repointed api to use one PG connection string. Removed the rest of an…

…y mysql connections
UW-Macrostrat · Aug 14, 2024 · 3ba9409 · 3ba9409
1 parent 5d9d20f
commit 3ba9409
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Showing 33 changed files with 84 additions and 58 deletions.
diff --git a/.gitignore b/.gitignore
@@ -15,8 +15,8 @@ v1/utilities/scripts/credentials.py
 .idea
 venv
 
-v2/credentials.ts
-credentials.ts
+!v2/credentials.ts
+!credentials.ts
 !v1/credentials.ts
 v2/utilities/scripts/credentials.py
 

diff --git a/v2/age_model.ts b/v2/age_model.ts
@@ -78,7 +78,7 @@ module.exports = function (req, res, next) {
     ? req.query.format
     : "json";
 
-  larkin.queryPgMaria("macrostrat_two", sql, params, function (error, response) {
+  larkin.queryPg("burwell", sql, params, function (error, response) {
     if (error) {
       larkin.error(req, res, next, error);
     } else {

diff --git a/v2/credentials.ts b/v2/credentials.ts
@@ -0,0 +1,21 @@
+exports.pgTwo = {
+  host: process.env.host,
+  port: process.env.port,
+  user: process.env.user,
+  password: process.env.password,
+  database: process.env.database
+};
+
+exports.postgresDatabases = {
+  burwell: "macrostrat",
+  geomacro: "geomacro"
+};
+
+// This is the default Redis port
+// NOTE: Redis is not configured at the moment
+exports.redis = {
+  port: 6379,
+};
+
+// Generate a hash by running: node -e "console.log(require('uuid/v4')())"
+exports.cacheRefreshKey = "put-hash-here";
diff --git a/v2/definitions/autocomplete.ts b/v2/definitions/autocomplete.ts
@@ -64,7 +64,7 @@ module.exports = function (req, res, next) {
       query =
         "sample" in req.query ? "ma%" : req.query.query.toLowerCase() + "%";
 
-    larkin.queryPgMaria("macrostrat_two",
+    larkin.queryPg("burwell",
       "SELECT id::integer, name, type, category FROM macrostrat_temp.autocomplete WHERE name ILIKE :query AND type = ANY(:types) LIMIT :limit",
       { query: query, types: types, limit: limit },
       function (error, result) {

diff --git a/v2/definitions/columns.ts b/v2/definitions/columns.ts
@@ -63,7 +63,7 @@ module.exports = function (req, res, next, cb) {
     sql += " LIMIT 5";
   }
 
-  larkin.queryPgMaria("macrostrat_two", sql, params, function (error, result) {
+  larkin.queryPg("burwell", sql, params, function (error, result) {
     if (error) {
       if (cb) {
         cb(error);

diff --git a/v2/definitions/drilling_sites.ts b/v2/definitions/drilling_sites.ts
@@ -68,7 +68,7 @@ module.exports = function (req, res, next, cb) {
   console.log(params)
 
 
-  larkin.queryPgMaria("macrostrat_two", sql, params, function (error, result) {
+  larkin.queryPg"burwell", sql, params, function (error, result) {
     if (error) {
       if (cb) {
         cb(error);

diff --git a/v2/definitions/econs.ts b/v2/definitions/econs.ts
@@ -50,7 +50,7 @@ module.exports = function (req, res, next, cb) {
     sql += "\nLIMIT 5";
   }
 
-  larkin.queryPgMaria("macrostrat_two", sql, params, function (error, data) {
+  larkin.queryPg("burwell", sql, params, function (error, data) {
     if (error) {
       if (cb) {
         cb(error);

diff --git a/v2/definitions/environments.ts b/v2/definitions/environments.ts
@@ -40,7 +40,7 @@ module.exports = function (req, res, next, cb) {
   if ("sample" in req.query) {
     sql += " LIMIT 5";
   }
-  larkin.queryPgMaria("macrostrat_two", sql, environ, function (error, data) {
+  larkin.queryPg("burwell", sql, environ, function (error, data) {
     if (error) {
       if (cb) {
         cb(error);

diff --git a/v2/definitions/groups.ts b/v2/definitions/groups.ts
@@ -9,7 +9,7 @@ module.exports = function (req, res, next, cb) {
   //change params from dict to array. add params.push to array
   //add schema to sql table in the from and join clauses
   //change sql where syntax to = ANY($1)
-  //update larkin.querypgmaria function
+  //update larkin.queryPg function
 
