Merge pull request #191 from indralab/fix-node-header

Fix node header and other docker issues

docker/Dockerfile

@@ -25,7 +25,7 @@ RUN wget -O /sw/nodes.tsv.gz https://askem-mira.s3.amazonaws.com/dkg/$domain/bui
     neo4j-admin import --delimiter='TAB' --skip-duplicate-nodes=true --skip-bad-relationships=true --nodes /sw/nodes.tsv.gz --relationships /sw/edges.tsv.gz
 
 # Python packages
-RUN python -m pip install git+https://github.com/indralab/mira.git@main#egg=mira[web,uvicorn] && \
+RUN python -m pip install git+https://github.com/indralab/mira.git@main#egg=mira[web,uvicorn,dkg-client] && \
     python -m pip uninstall -y flask_bootstrap && \
     python -m pip uninstall -y bootstrap_flask && \
     python -m pip install bootstrap_flask

docker/Dockerfile.local

@@ -24,7 +24,7 @@ RUN sed -i 's/#dbms.default_listen_address/dbms.default_listen_address/' /etc/ne
     neo4j-admin import --delimiter='TAB' --skip-duplicate-nodes=true --skip-bad-relationships=true --nodes /sw/nodes.tsv.gz --relationships /sw/edges.tsv.gz
 
 # Python packages
-RUN python -m pip install git+https://github.com/indralab/mira.git@$branch#egg=mira[web,uvicorn] && \
+RUN python -m pip install git+https://github.com/indralab/mira.git@$branch#egg=mira[web,uvicorn,dkg-client] && \
     python -m pip uninstall -y flask_bootstrap && \
     python -m pip uninstall -y bootstrap_flask && \
     python -m pip install bootstrap_flask

mira/dkg/client.py

@@ -382,13 +382,15 @@ def get_grounder(self, prefix: Union[str, List[str]]) -> "gilda.grounder.Grounde
 
         if isinstance(prefix, str):
             prefix = [prefix]
-        terms = list(
-            itt.chain.from_iterable(
+        terms = [
+            term
+            for term in itt.chain.from_iterable(
                 self.get_grounder_terms(p) for p in tqdm(
                     prefix, desc="Caching grounding terms"
                 )
             )
-        )
+            if term.norm_text
+        ]
         return Grounder(terms)
 
     def get_node_counter(self) -> Counter:
@@ -598,25 +600,29 @@ def get_terms(
     from gilda.process import normalize
     from gilda.term import Term
 
-    yield Term(
-        norm_text=normalize(name),
-        text=name,
-        db=prefix,
-        id=identifier,
-        entry_name=name,
-        status="name",
-        source=prefix,
-    )
-    for synonym in synonyms or []:
+    norm_text = normalize(name)
+    if norm_text:
         yield Term(
-            norm_text=normalize(synonym),
-            text=synonym,
+            norm_text=norm_text,
+            text=name,
             db=prefix,
             id=identifier,
             entry_name=name,
-            status="synonym",
+            status="name",
             source=prefix,
         )
+    for synonym in synonyms or []:
+        norm_text = normalize(synonym)
+        if norm_text:
+            yield Term(
+                norm_text=norm_text,
+                text=synonym,
+                db=prefix,
+                id=identifier,
+                entry_name=name,
+                status="synonym",
+                source=prefix,
+            )
 
 
 def build_match_clause(

mira/dkg/constants.py

@@ -12,6 +12,11 @@
     "xrefs:string[]",
     "alts:string[]",
     "version:string",
+    "property_predicates:string[]",
+    "property_values:string[]",
+    "xref_types:string[]",
+    "synonym_types:string[]",
+    "source:string",
 )
 
 #: The used for the edges files in the neo4j bulk import

setup.cfg

@@ -65,6 +65,7 @@ web =
     gilda
     click
     neo4j
+    networkx
     pystow
     tabulate
     pygraphviz