricultural pathogens like potato blight and sugar beet rhizomania disease. They have a greater range of body plans and lifestyles than the entire plant kingdom and more phyla than kingdoms Fungi or Protozoa."@en ;
   skos:prefLabel "Chromista"@en ;
+  skos:inScheme bioe:biologicentityvocabulary ;
 .
 bioe:crustacea
   rdf:type skos:Concept ;
@@ -434,6 +435,7 @@ sf:biologicalentity
   rdf:type skos:Concept ;
   rdfs:label "Biological entity"@en ;
   skos:definition "Sampled feature is an organism. Use for samples that represent some species of organism as the proximate sampled feature for which the focus is not the environment that the organism inhabits."@en ;
+  skos:inScheme bioe:biologicentityvocabulary ;
   skos:inScheme sf:sampledfeaturevocabulary ;
   skos:note "Based on DiSSCo listing in table 2 of https://docs.google.com/document/d/19OPyOm9VF2qfI3M6RmJPvRfo8JlZ3tt0II05aGCyBHQ/, draft DiSSCo specimen & collection classification (2023-03-27)"@en ;
   skos:prefLabel "Biological entity"@en ;