   //changing params from array back to dict
   let params = {};
@@ -46,7 +46,7 @@ module.exports = function (req, res, next, cb) {
     sql += " LIMIT 5";
   }
 
-  larkin.queryPgMaria("macrostrat_two",
+  larkin.queryPg("burwell",
     sql,
     params,
     function (error, data) {

diff --git a/v2/definitions/intervals.ts b/v2/definitions/intervals.ts
@@ -99,7 +99,7 @@ module.exports = function (req, res, next, cb) {
     sql += " LIMIT 5";
   }
 
-  larkin.queryPgMaria("macrostrat_two",
+  larkin.queryPg("burwell",
       sql,
       params, function (error, result) {
     if (error) {

diff --git a/v2/definitions/lithologies.ts b/v2/definitions/lithologies.ts
@@ -58,7 +58,7 @@ module.exports = function (req, res, next, cb) {
     sql += " LIMIT 5";
   }
 
-  larkin.queryPgMaria("macrostrat_two", sql, params, function (error, data) {
+  larkin.queryPg("burwell", sql, params, function (error, data) {
     if (error) {
       if (cb) {
         cb(error);

diff --git a/v2/definitions/lithology_attributes.ts b/v2/definitions/lithology_attributes.ts
@@ -34,7 +34,7 @@ module.exports = function (req, res, next, cb) {
     sql += " LIMIT 5";
   }
 
-  larkin.queryPgMaria("macrostrat_two", sql, params, function (error, data) {
+  larkin.queryPg("burwell", sql, params, function (error, data) {
     /*TODO Update t_units data type from str to bigint*/
     if (error) {
       if (cb) {

diff --git a/v2/definitions/measurement_sources.ts b/v2/definitions/measurement_sources.ts
@@ -51,7 +51,7 @@ FROM macrostrat_temp.refs
   }
 
 
-  larkin.queryPgMaria("macrostrat_two", sql, params, function (error, data) {
+  larkin.queryPg("burwell", sql, params, function (error, data) {
     if (error) {
       if (cb) {
         return cb(error);

diff --git a/v2/definitions/measurements.ts b/v2/definitions/measurements.ts
@@ -40,7 +40,7 @@ FROM macrostrat_temp.measurements
     sql += " LIMIT 5";
   }
 
-  larkin.queryPgMaria("macrostrat_two", sql, params, function (error, data) {
+  larkin.queryPg("burwell", sql, params, function (error, data) {
     if (error) {
       if (error) {
         return cb(error);

diff --git a/v2/definitions/minerals.ts b/v2/definitions/minerals.ts
@@ -52,7 +52,7 @@ module.exports = function (req, res, next, cb) {
     sql += " LIMIT 5";
   }
 
-  larkin.queryPgMaria("macrostrat_two", sql, params, function (error, data) {
+  larkin.queryPg("burwell", sql, params, function (error, data) {
     if (error) {
       if (cb) {
         cb(error);

diff --git a/v2/definitions/projects.ts b/v2/definitions/projects.ts
@@ -39,7 +39,7 @@ module.exports = function (req, res, next, cb) {
   sql += "\nGROUP BY projects.id, in_proc.c, obs.co";
 
 
-  larkin.queryPgMaria("macrostrat_two", sql, params, function (error, data) {
+  larkin.queryPg("burwell", sql, params, function (error, data) {
     if (error) {
       if (cb) {
         return cb(error);

diff --git a/v2/definitions/refs.ts b/v2/definitions/refs.ts
@@ -32,7 +32,7 @@ FROM macrostrat_temp.refs
     sql += " LIMIT 5";
   }
 
-  larkin.queryPgMaria("macrostrat_two", sql, params, function (error, data) {
+  larkin.queryPg("burwell", sql, params, function (error, data) {
     if (error) {
       if (cb) {
         return cb(error);

diff --git a/v2/definitions/strat_name_concepts.ts b/v2/definitions/strat_name_concepts.ts
@@ -54,7 +54,7 @@ module.exports = function (req, res, next, cb) {
     sql += " LIMIT 5";
   }
 
-  larkin.queryPgMaria("macrostrat_two", sql, params, function (error, result) {
+  larkin.queryPg("burwell", sql, params, function (error, result) {
     if (error) {
       if (cb) {
         return cb(error);

diff --git a/v2/definitions/strat_names.ts b/v2/definitions/strat_names.ts
@@ -132,7 +132,7 @@ module.exports = function (req, res, next, cb) {
     sql += " LIMIT 5";
   }
 
