Merge pull request #3199 from antgonza/fixes-after-2022.04

fixes after 2022.04

Author: charles-cowart

Diff for: qiita_db/artifact.py

@@ -55,6 +55,26 @@ class Artifact(qdb.base.QiitaObject):
     """
     _table = "artifact"
 
+    @classmethod
+    def iter(cls):
+        """Iterate over all artifacts in the database
+
+        Returns
+        -------
+        generator
+            Yields a `Artifact` object for each artifact in the database,
+            in order of ascending artifact_id
+        """
+        with qdb.sql_connection.TRN:
+            sql = """SELECT artifact_id FROM qiita.{}
+                     ORDER BY artifact_id""".format(cls._table)
+            qdb.sql_connection.TRN.add(sql)
+
+            ids = qdb.sql_connection.TRN.execute_fetchflatten()
+
+        for id_ in ids:
+            yield Artifact(id_)
+
     @classmethod
     def iter_by_visibility(cls, visibility):
         r"""Iterator over the artifacts with the given visibility
@@ -79,17 +99,6 @@ def iter_by_visibility(cls, visibility):
             for a_id in qdb.sql_connection.TRN.execute_fetchflatten():
                 yield cls(a_id)
 
-    @classmethod
-    def iter_public(cls):
-        r"""Iterator over the public artifacts available in the system
-
-        Returns
-        -------
-        generator of qiita_db.artifact.Artifact
-            The public artifacts available in the system
-        """
-        return cls.iter_by_visibility('public')
-
     @staticmethod
     def types():
         """Returns list of all artifact types available and their descriptions
@@ -615,12 +624,15 @@ def delete(cls, artifact_id):
                 qdb.util.move_filepaths_to_upload_folder(
                     study.id, filepaths)
 
-                sql = """UPDATE qiita.prep_template
-                         SET artifact_id = NULL
-                         WHERE prep_template_id IN %s"""
-                qdb.sql_connection.TRN.add(
-                    sql, [tuple(pt.id for a in all_artifacts
-                                for pt in a.prep_templates)])
+                # there are cases that an artifact would not be linked to a
+                # study
+                pt_ids = [tuple([pt.id]) for a in all_artifacts
+                          for pt in a.prep_templates]
+                if pt_ids:
+                    sql = """UPDATE qiita.prep_template
+                             SET artifact_id = NULL
+                             WHERE prep_template_id IN %s"""
+                    qdb.sql_connection.TRN.add(sql, pt_ids)
             else:
                 sql = """DELETE FROM qiita.parent_artifact
                          WHERE artifact_id IN %s"""

Diff for: qiita_db/test/test_artifact.py

@@ -40,10 +40,8 @@ def test_iter(self):
                qdb.artifact.Artifact(7)]
         self.assertEqual(obs, exp)
 
-    def test_iter_public(self):
-        obs = list(qdb.artifact.Artifact.iter_public())
-        exp = []
-        self.assertEqual(obs, exp)
+        exp.extend([qdb.artifact.Artifact(8), qdb.artifact.Artifact(9)])
+        self.assertEqual(list(qdb.artifact.Artifact.iter()), exp)
 
     def test_create_type(self):
         obs = qdb.artifact.Artifact.types()

Diff for: qiita_pet/support_files/doc/source/processingdata/processing-recommendations.rst

@@ -48,6 +48,14 @@ Qiita currently has one active shotgun metagenomics data analysis pipeline: a pe
 bowtie2 alignment step with Woltka classification using either the WoLr1 or Rep200 databases.
 Below you will find more information about each of these options.
 
+.. note::
+   The bowtie2 settings are maximum and minimum mismatch penalties (mp=[1,1]), a
+   penalty for ambiguities (np=1; default), read and reference gap open- and
+   extend penalties (rdg=[0,1], rfg=[0,1]), a minimum alignment score for an
+   alignment to be considered valid (score-min=[L,0,-0.05]), a defined number of
+   distinct, valid alignments (k=16), and the suppression of SAM records for
+   unaligned reads, as well as SAM headers (no-unal, no-hd).
+
 The current workflow is as follows:
 
 #. A single step per sample adapter removal (via `fastp <https://academic.oup.com/bioinformatics/article/34/17/i884/5093234>`_) and host filtering (via `minimap2 <https://academic.oup.com/bioinformatics/article/34/18/3094/4994778>`_); more information below.

Diff for: qiita_pet/templates/sitebase.html

@@ -532,11 +532,7 @@
                   </li>
                   <li role="separator" class="divider"></li>
                   <li>
-                    {% if qiita_sha=="" %}
-                      <a href="#">
-                    {% else %}
-                      <a href="https://github.com/biocore/qiita/commit/{{qiita_sha}}">
-                    {% end %}
+                    <a href="https://github.com/qiita-spots/qiita/releases">
                       <h6>
                         <b>Current version:</b></br>
                         {{qiita_version}} {{qiita_sha[0:7]}}

Diff for: qiita_ware/commands.py

@@ -43,11 +43,8 @@ def _ssh_session(p_url, private_key):
     """
     scheme = p_url.scheme
     hostname = p_url.hostname
-    # if port is '' Python 2.7.6 will raise an error
-    try:
-        port = p_url.port
-    except Exception:
-        port = 22
+
+    port = p_url.port
     username = p_url.username
 
     if scheme == 'scp':
@@ -61,8 +58,11 @@ def _ssh_session(p_url, private_key):
 
         # step 2: connect to fileserver
         key = RSAKey.from_private_key_file(private_key)
+        # we need pkeys now based on
+        # https://github.com/paramiko/paramiko/issues/1961
+        pkeys = dict(pubkeys=['rsa-sha2-256', 'rsa-sha2-512'])
         ssh.connect(hostname, port=port, username=username,
-                    pkey=key, look_for_keys=False)
+                    pkey=key, look_for_keys=False, disabled_algorithms=pkeys)
         return ssh
     else:
         raise ValueError(