Merge pull request #24 from antgonza/fix-after-rc-testing

fixes after rc testing
qiita-spots · Dec 20, 2023 · bd235f5 · bd235f5
2 parents 71fe32d + 01f1d02
commit bd235f5
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Showing 3 changed files with 19 additions and 11 deletions.
diff --git a/qp_woltka/tests/test_woltka.py b/qp_woltka/tests/test_woltka.py
@@ -577,11 +577,13 @@ def test_calculate_cell_counts(self):
             'SKB8.640193': {
                 'run_prefix': 'S22205_S104', 'syndna_pool_number': 1,
                 'raw_reads_r1r2': 10000, 'mass_syndna_input_ng': 120,
-                'minipico_dna_concentration_ng_ul': 10, 'vol_elute_ul': 5},
+                'extracted_gdna_concentration_ng_ul': 10,
+                'vol_extracted_elution_ul': 5},
             'SKD8.640184': {
                 'run_prefix': 'S22282_S102', 'syndna_pool_number': 1,
                 'raw_reads_r1r2': 10002, 'mass_syndna_input_ng': 120,
-                'minipico_dna_concentration_ng_ul': 11, 'vol_elute_ul': 6}}
+                'extracted_gdna_concentration_ng_ul': 11,
+                'vol_extracted_elution_ul': 6}}
         data = {'prep_info': dumps(prep_info_dict),
                 'study': 1,
                 'data_type': 'Metagenomic'}

diff --git a/qp_woltka/woltka.py b/qp_woltka/woltka.py
@@ -504,7 +504,7 @@ def woltka_syndna(qclient, job_id, parameters, out_dir):
         prep = pd.read_csv(
             f'{out_dir}/prep_info.tsv', index_col=None, sep='\t')
         output = fit_linear_regression_models_for_qiita(
-            prep, load_table(fp_biom), parameters['min_sample_counts'])
+            prep, load_table(fp_biom), int(parameters['min_sample_counts']))
         # saving results to disk
         lin_regress_results_fp = f'{out_dir}/lin_regress_by_sample_id.yaml'
         fit_syndna_models_log_fp = f'{out_dir}/fit_syndna_models_log.txt'

diff --git a/scripts/start_woltka b/scripts/start_woltka
@@ -34,6 +34,20 @@ def execute(url, job_id, out_dir):
 
         qclient.update_job_step(
             job_id, "Step 1 of 4: Collecting info and generating submission")
+
+        # these were defined in qp_woltka/__init.py__ while defining the
+        # available commands for this plugin
+        valid_commands = [
+            'Woltka v0.1.4', 'SynDNA Woltka', 'Calculate Cell Counts']
+
+        # this if/elif is the current solution for
+        # https://github.com/qiita-spots/qiita/issues/3340
+        if command not in valid_commands:
+            raise ValueError(f'Not a valid command: "{command}"')
+        elif command == 'Calculate Cell Counts':
+            plugin(url, job_id, out_dir)
+            exit(0)
+
         artifact_id = parameters['input']
         del parameters['input']
         files, prep = qclient.artifact_and_preparation_files(artifact_id)
@@ -47,14 +61,6 @@ def execute(url, job_id, out_dir):
         else:
             directory = directory.pop()
 
-        # these were defined in qp_woltka/__init.py__ while defining the
-        # available commands for this plugin
-        valid_commands = [
-            'Woltka v0.1.4', 'SynDNA Woltka', 'Calculate Cell Counts']
-
-        if command not in valid_commands:
-            raise ValueError(f'Not a valid command: "{command}"')
-
         if command == 'Woltka v0.1.4':
             main_fp, merge_fp = woltka_to_array(
                 files, out_dir, parameters['Database'], prep, url, job_id)