Develop

test/assays.js

@@ -0,0 +1,56 @@
+'use strict';
+const expect = require('chai').expect;
+const supertest = require('supertest');
+
+const dotenv = require('dotenv');
+dotenv.config();
+
+let testroute = process.env.APIPORT;
+
+if (typeof process.env.APIPATH === 'undefined') {
+  testroute = 'http://localhost:' + process.env.APIPORT + '/';
+} else {
+  testroute = process.env.APIPATH;
+}
+
+const api = supertest(testroute);
+
+// *************************************************
+// aeDNA assay data:
+//
+// This lives outside test/v*.js on purpose: genoatt.sh deletes and regenerates
+// those from openapi.yaml, and the generated tests only ever assert a status
+// code. The assay payload feeds the FAIRe exporter's projectMetadata sheet, so
+// a field silently dropped from assaysbydataset.sql would surface there as a
+// blank cell rather than as a failure.
+
+describe('Get aeDNA assays by datasetid:', function() {
+  this.timeout(5000);
+
+  it('every assay carries the FAIRe project terms:', function(done) {
+    api.get('v2.0/data/datasets/74666/assays')
+      .set('Accept', 'application/json')
+      .expect(200)
+      .expect(function(res) {
+        const assays = res.body.data.assays;
+        expect(assays).to.be.an('array');
+        assays.forEach(function(assay) {
+          // sterilise_method / neg_cont / pos_cont -> projectMetadata D6/D7/D8.
+          expect(assay).to.have.property('sterilisemethod');
+          expect(assay).to.have.property('negcont');
+          expect(assay).to.have.property('poscont');
+        });
+      })
+      .end(done);
+  });
+
+  it('a dataset with no assays returns an empty array, not an error:', function(done) {
+    api.get('v2.0/data/datasets/500/assays')
+      .set('Accept', 'application/json')
+      .expect(200)
+      .expect(function(res) {
+        expect(res.body.data.assays).to.be.an('array');
+      })
+      .end(done);
+  });
+});

test/v1.5-data-contacts-{contactid}-test.js

@@ -7,7 +7,7 @@ var expect = chakram.expect;
 describe('tests for /v1.5/data/contacts/{contactid}', function() {
     describe('tests for get', function() {
         it('should respond 200 for "Contact"', function() {
-            var response = request('get', 'http://localhost:3001/v1.5/data/contacts/-2097676', { 
+            var response = request('get', 'http://localhost:3001/v1.5/data/contacts/-90664163', { 
                 'time': true
             });
 

test/v1.5-data-geopoliticalunits-{gpid}-test.js

@@ -7,7 +7,7 @@ var expect = chakram.expect;
 describe('tests for /v1.5/data/geopoliticalunits/{gpid}', function() {
     describe('tests for get', function() {
         it('should respond 200 for "An array of geopolitical units."', function() {
-            var response = request('get', 'http://localhost:3001/v1.5/data/geopoliticalunits/7972', { 
+            var response = request('get', 'http://localhost:3001/v1.5/data/geopoliticalunits/4789', { 
                 'time': true
             });
 

test/v2.0-apps-constdb-datasetages-test.js

@@ -8,7 +8,7 @@ describe('tests for /v2.0/apps/constdb/datasetages', function() {
     describe('tests for get', function() {
         it('should respond 200 for "Returns an ordered array (from earliest to latest) of upload counts by month (YYYY/MM/DD; all days as 01). Months with no uploads are excluded. "', function() {
             var response = request('get', 'http://localhost:3001/v2.0/apps/constdb/datasetages', { 
-                'qs': {"dbid":25},
+                'qs': {"dbid":20},
                 'time': true
             });
 

test/v2.0-apps-constdb-datasets-test.js

@@ -8,7 +8,7 @@ describe('tests for /v2.0/apps/constdb/datasets', function() {
     describe('tests for get', function() {
         it('should respond 200 for "Returns the set of datasets contained within a constituent database, identified by the constituent database identifier. Used for quick landing page generation. "', function() {
             var response = request('get', 'http://localhost:3001/v2.0/apps/constdb/datasets', { 
-                'qs': {"dbid":7},
+                'qs': {"dbid":26},
                 'time': true
             });
 

