Human reads filter method (#3422)

* Update CHANGELOG.md

* human_reads_filter_method

* address @charles-cowart comment and expose value to the GUI

Author: antgonza

qiita_db/artifact.py

@@ -1684,3 +1684,51 @@ def get_commands(self):
                 cids = cmds & cids
 
             return [qdb.software.Command(cid) for cid in cids]
+
+    @property
+    def human_reads_filter_method(self):
+        """The human_reads_filter_method of the artifact
+
+        Returns
+        -------
+        str
+            The human_reads_filter_method name
+        """
+        with qdb.sql_connection.TRN:
+            sql = """SELECT human_reads_filter_method
+                     FROM qiita.artifact
+                     LEFT JOIN qiita.human_reads_filter_method
+                        USING (human_reads_filter_method_id)
+                     WHERE artifact_id = %s"""
+            qdb.sql_connection.TRN.add(sql, [self.id])
+            return qdb.sql_connection.TRN.execute_fetchlast()
+
+    @human_reads_filter_method.setter
+    def human_reads_filter_method(self, value):
+        """Set the human_reads_filter_method of the artifact
+
+        Parameters
+        ----------
+        value : str
+            The new artifact's human_reads_filter_method
+
+        Raises
+        ------
+        ValueError
+            If `value` doesn't exist in the database
+        """
+        with qdb.sql_connection.TRN:
+            sql = """SELECT human_reads_filter_method_id
+                     FROM qiita.human_reads_filter_method
+                     WHERE human_reads_filter_method = %s"""
+            qdb.sql_connection.TRN.add(sql, [value])
+            idx = qdb.sql_connection.TRN.execute_fetchflatten()
+
+            if len(idx) == 0:
+                raise ValueError(
+                    f'"{value}" is not a valid human_reads_filter_method')
+
+            sql = """UPDATE qiita.artifact
+                     SET human_reads_filter_method_id = %s
+                     WHERE artifact_id = %s"""
+            qdb.sql_connection.TRN.add(sql, [idx[0], self.id])

qiita_db/support_files/patches/92.sql

@@ -48,19 +48,18 @@ ALTER TABLE qiita.qiita_user ADD social_orcid character varying DEFAULT NULL;
 ALTER TABLE qiita.qiita_user ADD social_researchgate character varying DEFAULT NULL;
 ALTER TABLE qiita.qiita_user ADD social_googlescholar character varying DEFAULT NULL;
 
+-- Jul 1, 2024
 -- Add human_reads_filter_method so we can keep track of the available methods
 -- and link them to the preparations
 
-CREATE  TABLE qiita.human_reads_filter_method (
-	human_reads_filter_method_id    bigint  NOT NULL,
-	human_reads_filter_method_method character varying NOT NULL,
-	CONSTRAINT pk_human_reads_filter_method_id PRIMARY KEY (
-    human_reads_filter_method_id )
- );
+CREATE TABLE qiita.human_reads_filter_method (
+	human_reads_filter_method_id    SERIAL PRIMARY KEY,
+	human_reads_filter_method character varying NOT NULL
+);
 
-ALTER TABLE qiita.prep_template
+ALTER TABLE qiita.artifact
   ADD human_reads_filter_method_id bigint DEFAULT NULL;
-ALTER TABLE qiita.prep_template
+ALTER TABLE qiita.artifact
   ADD CONSTRAINT fk_human_reads_filter_method
   FOREIGN KEY ( human_reads_filter_method_id )
   REFERENCES qiita.human_reads_filter_method ( human_reads_filter_method_id );

