Merge branch 'dev' of github.com:biocore/qiita into dev

Author: antgonza

qiita_db/artifact.py

@@ -1574,7 +1574,15 @@ def being_deleted_by(self):
     @property
     def has_human(self):
         has_human = False
-        if self.artifact_type == 'per_sample_FASTQ':
+        # we are going to check the metadata if:
+        # - the prep data_type is _not_ target gene
+        # - the prep is not current_human_filtering
+        # - if the artifact_type is 'per_sample_FASTQ'
+        pts = self.prep_templates
+        tgs = qdb.metadata_template.constants.TARGET_GENE_DATA_TYPES
+        ntg = any([pt.data_type() not in tgs for pt in pts])
+        chf = any([not pt.current_human_filtering for pt in pts])
+        if ntg and chf and self.artifact_type == 'per_sample_FASTQ':
             st = self.study.sample_template
             if 'env_package' in st.categories:
                 sql = f"""SELECT DISTINCT sample_values->>'env_package'

qiita_db/metadata_template/prep_template.py

@@ -1082,3 +1082,28 @@ def creation_job_id(self, creation_job_id):
                      WHERE prep_template_id = %s"""
             qdb.sql_connection.TRN.add(sql, [creation_job_id, self.id])
             qdb.sql_connection.TRN.execute()
+
+    @property
+    def current_human_filtering(self):
+        """If the preparation is current with human filtering
+
+        Returns
+        -------
+        bool
+            The current_human_filtering of the prep information
+        """
+        with qdb.sql_connection.TRN:
+            sql = """SELECT current_human_filtering
+                     FROM qiita.prep_template
+                     WHERE prep_template_id = %s"""
+            qdb.sql_connection.TRN.add(sql, [self.id])
+            return qdb.sql_connection.TRN.execute_fetchlast()
+
+    @current_human_filtering.setter
+    def current_human_filtering(self, current_human_filtering):
+        with qdb.sql_connection.TRN:
+            sql = """UPDATE qiita.prep_template
+                     SET current_human_filtering = %s
+                     WHERE prep_template_id = %s"""
+            qdb.sql_connection.TRN.add(sql, [current_human_filtering, self.id])
+            qdb.sql_connection.TRN.execute()

qiita_db/metadata_template/test/test_prep_template.py

@@ -1905,6 +1905,15 @@ def test_name_setter(self):
         pt.name = 'Prep information 1'
         self.assertEqual(pt.name, 'Prep information 1')
 
+    def test_current_human_filtering(self):
+        pt = qdb.metadata_template.prep_template.PrepTemplate(1)
+        # by default it should be false
+        self.assertFalse(pt.current_human_filtering)
+        pt.current_human_filtering = True
+        self.assertTrue(pt.current_human_filtering)
+        pt.current_human_filtering = False
+        self.assertFalse(pt.current_human_filtering)
+
 
 EXP_PREP_TEMPLATE = (
     'sample_name\tbarcode\tcenter_name\tcenter_project_name\t'

qiita_db/support_files/patches/92.sql

@@ -18,3 +18,7 @@ ALTER TABLE qiita.slurm_resource_allocations
   ADD CONSTRAINT fk_slurm_resource_allocations
   FOREIGN KEY ( processing_job_id )
   REFERENCES qiita.processing_job ( processing_job_id );
+
+-- Apr 21, 2024
+-- Adding a new column: current_human_filtering to qiita.prep_template
+ALTER TABLE qiita.prep_template ADD current_human_filtering boolean DEFAULT False;

qiita_db/support_files/qiita-db.dbs

@@ -1001,6 +1001,9 @@
 			<column name="creation_job_id" type="uuid" jt="1111" >
 				<defo><![CDATA[NULL]]></defo>
 			</column>
+			<column name="current_human_filtering" type="boolean" jt="1111" >
+				<defo><![CDATA[false]]></defo>
+			</column>
 			<index name="pk_prep_template" unique="PRIMARY_KEY" >
 				<column name="prep_template_id" />
 			</index>
@@ -2148,10 +2151,10 @@ $function$
 		<entity schema="qiita" name="user_level" color="D1BEF4" x="64" y="1520" />
 		<entity schema="qiita" name="visibility" color="BED3F4" x="2160" y="880" />
 		<script name="Sample SQL Editor" id="Editor_19ad" language="SQL" >
-			<string><![CDATA[SELECT artifact_id, generated_timestamp, command_id, command_parameters, visibility_id, artifact_type_id, data_type_id, submitted_to_vamps, 
+			<string><![CDATA[SELECT artifact_id, generated_timestamp, command_id, command_parameters, visibility_id, artifact_type_id, data_type_id, submitted_to_vamps,
 	name
 FROM
 	qiita.artifact t;]]></string>
 		</script>
 	</layout>
-</project>
+</project>