test/v2.0-apps-constdb-datasetuploads-test.js

@@ -8,7 +8,7 @@ describe('tests for /v2.0/apps/constdb/datasetuploads', function() {
     describe('tests for get', function() {
         it('should respond 200 for "Returns an ordered array (from earliest to latest) of upload counts by month (YYYY/MM/DD; all days as 01). Months with no uploads are excluded. "', function() {
             var response = request('get', 'http://localhost:3001/v2.0/apps/constdb/datasetuploads', { 
-                'qs': {"dbid":2},
+                'qs': {"dbid":25},
                 'time': true
             });
 

test/v2.0-apps-depenvt-test.js

@@ -8,7 +8,7 @@ describe('tests for /v2.0/apps/depenvt', function() {
     describe('tests for get', function() {
         it('should respond 200 for "This returns the information about depositional environment for selected dataset/collection unit/site."', function() {
             var response = request('get', 'http://localhost:3001/v2.0/apps/depenvt', { 
-                'qs': {"siteid":8235,"datasetid":12990720,"collectionunitid":17491},
+                'qs': {"siteid":1610,"datasetid":80118037,"collectionunitid":46745},
                 'time': true
             });
 

test/v2.0-apps-taphonomysystems-test.js

@@ -8,7 +8,7 @@ describe('tests for /v2.0/apps/taphonomysystems', function() {
     describe('tests for get', function() {
         it('should respond 200 for "A table of Neotoma collection types."', function() {
             var response = request('get', 'http://localhost:3001/v2.0/apps/taphonomysystems', { 
-                'qs': {"datasettypeid":40},
+                'qs': {"datasettypeid":30},
                 'time': true
             });
 

test/v2.0-data-contacts-test.js

@@ -8,7 +8,7 @@ describe('tests for /v2.0/data/contacts', function() {
     describe('tests for get', function() {
         it('should respond 200 for "contact"', function() {
             var response = request('get', 'http://localhost:3001/v2.0/data/contacts', { 
-                'qs': {"contactid":2387,"familyname":"nU","contactname":"WwCt O'dJBx","contactstatus":"defunct","limit": 10,"offset": 0},
+                'qs': {"contactid":5583,"familyname":"Uum-WPAgUA","contactname":"m","contactstatus":"unknown","limit": 10,"offset": 0},
                 'time': true
             });
 

test/v2.0-data-contacts-{contactid}-publications-test.js

@@ -7,7 +7,7 @@ var expect = chakram.expect;
 describe('tests for /v2.0/data/contacts/{contactid}/publications', function() {
     describe('tests for get', function() {
         it('should respond 200 for "An array of publications associated with the contact."', function() {
-            var response = request('get', 'http://localhost:3001/v2.0/data/contacts/2594/publications', { 
+            var response = request('get', 'http://localhost:3001/v2.0/data/contacts/500/publications', { 
                 'time': true
             });
 

test/v2.0-data-contacts-{contactid}-sites-test.js

@@ -7,7 +7,7 @@ var expect = chakram.expect;
 describe('tests for /v2.0/data/contacts/{contactid}/sites', function() {
     describe('tests for get', function() {
         it('should respond 200 for "A Neotoma sites object."', function() {
-            var response = request('get', 'http://localhost:3001/v2.0/data/contacts/6889/sites', { 
+            var response = request('get', 'http://localhost:3001/v2.0/data/contacts/9929/sites', { 
                 'time': true
             });
 

test/v2.0-data-contacts-{contactid}-test.js

@@ -7,7 +7,7 @@ var expect = chakram.expect;
 describe('tests for /v2.0/data/contacts/{contactid}', function() {
     describe('tests for get', function() {
         it('should respond 200 for "A Neotoma contacts object."', function() {
-            var response = request('get', 'http://localhost:3001/v2.0/data/contacts/8026', { 
+            var response = request('get', 'http://localhost:3001/v2.0/data/contacts/500', { 
                 'time': true
             });
 

test/v2.0-data-datasets-db-test.js

@@ -8,7 +8,7 @@ describe('tests for /v2.0/data/datasets/db', function() {
     describe('tests for get', function() {
         it('should respond 200 for "Datasets"', function() {
             var response = request('get', 'http://localhost:3001/v2.0/data/datasets/db', { 
-                'qs': {"limit": 10,"offset": 0,"database":"Diatom Paleolimnology Data Cooperative (DPDC)"},
+                'qs': {"limit": 10,"offset": 0,"database":"Neotoma Testate Amoebae Database"},
                 'time': true
             });
 

