Merge branch 'dev' of github.com:biocore/qiita into 2021.07

Author: antgonza

qiita_db/support_files/patches/82.sql

@@ -11,3 +11,45 @@ BEGIN
      ALTER TABLE settings ADD COLUMN max_preparation_samples INT DEFAULT 800;
   END IF;
 END $do$;
+
+ALTER TABLE qiita.analysis
+  DROP CONSTRAINT fk_analysis_user,
+  ADD CONSTRAINT fk_analysis_user
+    FOREIGN KEY (email)
+    REFERENCES qiita.qiita_user(email)
+    ON UPDATE CASCADE;
+
+ALTER TABLE qiita.study_users
+  DROP CONSTRAINT fk_study_users_user,
+  ADD CONSTRAINT fk_study_users_user
+    FOREIGN KEY (email)
+    REFERENCES qiita.qiita_user(email)
+    ON UPDATE CASCADE;
+
+ALTER TABLE qiita.message_user
+  DROP CONSTRAINT fk_message_user_0,
+  ADD CONSTRAINT fk_message_user_0
+    FOREIGN KEY (email)
+    REFERENCES qiita.qiita_user(email)
+    ON UPDATE CASCADE;
+
+ALTER TABLE qiita.processing_job
+  DROP CONSTRAINT fk_processing_job_qiita_user,
+  ADD CONSTRAINT fk_processing_job_qiita_user
+    FOREIGN KEY (email)
+    REFERENCES qiita.qiita_user(email)
+    ON UPDATE CASCADE;
+
+ALTER TABLE qiita.processing_job_workflow
+  DROP CONSTRAINT fk_processing_job_workflow,
+  ADD CONSTRAINT fk_processing_job_workflow
+    FOREIGN KEY (email)
+    REFERENCES qiita.qiita_user(email)
+    ON UPDATE CASCADE;
+
+ALTER TABLE qiita.study
+  DROP CONSTRAINT fk_study_user,
+  ADD CONSTRAINT fk_study_user
+    FOREIGN KEY (email)
+    REFERENCES qiita.qiita_user(email)
+    ON UPDATE CASCADE;

qiita_db/test/test_user.py

@@ -498,6 +498,17 @@ def test_jobs(self):
         # no jobs
         self.assertEqual(qdb.user.User('[email protected]').jobs(), [])
 
+    def test_update_email(self):
+        user = qdb.user.User('[email protected]')
+        with self.assertRaisesRegex(IncorrectEmailError, 'Bad email given:'):
+            user.update_email('bladfa.adferqerq@$EWE')
+
+        with self.assertRaisesRegex(IncorrectEmailError,
+                                    'This email already exists'):
+            user.update_email('[email protected]')
+
+        user.update_email('[email protected]')
+
 
 if __name__ == "__main__":
     main()

qiita_db/user.py

@@ -708,6 +708,17 @@ def jobs(self, limit=30, ignore_status=['success'], show_hidden=False):
             return [qdb.processing_job.ProcessingJob(p[0])
                     for p in qdb.sql_connection.TRN.execute_fetchindex()]
 
+    def update_email(self, email):
+        if not validate_email(email):
+            raise IncorrectEmailError(f'Bad email given: {email}')
+
+        if self.exists(email):
+            raise IncorrectEmailError(f'This email already exists: {email}')
+
+        with qdb.sql_connection.TRN:
+            sql = 'UPDATE qiita.qiita_user SET email = %s where email = %s'
+            qdb.sql_connection.TRN.add(sql, [email, self.email])
+
 
 def validate_email(email):
     """Validates an email

qiita_pet/support_files/doc/source/faq.rst

@@ -231,8 +231,33 @@ for close reference picking), and summaries.
 How to convert Qiita files to QIIME2 artifacts?
 -----------------------------------------------
 
-Please visit the `Transferring Qiita Artifacts to Qiime2 Tutorial <https://forum.qiime2.org/t/transferring-qiita-artifacts-to-qiime2/4790>`__
-in the `QIIME2 forum <https://forum.qiime2.org>`__. Note that all feature table (bioms) and analytical steps will generate qza and qzv, which are QIIME2 artifacts.
+As a reminder, Qiita and QIIME 2 artifacts are similar as they encapsulate multiple files. However, a big
+difference is that QIIME 2 only has 2 main artifact types: QZA (all kinds of files) and QZV (visualization).
+
+Here is quick reference conversion table, but please visit the `Transferring Qiita Artifacts to Qiime2 Tutorial <https://forum.qiime2.org/t/transferring-qiita-artifacts-to-qiime2/4790>`__
+in the `QIIME2 forum <https://forum.qiime2.org>`__. for more details:
+
++----------------------------+----------------------------------------------------------------------+
+| Qiita                      | QIIME 2                                                              |
++============================+======================================================================+
+| beta diversity .tsv        |  DistanceMatrix (QZA)                                                |
++----------------------------+----------------------------------------------------------------------+
+| FASTA sequence files       | FeatureData[Taxonomy | Sequence] (QZA)                               |
++----------------------------+----------------------------------------------------------------------+
+| .biom tables               | FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] (QZA)  |
++----------------------------+----------------------------------------------------------------------+
+| ordination .txt            | PCoAResults (QZA)                                                    |
++----------------------------+----------------------------------------------------------------------+
+| phylogentic tree .txt      | Phylogeny[Rooted] (QZA)                                              |
++----------------------------+----------------------------------------------------------------------+
+| alpha diversity .tsv       | SampleData[AlphaDiversity] (QZA)                                     |
++----------------------------+----------------------------------------------------------------------+
+| taxonomic classifier       | Taxonomic Classifier (QZA)                                           |
++----------------------------+----------------------------------------------------------------------+
+| all QIIME 2 visualizations | Visualization (QZV)                                                  |
++----------------------------+----------------------------------------------------------------------+
+
+Note that all feature table (bioms) and analytical steps will generate QZA and QZV, which are native QIIME2 artifacts.
 
 
 How to add extra files to a Qiita study?