need to figure out a way to bring over the pbdb tables that are used …

…in the api

api-tests/app.ts

@@ -9,16 +9,13 @@ import * as path from 'path';
 
 
 const testFiles = [
-    'defs_sources.ts'
-    /*'defs_strat_name_concepts.ts',
-    'defs_strat_names.ts',
-    'defs_structures.ts',
-    'defs_timescales.ts',
-    'fossils.ts',
+    //'defs_sources.ts'
+  //'defs_structures.ts'
+    //'fossils.ts',
     'geologic_units_burwell.ts',
     'geologic_units_gmna.ts',
-    'geologic_units_gmus.ts',
-    'index.ts',
+    'geologic_units_gmus.ts'
+    /*'index.ts',
     'mancos_test_cases.ts',
     'mobile_fossil_collections.ts',
     'mobile_macro_summary.ts',

api-tests/v2Tests/defs_strat_name_concepts.ts

@@ -37,7 +37,7 @@
         done();
       });
   });
-/*
+
   it("should output CSV", function (done) {
     request(settings.host)
       .get("/defs/strat_name_concepts?all&format=csv")
@@ -49,4 +49,3 @@
         done();
       });
   });
-*/

api-tests/v2Tests/defs_strat_names.ts

@@ -80,8 +80,9 @@
         done();
       });
   });
-/*
+
   it("should return all strat names", function (done) {
+    this.timeout(5000)
     request(settings.host)
       .get("/defs/strat_names?all")
       .expect(validators.aSuccessfulRequest)
@@ -92,7 +93,7 @@
         done();
       });
   });
-*/
+
   it("should output CSV", function (done) {
     request(settings.host)
       .get("/defs/strat_names?strat_name=Abercrombie&format=csv")

api-tests/v2Tests/defs_structures.ts

@@ -92,7 +92,7 @@
         done();
       });
   });
-/*
+
   it("should return CSV", function (done) {
     request(settings.host)
       .get("/defs/structures?structure_type=fabric&format=csv")
@@ -104,4 +104,3 @@
         done();
       });
   });
-*/

api-tests/v2Tests/fossils.ts

@@ -13,7 +13,7 @@
         done();
       });
   });
-/*
+
   it("should return a sample", function (done) {
     request(settings.host)
       .get("/fossils?sample")
@@ -119,4 +119,3 @@
         done();
       });
   });
-*/

api-tests/v2Tests/geologic_units_burwell.ts

@@ -13,7 +13,7 @@
         done();
       });
   });
-/*
+
   it("should return a sample", function (done) {
     request(settings.host)
       .get("/geologic_units/burwell?sample")
@@ -107,4 +107,4 @@
         done();
       });
   });
-  */
+

api-tests/v2Tests/geologic_units_gmna.ts

@@ -13,7 +13,7 @@
         done();
       });
   });
-/*
+
   it("should return a sample", function (done) {
     request(settings.host)
       .get("/geologic_units/gmna?sample")
@@ -90,4 +90,4 @@
       });
   });
 
- */
+

api-tests/v2Tests/geologic_units_gmus.ts

@@ -13,7 +13,7 @@
         done();
       });
   });
-/*
+
   it("should return a sample", function (done) {
     request(settings.host)
       .get("/geologic_units/gmus?sample")
@@ -182,4 +182,4 @@
       });
   });
 
- */
+

v2/credentials.ts

@@ -7,6 +7,7 @@ if (process.env.MACROSTRAT_DATABASE != null) {
   // Connect using a database URL
   const macrostratDatabaseURL = process.env.MACROSTRAT_DATABASE
   const elevationDatabaseURL = process.env.ELEVATION_DATABASE ?? macrostratDatabaseURL.replace("5432/macrostrat", "5432/elevation");
+  //add alice db connection
   exports.pg = {
     macrostratDatabaseURL,
     elevationDatabaseURL
@@ -29,6 +30,7 @@ exports.postgresDatabases = {
   burwell: "macrostrat",
   geomacro: "geomacro",
   elevation: "elevation",
+  alice: "alice"
 };
 
 // This is the default Redis port

v2/fossils.ts

@@ -130,6 +130,11 @@ module.exports = function (req, res, next) {
           //TODO there is no pbdb table, so I removed LEFT JOIN pbdb.occ_matrix ON pbdb.coll_matrix.collection_no = pbdb.occ_matrix.collection_no
           //I also removed           LEFT JOIN pbdb.taxon_lower ON pbdb.occ_matrix.orig_no = pbdb.taxon_lower.orig_no
           //removed           JOIN pbdb.coll_matrix ON pbdb_matches.collection_no = pbdb.coll_matrix.collection_no
+
+          //need dump and restore of pbdb or a copy of only the tables needed for the api to function in postgresql
+          //find number of routes affected
+          //find mariadb endpoint notes
+          //"genus_no": [], "taxon_no": "" are always null
           larkin.queryPg("burwell",
             "SELECT pbdb_matches.collection_no AS cltn_id, collection_name AS cltn_name, lookup_unit_intervals.t_age, lookup_unit_intervals.b_age, n_occs AS pbdb_occs, COALESCE(GROUP_CONCAT(distinct pbdb.taxon_lower.genus_no), '') AS genus_no,  COALESCE(GROUP_CONCAT(distinct pbdb.occ_matrix.taxon_no), '') AS taxon_no, \
           pbdb_matches.unit_id, cols.id as col_id, CONCAT(pbdb_matches.ref_id, '|') AS refs " +

v2/larkin.ts

@@ -91,13 +91,15 @@ const { Client, Pool } = require("pg");
         connectionString = postgresCfg.elevationDatabaseURL
       }
       connectionDetails = { connectionString }
+      //add alice db connection
 
     } else {
       connectionDetails = { ...credentials.pg }
       if (dbName == "elevation") {
         /* Special case for elevation database (temporary) */
         connectionDetails.database = 'elevation'
       }
+      //add alice db connection
     }
 
     const pool = new Pool(connectionDetails);