test/v2.0-data-datasets-test.js

@@ -8,7 +8,7 @@ describe('tests for /v2.0/data/datasets', function() {
     describe('tests for get', function() {
         it('should respond 200 for "An array of datasets."', function() {
             var response = request('get', 'http://localhost:3001/v2.0/data/datasets', { 
-                'qs': {"sitename":"ea reprehenderit Duis exercitation","database":"FAUNMAP","datasettype":"specimen stable isotope","altmin": 10,"altmax": 100,"loc":"{\"type\":\"Polygon\",\"crs\":{\"type\":\"name\",\"properties\":{\"name\":\"EPSG:4326\"}},\"coordinates\":[[[13.4,55.92],[13.5,55.92],[13.5,55.95],[13.4,55.95],[13.4,55.92]]]}","siteid":1671,"datasetid":33225555,"doi":"10F3028263/I","gpid":5392,"keyword":"beyond radiocarbon","contactid":952,"taxa":"occaecat ut elit est et","ageyoung": 1000,"ageold": 10000,"ageof":21061821,"limit": 10,"offset": 0},
+                'qs': {"sitename":"in nisi amet deserunt ea","database":"Chinese Pollen Database","datasettype":"chironomid","altmin": 10,"altmax": 100,"loc":"{\"type\":\"Polygon\",\"crs\":{\"type\":\"name\",\"properties\":{\"name\":\"EPSG:4326\"}},\"coordinates\":[[[13.4,55.92],[13.5,55.92],[13.5,55.95],[13.4,55.95],[13.4,55.92]]]}","siteid":26747,"datasetid":69182564,"doi":"10A45156150/-","gpid":5392,"keyword":"bottom","contactid":6816,"taxa":"adipisicing laborum deserunt sunt","ageyoung": 1000,"ageold": 10000,"ageof":1987576,"limit": 10,"offset": 0},
                 'time': true
             });
 

test/v2.0-data-datasets-{datasetid}-assays-test.js

@@ -0,0 +1,19 @@
+'use strict';
+var mocha = require('mocha');
+var chakram = require('chakram');
+var request = chakram.request;
+var expect = chakram.expect;
+
+describe('tests for /v2.0/data/datasets/{datasetid}/assays', function() {
+    describe('tests for get', function() {
+        it('should respond 200 for "Assays"', function() {
+            var response = request('get', 'http://localhost:3001/v2.0/data/datasets/500/assays', { 
+                'time': true
+            });
+
+            expect(response).to.have.status(200);
+            return chakram.wait();
+        });
+
+    });
+});

test/v2.0-data-datasets-{datasetid}-projects-test.js

@@ -0,0 +1,19 @@
+'use strict';
+var mocha = require('mocha');
+var chakram = require('chakram');
+var request = chakram.request;
+var expect = chakram.expect;
+
+describe('tests for /v2.0/data/datasets/{datasetid}/projects', function() {
+    describe('tests for get', function() {
+        it('should respond 200 for "Projects"', function() {
+            var response = request('get', 'http://localhost:3001/v2.0/data/datasets/500/projects', { 
+                'time': true
+            });
+
+            expect(response).to.have.status(200);
+            return chakram.wait();
+        });
+
+    });
+});

test/v2.0-data-datasets_elc-test.js

@@ -8,7 +8,7 @@ describe('tests for /v2.0/data/datasets_elc', function() {
     describe('tests for get', function() {
         it('should respond 200 for "A Neotoma datasets object suitable for the EarthLife Consortium API."', function() {
             var response = request('get', 'http://localhost:3001/v2.0/data/datasets_elc', { 
-                'qs': {"siteid":7265,"contactid":10455,"datasettype":"geochronologic","altmin": 10,"altmax": 100,"loc":"{\"type\":\"Polygon\",\"crs\":{\"type\":\"name\",\"properties\":{\"name\":\"EPSG:4326\"}},\"coordinates\":[[[13.4,55.92],[13.5,55.92],[13.5,55.95],[13.4,55.95],[13.4,55.92]]]}","ageyoung": 1000,"ageold": 10000,"ageof":16732658},
+                'qs': {"siteid":24832,"contactid":6896,"datasettype":"geochemistry","altmin": 10,"altmax": 100,"loc":"{\"type\":\"Polygon\",\"crs\":{\"type\":\"name\",\"properties\":{\"name\":\"EPSG:4326\"}},\"coordinates\":[[[13.4,55.92],[13.5,55.92],[13.5,55.95],[13.4,55.95],[13.4,55.92]]]}","ageyoung": 1000,"ageold": 10000,"ageof":6017958},
                 'time': true
             });
 