qiita_db/support_files/patches/test_db_sql/92.sql

@@ -942,3 +942,13 @@ WHERE email = 'test@foo.bar';
 INSERT INTO qiita.qiita_user VALUES ('justnow@nonvalidat.ed', 5, '$2a$12$gnUi8Qg.0tvW243v889BhOBhWLIHyIJjjgaG6dxuRJkUM8nXG9Efe', 'JustNow', 'NonVeriUser', '1634 Edgemont Avenue', '303-492-1984', NULL, NULL, NULL, false, NOW(), NULL, NULL, NULL);
 INSERT INTO qiita.qiita_user VALUES ('ayearago@nonvalidat.ed', 5, '$2a$12$gnUi8Qg.0tvW243v889BhOBhWLIHyIJjjgaG6dxuRJkUM8nXG9Efe', 'Oldie', 'NonVeriUser', '172 New Lane', '102-111-1984', NULL, NULL, NULL, false, NOW() - INTERVAL '1 YEAR', NULL, NULL, NULL);
 INSERT INTO qiita.qiita_user VALUES ('3Xdays@nonvalidat.ed', 5, '$2a$12$gnUi8Qg.0tvW243v889BhOBhWLIHyIJjjgaG6dxuRJkUM8nXG9Efe', 'TooLate', 'NonVeriUser', '564 C Street', '508-492-222', NULL, NULL, NULL, false, NOW() - INTERVAL '30 DAY', NULL, NULL, NULL);
+
+-- Jul 1, 2024
+-- Inserting a human_reads_filter_method and assigning it to the raw data in prep/artifact 1
+INSERT INTO qiita.human_reads_filter_method (
+    human_reads_filter_method)
+  VALUES (
+    'The greatest human filtering method');
+UPDATE qiita.artifact
+  SET human_reads_filter_method_id = 1
+  WHERE artifact_id = 1;

qiita_db/support_files/qiita-db.dbs

@@ -1243,6 +1243,7 @@ def test_name_setter(self):
     def test_visibility_setter(self):
         a = qdb.artifact.Artifact.create(
             self.filepaths_root, "FASTQ", prep_template=self.prep_template)
+
         self.assertEqual(a.visibility, "sandbox")
         a.visibility = "awaiting_approval"
         self.assertEqual(a.visibility, "awaiting_approval")
@@ -1285,6 +1286,24 @@ def test_visibility_setter(self):
         self.assertEqual(a5.visibility, "private")
         self.assertEqual(a6.visibility, "private")
 
+        # testing human_reads_filter_method here as in the future we might
+        # want to check that this property is inherited as visibility is;
+        # however, for the time being we don't need to do that and there is
+        # no downside on adding it here.
+        mtd = 'The greatest human filtering method'
+        self.assertEqual(mtd, a1.human_reads_filter_method)
+        self.assertIsNone(a2.human_reads_filter_method)
+        self.assertIsNone(a3.human_reads_filter_method)
+
+        # let's change some values
+        with self.assertRaisesRegex(ValueError, '"This should fail" is not a '
+                                    'valid human_reads_filter_method'):
+            a2.human_reads_filter_method = 'This should fail'
+        self.assertIsNone(a2.human_reads_filter_method)
+        a2.human_reads_filter_method = mtd
+        self.assertEqual(mtd, a2.human_reads_filter_method)
+        self.assertIsNone(a3.human_reads_filter_method)
+
     def test_ebi_run_accessions_setter(self):
         a = qdb.artifact.Artifact(3)
         self.assertEqual(a.ebi_run_accessions, dict())

qiita_db/support_files/qiita-db.html

@@ -88,6 +88,13 @@ def get(self):
                         'output'].html_summary_fp[1]
                     summary = relpath(_file, qiita_config.base_data_dir)
             res['creation_job_artifact_summary'] = summary
+        # res['']
+        res['human_reads_filter_method'] = None
+        a = PrepTemplate(prep_id).artifact
+        if a is not None:
+            hrfm = a.human_reads_filter_method
+            if hrfm is not None:
+                res['human_reads_filter_method'] = hrfm
 
         self.render('study_ajax/prep_summary.html', **res)
 

qiita_db/test/test_artifact.py

@@ -467,6 +467,10 @@ <h5>
 
 <div class="row">
   <div class="col-md-12">
+    {% if human_reads_filter_method is not None %}
+      <h7> The raw data of this preparation was pre-processed via: <b>{{ human_reads_filter_method }}</b></h7>
+    {% end %}
+
     <ul class="nav nav-pills">
       <li style="border: 1px solid #428bca; border-radius: 5px"><a data-toggle="tab" href="#sample-listing-tab-div">Sample Listing</a></li>
       <li style="border: 1px solid #428bca; border-radius: 5px"><a data-toggle="tab" href="#summary-tab-div">Summary</a></li>