Merge branch 'dev' of https://github.com/qiita-spots/qiita into dev

CHANGELOG.md

@@ -1,5 +1,24 @@
 # Qiita changelog
 
+Version 2024.07
+---------------
+
+Deployed on July 15th, 2024
+
+* On June 14th, 2024 we modified the SPP to use ["fastp & minimap2 against GRCh38.p14 + Phi X 174 + T2T-CHM13v2.0, then Movi against GRCh38.p14, T2T-CHM13v2.0 + Human Pangenome Reference Consortium release 2023"](https://github.com/cguccione/human_host_filtration) to filter human-reads.
+* Full refactor of the [DB patching system](https://github.com/qiita-spots/qiita/blob/master/CONTRIBUTING.md#patch-91sql) to make sure that a new production deployment has a fully empty database.
+* Fully removed Qiimp from Qiita.
+* Users can now add `ORCID`, `ResearchGate` and/or `GoogleScholar` information to their profile and the creation (registration) timestamp is kept in the database. Thank you @jlab.
+* Admins can now track and purge non-confirmed users from the database via the GUI (`/admin/purge_users/`). Thank you @jlab.
+* Added `qiita.slurm_resource_allocations` to store general job resource usage, which can be populated by `qiita_db.util.update_resource_allocation_table`.
+* Added `qiita_db.util.resource_allocation_plot` to generate different models to allocate resources from a given software command based on previous jobs, thank you @Gossty !
+* The stats page map can be centered via the configuration file; additionally, the Help and Admin emails are defined also via the configuration files, thank you @jlab !
+* ``Sequel IIe``, ``Revio``, and ``Onso`` are now valid instruments for the ``PacBio_SMRT`` platform.
+* Added `current_human_filtering` to the prep-information and `human_reads_filter_method` to the artifact to keep track of the method that it was used to human reads filter the raw artifact and know if it's up to date with what is expected via the best practices.
+* Added `reprocess_job_id` to the prep-information so we keep track if a preparation has been reprocessed with another job.
+* Other general fixes, like [#3385](https://github.com/qiita-spots/qiita/pull/3385), [#3397](https://github.com/qiita-spots/qiita/pull/3397), [#3399](https://github.com/qiita-spots/qiita/pull/3399), [#3400](https://github.com/qiita-spots/qiita/pull/3400), [#3409](https://github.com/qiita-spots/qiita/pull/3409), [#3410](https://github.com/qiita-spots/qiita/pull/3410).
+
+
 Version 2024.02
 ---------------
 

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/91.sql

@@ -0,0 +1,3 @@
+-- Just an empty SQL to allow the changes implemented in
+-- https://github.com/qiita-spots/qiita/pull/3403 to take effect
+SELECT 1;

qiita_db/support_files/patches/test_db_sql/92.sql

@@ -942,3 +942,13 @@ WHERE email = '[email protected]';
 INSERT INTO qiita.qiita_user VALUES ('[email protected]', 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 ('[email protected]', 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 ('[email protected]', 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;