qiita-spots · ElDeveloper · Sep 16, 2020 · Sep 11, 2020 · Sep 14, 2020 · Sep 15, 2020
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,16 @@
 # Qiita changelog
 
+Version 092020
+--------------
+
+* Added a new endpoint to inject artifacts to existing preparations or jobs: `/qiita_db/artifact/`
+* Outdated commands with the exact same name than newer commands will be marked as not outdated. This is helpful for cases where the commands haven't changed between version
+* Added the `add_ebi_accessions` to the `to_dataframe()` method of the information files so it can be used to `redbiom`. This will allow searching via sample or experiment accessions
+* Added the `release_validator_job` method to `ProcessingJob` method to easily retrieve the `release_validator` job of a `processing_job`
+* Re-added `STUDY_TYPE` to the EBI-ENA submission as they are required but deprecated so just adding as Other
+* Added qiime2.2020.08 to the system; which updated these plugins: qp-qiime2, qtp-biom, qtp-diversity, qtp-visualization
+* Shogun processing using Woltka will now produce 2 extra artifacts: a per genome and per gene artifacts
+
 Version 072020
 --------------
 

diff --git a/qiita_core/__init__.py b/qiita_core/__init__.py
@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "052020"
+__version__ = "092020"
diff --git a/qiita_db/__init__.py b/qiita_db/__init__.py
@@ -27,7 +27,7 @@
 from . import user
 from . import processing_job
 
-__version__ = "052020"
+__version__ = "092020"
 
 __all__ = ["analysis", "artifact",  "archive", "base", "commands",
            "environment_manager", "exceptions", "investigation", "logger",

diff --git a/qiita_db/handlers/artifact.py b/qiita_db/handlers/artifact.py
@@ -285,7 +285,8 @@ def post(self):
                           'direct_creation': True,
                           'name': aname}
             values['provenance'] = dumps(provenance)
-            prep_id = job.input_artifacts[0].id
+            # inherint the first prep info file from the first input artifact
+            prep_id = job.input_artifacts[0].prep_templates[0].id
         else:
             prep_id = int(prep_id)
 

diff --git a/qiita_db/handlers/tests/test_artifact.py b/qiita_db/handlers/tests/test_artifact.py
@@ -340,7 +340,9 @@ def test_post(self):
         # tests success by inserting a new artifact into an existing job
         original_job = qdb.processing_job.ProcessingJob(data['job_id'])
         input_artifact = original_job.input_artifacts[0]
-        self.assertEqual(len(input_artifact.children), 3)
+        original_children = input_artifact.children
+        self.assertEqual(len(original_children), 3)
+
         # send the new data
         del data['prep_id']
         obs = self.post('/qiita_db/artifact/', headers=self.header, data=data)
@@ -353,12 +355,17 @@ def test_post(self):
         # now the original job should have 4 children and make sure they have
         # the same parent and parameters
         children = input_artifact.children
+        new_children = list(set(children) - set(original_children))[0]
         self.assertEqual(len(children), 4)
         for c in children[1:]:
             self.assertCountEqual(children[0].processing_parameters.values,
                                   c.processing_parameters.values)
             self.assertEqual(children[0].parents, c.parents)
 
+        # making sure the new artifact is part of the descendants, which is a
+        # different method and usage than children method
+        self.assertIn(new_children, input_artifact.descendants.nodes)
+
         # now let's test adding an artifact directly to a new prep
         new_prep = qdb.metadata_template.prep_template.PrepTemplate.create(
             pd.DataFrame({'new_col': {'1.SKB1.640202': 1,

diff --git a/qiita_db/processing_job.py b/qiita_db/processing_job.py
@@ -1133,12 +1133,23 @@ def _complete_artifact_definition(self, artifact_data):
                 provenance = loads(job_params['provenance'])
                 if provenance.get('direct_creation', False):
                     original_job = ProcessingJob(provenance['job'])
-                    qdb.artifact.Artifact.create(
+                    artifact = qdb.artifact.Artifact.create(
                         filepaths, atype,
                         parents=original_job.input_artifacts,
                         processing_parameters=original_job.parameters,
                         analysis=job_params['analysis'],
                         name=job_params['name'])
+
+                    sql = """
+                        INSERT INTO qiita.artifact_output_processing_job
+                            (artifact_id, processing_job_id,
+                             command_output_id)
+                         VALUES (%s, %s, %s)"""
+                    qdb.sql_connection.TRN.add(
+                        sql, [artifact.id, original_job.id,
+                              provenance['cmd_out_id']])
+                    qdb.sql_connection.TRN.execute()
+
                     self._set_status('success')
                 else:
                     if provenance.get('data_type') is not None:

