WIP Gen shotgun prep files

labcontrol/db/composition.py

@@ -1005,7 +1005,8 @@ def create(cls, process, container, volume, norm_gdna_composition,
             The container with the composition
         volume: float
             The initial volume
-        norm_gdna_composition: labcontrol.db.composition.NormalizedGDNAComposition
+        norm_gdna_composition:
+            labcontrol.db.composition.NormalizedGDNAComposition
             The source normalized gDNA composition
         i5_composition: labcontrol.db.composition.PrimerComposition
             The i5 composition

labcontrol/db/support_files/patches/1.sql

@@ -1,3 +1,8 @@
 -- April 2, 2019
 -- Implicitly track the date and time of plate creation
 ALTER TABLE labman.plate ADD COLUMN creation_timestamp timestamp NOT NULL default now();
+
+-- May 9, 2019
+-- Add constraints to existing columns for wells.
+ALTER TABLE labman.well ADD CONSTRAINT rowchk CHECK (row_num > 0);
+ALTER TABLE labman.well ADD CONSTRAINT colchk CHECK (col_num > 0);

labcontrol/db/testing.py

@@ -35,8 +35,8 @@ def reset_test_db():
     client_secret = ('J7FfQ7CQdOxuKhQAf1eoGgBAE81Ns8Gu3EKaWFm3IO2JKh'
                      'AmmCWZuabe0O5Mp28s1')
     qclient = QiitaClient(
-        "https://localhost:8383", client_id, client_secret,
-        server_cert=labcontrol.db.settings.labcontrol_settings.qiita_server_cert)
+      "https://localhost:8383", client_id, client_secret,
+      server_cert=labcontrol.db.settings.labcontrol_settings.qiita_server_cert)
     qclient.post("/apitest/reset/")
     # The above call resets the qiita schema. Qiita does not create the
     # LabControl structures, so create them here

labcontrol/db/tests/test_process.py

@@ -44,8 +44,10 @@ def load_data(filename):
 
 NORM_PROCESS_PICKLIST = load_data('norm-process-picklist.txt')
 NORM_PROCESS_PICKLIST_SID = load_data('norm-process-picklist-specimen-id.txt')
-COMBINED_SAMPLES_PREP_EXAMPLE = load_data(
-    'experimental-plus-samples-prep-example.txt')
+COMBINED_SAMPLES_AMPLICON_PREP_EXAMPLE = load_data(
+    'experimental-plus-samples-amplicon-prep-example.txt')
+COMBINED_SAMPLES_METAGENOMICS_PREP_EXAMPLE = load_data(
+    'experimental-plus-samples-metagenomics-prep-example.txt')
 SHOTGUN_SAMPLE_SHEET = load_data("shotgun_sample_sheet.txt")
 POOLING_PROCESS_ECHO_PICKLIST = load_data("pooling-process-echo-picklist.txt")
 
@@ -1935,20 +1937,19 @@ def test_generate_amplicon_prep_information(self):
         tester = SequencingProcess(1)
         obs = tester.generate_prep_information()
         exp_key = 'Test Run.1'
-        exp = {exp_key: COMBINED_SAMPLES_PREP_EXAMPLE}
+        exp = {exp_key: COMBINED_SAMPLES_AMPLICON_PREP_EXAMPLE}
         self.assertEqual(len(obs), len(exp))
         self.assertEqual(obs[exp_key], exp[exp_key])
 
     def test_generate_metagenomics_prep_information(self):
-        # Shotgun run--prep not implemented
-        exp_err = "Prep file generation is not implemented for " \
-                  "Metagenomics assays."
         tester = SequencingProcess(2)
-        with self.assertRaisesRegex(ValueError, exp_err):
-            tester.generate_prep_information()
+        obs = tester.generate_prep_information()
+        exp_key = 'TestShotgunRun1'
+        exp = {exp_key: COMBINED_SAMPLES_METAGENOMICS_PREP_EXAMPLE}
+        self.assertEqual(len(obs), len(exp))
+        self.assertEqual(obs[exp_key], exp[exp_key])
 
     def test_generate_prep_information_error(self):
-        # Shotgun run--prep not implemented
         exp_err = "Prep file generation is not implemented for this assay " \
                   "type."
         tester = SequencingProcess(3)

labcontrol/gui/templates/sequence_run_list.html

@@ -24,15 +24,11 @@
           "<span class='glyphicon glyphicon-download'></span> " +
           "Download Sample Sheet</a>";
 
-        // ToDo: #327
-        var preparationSheets = '';
-        if (row[assay_type] == 'Amplicon') {
-          preparationSheets = "<a href='/process/sequencing/" +
+        var preparationSheets = "<a href='/process/sequencing/" +
             row[sequencing_process_id] +
             "/preparation_sheets' class='btn btn-success'>" +
             "<span class='glyphicon glyphicon-download'></span> " +
             "Download Preparation Sheets</a>";
-        }
         newData.push([row[process_id], row[run_name], row[experiment_name],
             row[assay_type], row[pi_name], sampleSheet, preparationSheets]);
       }