more fixes

agr_literature_service/api/triggers/citation.py

@@ -28,7 +28,7 @@
 --   <year>,
 --   <resource abbrev>
 --   <volume>(<issue>):<page(s)>
-   short_citation TEXT;
+   short_citation TEXT default '';
    author_short author.name%type default '';
    ref_year reference.page_range%type;
    res_abbr TEXT default '';
@@ -43,17 +43,19 @@
    iso resource.iso_abbreviation%type;
    medline resource.iso_abbreviation%type;
 
-   citation TEXT default '';
+
 -- Long citation
 --  citation = get_citation_from_args(authorNames, year, title, journal,
 --                                     ref_db_obj.volume or '',
 --                                     ref_db_obj.issue_name or '',
 --                                     ref_db_obj.page_range or '')
+   citation TEXT default '';
    -- volume, issue and page range same as short citation
    title reference.title%type;
-   authors author.name%type default '';
+   authors author.name%type default ' ';
    auth record;
 BEGIN
+    raise notice 'update citations for %', ref_id;
     -- Get first author for short citation
     SELECT CONCAT(SUBSTRING(author.first_name, 1 ,1), ' ', author.last_name) FROM author into author_short
       WHERE author.reference_id = ref_id AND
@@ -78,15 +80,20 @@
       -- raise notice 'Record %', auth;
       authors := authors || auth.name || '; ';
     end loop;
-    authors := SUBSTRING(authors, 1, LENGTH(authors)-2);
+    raise notice 'Authors %', authors;
+    IF authors != ' ' THEN
+      authors := SUBSTRING(authors, 1, LENGTH(authors)-2);
+    ELSE
+       authors := '';
+    END IF;
     -- raise notice 'Authors %', authors;
 
     -- Get the resource abbr
     SELECT res.iso_abbreviation, res.medline_abbreviation, res.title into iso, medline, journal
       FROM reference ref, resource res
       WHERE ref.resource_id = res.resource_id AND
             ref.reference_id = ref_id;
-    IF iso is NULL THEN
+    IF iso is not NULL THEN
         res_abbr := iso;
     ELSIF  medline is not NULL THEN
         res_abbr :=  medline;
@@ -101,19 +108,36 @@
     if title is NULL THEN
       title := '';
     END IF;
-
+    if volume is NULL THEN
+      volume := '';
+    END IF;
+    if issue_name is NULL THEN
+      issue_name := '';
+    END IF;
+    if page_range is NULL THEN
+      page_range := '';
+    END IF;
+    if ref_year is NULL THEN
+      ref_year := '';
+    END IF;
+    if journal is NULL THEN
+      journal := '';
+    END IF;
     -- build the ref_details
     -- <volume>(<issue>):<page(s)>
     ref_details := volume || ' (' || issue_name || '): ' || page_range;
-
+    raise notice 'rd: %', ref_details;
+    raise notice 'tit: %', title;
     citation := authors || ', (' || ref_year || ') ' || title;
     citation := citation || ' ' || journal || ' ' || ref_details;
-    -- raise notice '%', citation;
+    raise notice '%', citation;
 
 
     short_citation :=  author_short || ', ' || ref_year || ', ' || res_abbr || ', ' || ref_details;
     -- raise notice '%', short_citation;
     IF citation_id is NULL THEN
+      raise notice 'sh cit: %', short_citation;
+      raise notice 'cit: %', citation;
       INSERT INTO citation (citation, short_citation) VALUES (citation, short_citation);
       citation_id := (SELECT currval('citation_citation_id_seq'));
       raise notice 'citation_id %', citation_id;
@@ -176,13 +200,32 @@
 returns TRIGGER
 as $$
 BEGIN
+    raise notice 'trgfunc_reference_update_citation: %: % % %', NEW.reference_id, NEW.title, OLD.title, OLD.curie;
     IF NEW.title != OLD.title OR
        NEW.volume != OLD.volume OR
        NEW.issue_name != OLD.issue_name OR
        NEW.page_range != OLD.page_range OR
        NEW.date_published != OLD.date_published THEN
+         raise notice 'Calling update_citations with %', NEW.title; 
          PERFORM update_citations(NEW.reference_id);
+    ELSE
+       raise notice 'Failed update critieria?';
     END IF;
+    raise notice 'Exiting trgfunc_reference_update_citation';
+    return NEW;
+END $$ language plpgsql;
+""")
+
+trgfunc_reference_create_citation = PGFunction(
+    schema="public",
+    signature="trgfunc_reference_create_citation()",
+    definition="""
+returns TRIGGER
+as $$
+BEGIN
+    raise notice 'trgfunc_reference_create_citation: %: % % %', NEW.reference_id, NEW.title, OLD.title, OLD.curie;
+    PERFORM update_citations(NEW.reference_id);
+    raise notice 'Exiting trgfunc_reference_create_citation';
     return NEW;
 END $$ language plpgsql;
 """)
@@ -204,7 +247,7 @@
     is_constraint=False,
     definition="""AFTER INSERT ON reference
         FOR EACH ROW
-        EXECUTE FUNCTION trgfunc_reference_update_citation()""",
+        EXECUTE FUNCTION trgfunc_reference_create_citation()""",
 )
 
 trgfunc_resource_update_citation = PGFunction(

alembic.ini

@@ -6,6 +6,7 @@ script_location = alembic
 
 # template used to generate migration files
 # file_template = %%(rev)s_%%(slug)s
+file_template = %%(year)d%%(month).2d%%(day).2d_%%(rev)s_%%(slug)s
 
 # sys.path path, will be prepended to sys.path if present.
 # defaults to the current working directory.

alembic/env.py

@@ -20,6 +20,7 @@
     trg_reference_update_citation,
     trg_reference_create_citation,
     trgfunc_reference_update_citation,
+    trgfunc_reference_create_citation,
     trg_resource_update_citation,
     trgfunc_resource_update_citation)
 
@@ -32,6 +33,7 @@
                    trg_reference_update_citation,
                    trg_reference_create_citation,
                    trgfunc_reference_update_citation,
+                   trgfunc_reference_create_citation,
                    trg_resource_update_citation,
                    trgfunc_resource_update_citation])