some cleanup + sample_info PrepTemplateDataHandler

qiita-spots · Dec 12, 2023 · e8997e0 · e8997e0
1 parent baf66af
commit e8997e0
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Showing 6 changed files with 47 additions and 5 deletions.
diff --git a/qiita_db/handlers/prep_template.py b/qiita_db/handlers/prep_template.py
@@ -108,9 +108,16 @@ def get(self, prep_id):
         dict
             The contents of the prep information keyed by sample id
         """
+        sample_info = self.get_argument('sample_information', False)
+
         with qdb.sql_connection.TRN:
             pt = _get_prep_template(prep_id)
-            response = {'data': pt.to_dataframe().to_dict(orient='index')}
+            if not sample_info:
+                response = {'data': pt.to_dataframe().to_dict(orient='index')}
+            else:
+                ST = qdb.metadata_template.sample_template.SampleTemplate
+                response = {'data': ST(pt.study_id).to_dataframe(
+                    samples=list(pt)).to_dict(orient='index')}
 
         self.write(response)
 

diff --git a/qiita_db/handlers/tests/test_prep_template.py b/qiita_db/handlers/tests/test_prep_template.py
@@ -130,6 +130,41 @@ def test_get(self):
             'qiita_prep_id': '1'}
         self.assertEqual(obs, exp)
 
+    def test_get_sample_information(self):
+        obs = self.get(
+            '/qiita_db/prep_template/1/data/?sample_information=true',
+            headers=self.header)
+        self.assertEqual(obs.code, 200)
+
+        obs = loads(obs.body)
+        self.assertCountEqual(obs.keys(), ['data'])
+
+        # let's just check that the samples and the keys from the first element
+        # match - this assures us that is the sample_info, the rest is
+        # basically the same as the regular prep_info
+        obs = obs['data']
+        exp = ['1.SKB2.640194', '1.SKM4.640180', '1.SKB3.640195',
+               '1.SKB6.640176', '1.SKD6.640190', '1.SKM6.640187',
+               '1.SKD9.640182', '1.SKM8.640201', '1.SKM2.640199',
+               '1.SKD2.640178', '1.SKB7.640196', '1.SKD4.640185',
+               '1.SKB8.640193', '1.SKM3.640197', '1.SKD5.640186',
+               '1.SKB1.640202', '1.SKM1.640183', '1.SKD1.640179',
+               '1.SKD3.640198', '1.SKB5.640181', '1.SKB4.640189',
+               '1.SKB9.640200', '1.SKM9.640192', '1.SKD8.640184',
+               '1.SKM5.640177', '1.SKM7.640188', '1.SKD7.640191']
+        self.assertCountEqual(list(obs.keys()), exp)
+        exp = ['ph', 'temp', 'depth', 'country', 'texture', 'altitude',
+               'latitude', 'taxon_id', 'elevation', 'env_biome', 'longitude',
+               'tot_nitro', 'host_taxid', 'common_name', 'description',
+               'env_feature', 'env_package', 'sample_type', 'tot_org_carb',
+               'dna_extracted', 'samp_salinity', 'anonymized_name',
+               'host_subject_id', 'scientific_name', 'assigned_from_geo',
+               'season_environment', 'water_content_soil',
+               'collection_timestamp', 'description_duplicate',
+               'physical_specimen_location', 'physical_specimen_remaining',
+               'qiita_study_id']
+        self.assertCountEqual(obs['1.SKB2.640194'].keys(), exp)
+
 
 class PrepTemplateAPItestHandlerTests(OauthTestingBase):
     def test_post(self):

diff --git a/qiita_db/metadata_template/prep_template.py b/qiita_db/metadata_template/prep_template.py
@@ -328,7 +328,7 @@ def columns_restrictions(self):
         Returns
         -------
         dict
-            The dict of restictions based on the data_type
+            The dict of restrictions based on the data_type
         """
         pt_cols = deepcopy(PREP_TEMPLATE_COLUMNS)
         if self.data_type() in TARGET_GENE_DATA_TYPES:

diff --git a/qiita_db/metadata_template/sample_template.py b/qiita_db/metadata_template/sample_template.py
@@ -168,7 +168,7 @@ def columns_restrictions(self):
         Returns
         -------
         dict
-            The dict of restictions
+            The dict of restrictions
         """
         return qdb.metadata_template.constants.SAMPLE_TEMPLATE_COLUMNS
 

diff --git a/qiita_pet/templates/workflows.html b/qiita_pet/templates/workflows.html
@@ -90,7 +90,7 @@ <h5>Hover on the spheres to get more information</h5>
             <h4>
               Application: {{', '.join(w['data_types'])}} ->
               {% if w['parameters_sample'] or w['parameters_prep'] %}
-                  parameter restictions:
+                  parameter restrictions:
                   <br/>
                   <ul>
                   {% if w['parameters_sample'] %}

diff --git a/qiita_ware/ebi.py b/qiita_ware/ebi.py
@@ -191,7 +191,7 @@ def __init__(self, artifact_id, action):
         st_restrictions = [self.sample_template.columns_restrictions['EBI']]
         pt_restrictions = [self.prep_template.columns_restrictions['EBI']]
         if self.artifact.data_type in TARGET_GENE_DATA_TYPES:
-            # adding restictions on primer and barcode as these are
+            # adding restrictions on primer and barcode as these are
             # conditionally requiered for target gene
             pt_restrictions.append(
                 PREP_TEMPLATE_COLUMNS_TARGET_GENE['demultiplex'])