-  larkin.queryPgMaria("macrostrat_two", sql, params, function (error, response) {
+  larkin.queryPg("burwell", sql, params, function (error, response) {
     if (error) {
       console.log(error);
       if (cb) {

diff --git a/v2/definitions/structures.ts b/v2/definitions/structures.ts
@@ -48,7 +48,7 @@ module.exports = function (req, res, next, cb) {
     ${limit}
   `
 
-  larkin.queryPgMaria("macrostrat_two",
+  larkin.queryPg("burwell",
     sql,
     params,
     function (error, data) {

diff --git a/v2/definitions/timescales.ts b/v2/definitions/timescales.ts
@@ -22,7 +22,7 @@ module.exports = function (req, res, next, cb) {
     sql += " LIMIT 5";
   }
 
-  larkin.queryPgMaria("macrostrat_two", sql, [], function (error, data) {
+  larkin.queryPg("burwell", sql, [], function (error, data) {
     if (error) {
       if (cb) {
         return cb(error);

diff --git a/v2/editing/section.ts b/v2/editing/section.ts
@@ -5,7 +5,7 @@ module.exports = function (req, res, next) {
   if (!req.query.section_id) {
     res.json("Need a section_id");
   } else {
-    larkin.queryPgMaria("macrostrat_two",
+    larkin.queryPg("burwell",
       `SELECT ub.id, 
        u1.strat_name AS below, 
        u2.strat_name AS above, 

diff --git a/v2/editing/units_update.ts b/v2/editing/units_update.ts
@@ -7,7 +7,7 @@ module.exports = function (req, res, next) {
     async.each(
       req.body.units,
       function (each, callback) {
-        larkin.queryPgMaria("macrostrat_two",
+        larkin.queryPg("burwell",
           "UPDATE macrostrat_temp.units SET position_bottom = :position_bottom WHERE id = :units",
           [each.position_bottom, each.unit],
           function (error, result) {

diff --git a/v2/eodp.ts b/v2/eodp.ts
@@ -70,7 +70,7 @@ module.exports = function (req, res, next) {
   }
 
 
-  larkin.queryPgMaria("macrostrat_two",sql, params, function (error, response) {
+  larkin.queryPg("burwell",sql, params, function (error, response) {
     if (error) {
       larkin.error(req, res, next, error);
     } else {

diff --git a/v2/fossils.ts b/v2/fossils.ts
@@ -130,7 +130,7 @@ 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
-          larkin.queryPgMaria("macrostrat_two",
+          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 " +
               (geo ? ", AsWKT(pbdb_matches.coordinate) AS geometry" : "") +

diff --git a/v2/index.ts b/v2/index.ts
@@ -2,7 +2,7 @@ var api = require("./api"),
   larkin = require("./larkin");
 
 // Establish a connection to the database
-larkin.connectMySQL();
+//larkin.connectMySQL();
 
 // Set up the column and unit cache
 larkin.setupCache();

diff --git a/v2/larkin.ts b/v2/larkin.ts
@@ -1,4 +1,4 @@
-var mysql = require("mysql"),
+var //mysql = require("mysql"),
   async = require("async"),
   _ = require("underscore"),
   credentials = require("./credentials"),
@@ -14,7 +14,7 @@ const { Client, Pool } = require("pg");
 (function () {
   var larkin = {};
 
-  larkin.connectMySQL = function () {
+  /* larkin.connectMySQL = function () {
     // Non-blocking FTW
     this.pool = mysql.createPool(credentials.mysql);
 
@@ -26,9 +26,10 @@ const { Client, Pool } = require("pg");
         );
       }
     });
-  };
+  };*/
 
-  larkin.queryPg = function (db, sql, params, callback) {
+
+  /*larkin.queryPg = function (db, sql, params, callback) {
     const nameMapping = credentials.postgresDatabases ?? {};
     const dbName = nameMapping[db] ?? db;
 
@@ -41,7 +42,7 @@ const { Client, Pool } = require("pg");
     }
 
     if (dbName == "elevation") {
-      /** Special case for elevation database (temporary) */
+      //Special case for elevation database (temporary)
       connectionString = credentials.elevationDatabase;
     }
     const pool = new Pool({
@@ -66,16 +67,17 @@ const { Client, Pool } = require("pg");
       }
     });
   };
+*/
 