test/v2.0-data-dbtables-test.js

@@ -8,7 +8,7 @@ describe('tests for /v2.0/data/dbtables', function() {
     describe('tests for get', function() {
         it('should respond 200 for "Returned table."', function() {
             var response = request('get', 'http://localhost:3001/v2.0/data/dbtables', { 
-                'qs': {"table":"voluptate pariatur","count":true,"limit": 10,"offset": 0},
+                'qs': {"table":"fugiat","count":false,"limit": 10,"offset": 0},
                 'time': true
             });
 

test/v2.0-data-dbtables-{table}-test.js

@@ -7,8 +7,8 @@ var expect = chakram.expect;
 describe('tests for /v2.0/data/dbtables/{table}', function() {
     describe('tests for get', function() {
         it('should respond 200 for "Returned table."', function() {
-            var response = request('get', 'http://localhost:3001/v2.0/data/dbtables/minimLoremExcepteur', { 
-                'qs': {"count":true,"limit": 10,"offset": 0},
+            var response = request('get', 'http://localhost:3001/v2.0/data/dbtables/deseruntaliquapariatur', { 
+                'qs': {"count":false,"limit": 10,"offset": 0},
                 'time': true
             });
 

test/v2.0-data-geopoliticalunits-test.js

@@ -8,7 +8,7 @@ describe('tests for /v2.0/data/geopoliticalunits', function() {
     describe('tests for get', function() {
         it('should respond 200 for "An array of geopolitical units."', function() {
             var response = request('get', 'http://localhost:3001/v2.0/data/geopoliticalunits', { 
-                'qs': {"gpid":5392,"gpname":"Canada","rank":2,"lower":false},
+                'qs': {"gpid":5392,"gpname":"Canada","rank":4,"lower":true},
                 'time': true
             });
 

test/v2.0-data-geopoliticalunits-{gpid}-datasets-test.js

@@ -7,7 +7,7 @@ var expect = chakram.expect;
 describe('tests for /v2.0/data/geopoliticalunits/{gpid}/datasets', function() {
     describe('tests for get', function() {
         it('should respond 200 for "An array of datasets."', function() {
-            var response = request('get', 'http://localhost:3001/v2.0/data/geopoliticalunits/90/datasets', { 
+            var response = request('get', 'http://localhost:3001/v2.0/data/geopoliticalunits/500/datasets', { 
                 'qs': {"limit": 10,"offset": 0},
                 'time': true
             });

test/v2.0-data-geopoliticalunits-{gpid}-sites-test.js

@@ -7,7 +7,7 @@ var expect = chakram.expect;
 describe('tests for /v2.0/data/geopoliticalunits/{gpid}/sites', function() {
     describe('tests for get', function() {
         it('should respond 200 for "An array of sites."', function() {
-            var response = request('get', 'http://localhost:3001/v2.0/data/geopoliticalunits/4371/sites', { 
+            var response = request('get', 'http://localhost:3001/v2.0/data/geopoliticalunits/1467/sites', { 
                 'qs': {"limit": 10,"offset": 0},
                 'time': true
             });

test/v2.0-data-geopoliticalunits-{gpid}-test.js

@@ -7,7 +7,7 @@ var expect = chakram.expect;
 describe('tests for /v2.0/data/geopoliticalunits/{gpid}', function() {
     describe('tests for get', function() {
         it('should respond 200 for "An array of geopolitical units."', function() {
-            var response = request('get', 'http://localhost:3001/v2.0/data/geopoliticalunits/4982', { 
+            var response = request('get', 'http://localhost:3001/v2.0/data/geopoliticalunits/5778', { 
                 'time': true
             });
 