diff --git a/qiita_db/test/test_software.py b/qiita_db/test/test_software.py
@@ -383,23 +383,24 @@ def test_create(self):
             'analysis': ('analysis', None),
             'files': ('string', None),
             'artifact_type': ('string', None)}
-        obs = qdb.software.Command.create(
+        validate = qdb.software.Command.create(
             software, "Validate", "Test creating a validate command",
             parameters)
-        self.assertEqual(obs.name, "Validate")
-        self.assertEqual(obs.description, "Test creating a validate command")
+        self.assertEqual(validate.name, "Validate")
+        self.assertEqual(
+            validate.description, "Test creating a validate command")
         exp_required = {
             'template': ('prep_template', [None]),
             'analysis': ('analysis', [None]),
             'files': ('string', [None]),
             'artifact_type': ('string', [None])}
-        self.assertEqual(obs.required_parameters, exp_required)
+        self.assertEqual(validate.required_parameters, exp_required)
         exp_optional = {'name': ['string', 'dflt_name'],
                         'provenance': ['string', None]}
-        self.assertEqual(obs.optional_parameters, exp_optional)
-        self.assertFalse(obs.analysis_only)
-        self.assertEqual(obs.naming_order, [])
-        self.assertEqual(obs.merging_scheme,
+        self.assertEqual(validate.optional_parameters, exp_optional)
+        self.assertFalse(validate.analysis_only)
+        self.assertEqual(validate.naming_order, [])
+        self.assertEqual(validate.merging_scheme,
                          {'parameters': [], 'outputs': [],
                           'ignore_parent_command': False})
 
@@ -440,11 +441,21 @@ def test_create(self):
         self.assertFalse(old_cmd.active)
 
         # 2. let's create a new command with the same name and check that now
-        #    the old and the new are active
+        #    the old and the new are active. Remember the new command is going
+        #    to be created in a new software that has a Validate command which
+        #    is an 'artifact definition', so this will allow us to test that
+        #    a previous Validate command is not active
         new_cmd = qdb.software.Command.create(
             software, cmd_name, cmd_name, parameters, outputs=outputs)
+        self.assertEqual(old_cmd.name, new_cmd.name)
         self.assertTrue(old_cmd.active)
         self.assertTrue(new_cmd.active)
+        # find an old Validate command
+        old_validate = [c for c in qdb.software.Software.from_name_and_version(
+            'BIOM type', '2.1.4 - Qiime2').commands if c.name == 'Validate'][0]
+        self.assertEqual(old_validate.name, validate.name)
+        self.assertTrue(validate.active)
+        self.assertFalse(old_validate.active)
 
     def test_activate(self):
         qdb.software.Software.deactivate_all()

diff --git a/qiita_pet/__init__.py b/qiita_pet/__init__.py
@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "052020"
+__version__ = "092020"
diff --git a/qiita_pet/handlers/api_proxy/__init__.py b/qiita_pet/handlers/api_proxy/__init__.py
@@ -38,7 +38,7 @@
 from .user import (user_jobs_get_req)
 from .util import check_access, check_fp
 
-__version__ = "052020"
+__version__ = "092020"
 
 __all__ = ['prep_template_summary_get_req', 'data_types_get_req',
            'study_get_req', 'sample_template_filepaths_get_req',

diff --git a/qiita_pet/support_files/doc/source/dev/rest.rst b/qiita_pet/support_files/doc/source/dev/rest.rst
@@ -43,6 +43,14 @@ the important parts of the values are described in the Parameters column.
 |PATCH   | ``/qiita_db/artifacts/<artifact_id>/``                                            | ``op: operation``, ``path: path``,      | Retrieves the artifact information                  | ArtifactHandler            |
 |        |                                                                                   | ``value: value``                        |                                                     |                            |
 +--------+-----------------------------------------------------------------------------------+-----------------------------------------+-----------------------------------------------------+----------------------------+
+|POST    | ``/qiita_db/artifact/``                                                           | ``user_email: str``,                    | Injects artifacts to existing prep templates or     | APIArtifactHandler         |
+|        |                                                                                   | ``artifact_type: str``,                 | jobs                                                |                            |
+|        |                                                                                   | ``files: JSON of {'filepath_types':     |                                                     |                            |
+|        |                                                                                   | [filepaths]}``                          |                                                     |                            |
+|        |                                                                                   | ``command_artifact_name: str``,         |                                                     |                            |
+|        |                                                                                   | ``job_id: str, optional``,              |                                                     |                            |
+|        |                                                                                   | ``prep_id: int, optional``,             |                                                     |                            |
++--------+-----------------------------------------------------------------------------------+-----------------------------------------+-----------------------------------------------------+----------------------------+
 |GET     | ``/qiita_db/users/``                                                              |                                         | Retrieves the email and name of all the users       | UsersListDBHandler         |
 +--------+-----------------------------------------------------------------------------------+-----------------------------------------+-----------------------------------------------------+----------------------------+
 |GET     | ``/qiita_db/user/<email>/data/``                                                  |                                         | Retrieves the user information                      | UserInfoDBHandlerTests     |

diff --git a/qiita_ware/__init__.py b/qiita_ware/__init__.py
@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "052020"
+__version__ = "092020"
diff --git a/setup.py b/setup.py
@@ -10,7 +10,7 @@
 from setuptools import setup
 from glob import glob
 
-__version__ = "052020"
+__version__ = "092020"
 
 
 classes = """