   //added new method to query from Maria data in the new PG database after migration
-  larkin.queryPgMaria = function (db, sql, params, callback) {
+  larkin.queryPg = function (db, sql, params, callback) {
     //add console.logs for debug mode in the future
     console.log(sql)
     console.log(params)
     const nameMapping = credentials.postgresDatabases ?? {};
     const dbName = nameMapping[db] ?? db;
 
-    let { connectionString, ...otherConnectionDetails } = credentials.pgMaria;
+    let { connectionString, ...otherConnectionDetails } = credentials.pg;
 
     if (dbName == "geomacro") {
       console.warn(
@@ -135,6 +137,7 @@ const { Client, Pool } = require("pg");
     return [sql, newParams];
   };
 
+  /*
   larkin.query = function (sql, params, callback) {
     //console.warn(`Deprecated MySQL query:\n${sql}`);
     if (sql.indexOf(":") > -1 && Object.keys(params).length > 0) {
@@ -164,7 +167,7 @@ const { Client, Pool } = require("pg");
         );
       }.bind(this),
     );
-  };
+  }; */
 
   larkin.sendImage = function (req, res, next, data, isCached) {
     //  console.log(data)
@@ -557,23 +560,25 @@ const { Client, Pool } = require("pg");
       ),
     );
 
+
+
     // Macrostrat refs
     if (key === "refs" || key === "ref_id") {
-      larkin.query(
-        "SELECT refs.id AS ref_id, pub_year, author, ref, doi, url, COUNT(DISTINCT units_sections.unit_id) AS t_units FROM refs LEFT JOIN col_refs ON col_refs.ref_id = refs.id LEFT JOIN units_sections ON units_sections.col_id = col_refs.col_id WHERE refs.id IN (:ref_id) GROUP BY refs.id",
+      larkin.queryPg("burwell",
+        "SELECT refs.id AS ref_id, pub_year, author, ref, doi, url, COUNT(DISTINCT units_sections.unit_id) AS t_units FROM macrostrat_temp.refs LEFT JOIN macrostrat_temp.col_refs ON col_refs.ref_id = refs.id LEFT JOIN macrostrat_temp.units_sections ON units_sections.col_id = col_refs.col_id WHERE refs.id = ANY(:ref_id) GROUP BY refs.id",
         { ref_id: ref_ids },
         function (error, data) {
           var refs = {};
-          if (!data) {
+          if (!data.rows) {
             return callback(null);
           }
-          for (var i = 0; i < data.length; i++) {
-            refs[data[i]["ref_id"]] =
-              larkin.normalizeRefField(data[i].author) +
-              larkin.normalizeRefField(data[i].ref) +
-              larkin.normalizeRefField(data[i].pub_year) +
-              larkin.normalizeRefField(data[i].doi) +
-              larkin.normalizeRefField(data[i].url);
+          for (var i = 0; i < data.rows.length; i++) {
+            refs[data.rows[i]["ref_id"]] =
+              larkin.normalizeRefField(data.rows[i].author) +
+              larkin.normalizeRefField(data.rows[i].ref) +
+              larkin.normalizeRefField(data.rows[i].pub_year) +
+              larkin.normalizeRefField(data.rows[i].doi) +
+              larkin.normalizeRefField(data.rows[i].url);
           }
           callback(refs);
         },

diff --git a/v2/measurements.ts b/v2/measurements.ts
@@ -205,7 +205,7 @@ module.exports = function (req, res, next) {
   `;
   // console.log(sql)
 
-  larkin.queryPgMaria("macrostrat_two", sql, params, function (error, response) {
+  larkin.queryPg("burwell", sql, params, function (error, response) {
     if (error) {
       larkin.error(req, res, next, error);
     } else {

diff --git a/v2/mobile/fossil_collections.ts b/v2/mobile/fossil_collections.ts
@@ -6,7 +6,7 @@ module.exports = function (req, res, next) {
     if ("sample" in req.query) {
       req.query.unit_id = 15176;
     }
-    larkin.queryPgMaria("macrostrat_two",
+    larkin.queryPg("burwell",
       "SELECT DISTINCT collection_no AS cltn_id, collection_name AS cltn_name FROM macrostrat_temp.pbdb_matches WHERE unit_id = ? AND occs > 0 and release_date<NOW()",
       [req.query.unit_id],
       function (error, result) {