test/v2.0-data-occurrences-test.js

@@ -8,7 +8,7 @@ describe('tests for /v2.0/data/occurrences', function() {
     describe('tests for get', function() {
         it('should respond 200 for "occurrence"', function() {
             var response = request('get', 'http://localhost:3001/v2.0/data/occurrences', { 
-                'qs': {"taxonname":"occaecat cupidatat labore sunt ad","taxonid":20557,"siteid":41770,"sitename":"et","datasettype":"geochemistry","altmin": 10,"altmax": 100,"loc":"{\"type\":\"Polygon\",\"crs\":{\"type\":\"name\",\"properties\":{\"name\":\"EPSG:4326\"}},\"coordinates\":[[[13.4,55.92],[13.5,55.92],[13.5,55.95],[13.4,55.95],[13.4,55.92]]]}","ageof":10629033,"ageyoung": 1000,"ageold": 10000,"limit": 10,"offset": 0},
+                'qs': {"taxonname":"magna irure anim consectetur ullamco","taxonid":21012,"siteid":49855,"sitename":"mollit","datasettype":"stable isotope","altmin": 10,"altmax": 100,"loc":"{\"type\":\"Polygon\",\"crs\":{\"type\":\"name\",\"properties\":{\"name\":\"EPSG:4326\"}},\"coordinates\":[[[13.4,55.92],[13.5,55.92],[13.5,55.95],[13.4,55.95],[13.4,55.92]]]}","ageof":2647566,"ageyoung": 1000,"ageold": 10000,"limit": 10,"offset": 0},
                 'time': true
             });
 

test/v2.0-data-pollen-test.js

@@ -8,7 +8,7 @@ describe('tests for /v2.0/data/pollen', function() {
     describe('tests for get', function() {
         it('should respond 200 for "A record of all pollen samples in time/space for a particular taxon."', function() {
             var response = request('get', 'http://localhost:3001/v2.0/data/pollen', { 
-                'qs': {"taxonname":"dolor proident dolore cillum","taxonid":45760,"siteid":7899,"sitename":"fugiat eiusmod","datasettype":"macroinvertebrate","altmin": 10,"altmax": 100,"loc":"{\"type\":\"Polygon\",\"crs\":{\"type\":\"name\",\"properties\":{\"name\":\"EPSG:4326\"}},\"coordinates\":[[[13.4,55.92],[13.5,55.92],[13.5,55.95],[13.4,55.95],[13.4,55.92]]]}","ageof":3490473,"ageyoung": 1000,"ageold": 10000,"limit": 10,"offset": 0},
+                'qs': {"taxonname":"et ad non irure quis","taxonid":45362,"siteid":39084,"sitename":"eiusmod esse ipsum","datasettype":"geochronologic","altmin": 10,"altmax": 100,"loc":"{\"type\":\"Polygon\",\"crs\":{\"type\":\"name\",\"properties\":{\"name\":\"EPSG:4326\"}},\"coordinates\":[[[13.4,55.92],[13.5,55.92],[13.5,55.95],[13.4,55.95],[13.4,55.92]]]}","ageof":5395162,"ageyoung": 1000,"ageold": 10000,"limit": 10,"offset": 0},
                 'time': true
             });
 

test/v2.0-data-pollen-{id}-test.js

@@ -7,7 +7,7 @@ var expect = chakram.expect;
 describe('tests for /v2.0/data/pollen/{id}', function() {
     describe('tests for get', function() {
         it('should respond 200 for "A record of all pollen samples in time/space for a particular taxon."', function() {
-            var response = request('get', 'http://localhost:3001/v2.0/data/pollen/9055', { 
+            var response = request('get', 'http://localhost:3001/v2.0/data/pollen/500', { 
                 'time': true
             });
 

test/v2.0-data-publications-test.js

@@ -8,7 +8,7 @@ describe('tests for /v2.0/data/publications', function() {
     describe('tests for get', function() {
         it('should respond 200 for "A list of publications."', function() {
             var response = request('get', 'http://localhost:3001/v2.0/data/publications', { 
-                'qs': {"publicationid":1255,"datasetid":13617827,"siteid":44696,"familyname":"MpTf-oof","pubtype":"Book Chapter","year":1521,"search":"ad veniam occaecat","limit": 10,"offset": 0},
+                'qs': {"publicationid":3227,"datasetid":62171686,"siteid":15473,"familyname":"Tm-","pubtype":"Other Edited","year":1958,"search":"dolor laboris ullamco ut","limit": 10,"offset": 0},
                 'time': true
             });
 

test/v2.0-data-publications-{publicationid}-test.js

@@ -7,7 +7,7 @@ var expect = chakram.expect;
 describe('tests for /v2.0/data/publications/{publicationid}', function() {
     describe('tests for get', function() {
         it('should respond 200 for "A list of publications."', function() {
-            var response = request('get', 'http://localhost:3001/v2.0/data/publications/1784', { 
+            var response = request('get', 'http://localhost:3001/v2.0/data/publications/500', { 
                 'time': true
             });