don't restrict species search to ncbi

scripts/run_tests.sh

@@ -16,8 +16,8 @@ sh /app/scripts/start_server.sh &
 coverage erase
 # spec validation
 python -m spec.validate
-# run importer/, relation_engine_server/, and spec/ tests, skip test_query.py
-coverage run --branch -m pytest --ignore=spec/test/stored_queries/test_query.py
+# run importer/, relation_engine_server/, and spec/ tests
+coverage run --branch -m pytest
 # RE client tests
 PYTHONPATH=client_src python -m pytest client_src/test
 coverage html --omit=*/test_*

spec/stored_queries/generic/fulltext_search.yaml

@@ -1,4 +1,6 @@
 # Search a collection with a fulltext index with an attribute name and search text
+# Also supports filtering by outer-level attributes
+# Not recommended for fast searching because it can be very slow and even timeout at 60s
 name: fulltext_search
 params:
   type: object

spec/stored_queries/taxonomy/taxonomy_search_sci_name.yaml

@@ -1,3 +1,5 @@
+# Should be REVISED then DEPRECATED
+# 
 # Search for a taxon with a scientific name
 # Offset is limited to 10k
 name: taxonomy_search_sci_name

spec/stored_queries/taxonomy/taxonomy_search_species.yaml

@@ -1,3 +1,5 @@
+# DEPRECATED. See taxonomy_search_species_strains and taxonomy_search_species_strains_no_sort
+#
 # Search for a species/strain. Similar to search_sci_name, but simpler and quicker
 name: taxonomy_search_species
 params:

spec/stored_queries/taxonomy/taxonomy_ncbi_species.yaml → spec/stored_queries/taxonomy/taxonomy_search_species_strain.yaml

@@ -1,15 +1,23 @@
 # Search ncbi_taxon collection for species/strains by scientific name
-name: taxonomy_ncbi_species
+name: taxonomy_search_species_strain
 params:
   type: object
-  required: [search_text]
+  required: ["@taxon_coll", sciname_field, search_text]
   additionalProperties: false
   properties:
+    "@taxon_coll":
+      type: string
+      title: Taxon collection name
+      examples: [ncbi_taxon, gtdb_taxon]
     search_text:
       type: string
       title: Search text
       examples: [escherichia, es]
       description: Text to search on the search attribute values
+    sciname_field:
+      type: string
+      title: Scientific name field name
+      examples: [scientific_name, name]
     ts:
       type: [integer, "null"]
       title: Versioning timestamp
@@ -43,7 +51,7 @@ query: |
       FOR tok IN search_text__wordboundmod_icu_toks  // prepend "prefix:"
           RETURN CONCAT("prefix:", tok)
   )
-  FOR doc IN FULLTEXT(ncbi_taxon, "scientific_name", search_text__fulltext)
+  FOR doc IN FULLTEXT(@@taxon_coll, @sciname_field, search_text__fulltext)
       FILTER @ts ? doc.created <= @ts AND doc.expired >= @ts : true
       FILTER doc.rank IN ["species", "strain"] OR doc.strain
       LET doc_sciname__norm = REGEX_REPLACE(LOWER(TRIM(doc.scientific_name)), "\\s+", " ")  // for exact matching

spec/stored_queries/taxonomy/taxonomy_ncbi_species_no_sort.yaml → spec/stored_queries/taxonomy/taxonomy_search_species_strain_no_sort.yaml

@@ -1,12 +1,20 @@
 # Search ncbi_taxon collection for species/strains by scientific name
 # Except do not sort, just return the first however many documents
 # Useful for short prefixes (e.g., "s")  that would be expensive yet not meaningful to sort
-name: taxonomy_ncbi_species_no_sort
+name: taxonomy_search_species_strain_no_sort
 params:
   type: object
-  required: [search_text]
+  required: ["@taxon_coll", sciname_field, search_text]
   additionalProperties: false
   properties:
+    "@taxon_coll":
+      type: string
+      title: Taxon collection name
+      examples: [ncbi_taxon, gtdb_taxon]
+    sciname_field:
+      type: string
+      title: Scientific name field name
+      examples: [scientific_name, name]
     search_text:
       type: string
       title: Search text
@@ -43,7 +51,7 @@ query: |
       FOR tok IN search_text__wordboundmod_icu_toks  // prepend "prefix:"
           RETURN CONCAT("prefix:", tok)
   )
-  FOR doc IN FULLTEXT(ncbi_taxon, "scientific_name", search_text__fulltext)
+  FOR doc IN FULLTEXT(@@taxon_coll, @sciname_field, search_text__fulltext)
       FILTER @ts ? doc.created <= @ts AND doc.expired >= @ts : true
       FILTER doc.rank IN ["species", "strain"] OR doc.strain
       LIMIT @offset ? @offset : 0, @limit ? @limit : 20