add execute_pipeline to StandardMetatranscriptomicWorkflow (#101)

antgonza · web-flow · commit d7aec03a61bb · 2025-03-17T12:04:00.000-06:00
* add execute_pipeline to StandardMetatranscriptomicWorkflow

* fix CI

* fix configure_klp.py
diff --git a/.github/workflows/qiita-plugin-ci.yml b/.github/workflows/qiita-plugin-ci.yml
@@ -2,7 +2,7 @@
 
 on:
   push:
-    branches: [ dev ]
+    branches: [dev]
   pull_request:
 
 jobs:
@@ -83,7 +83,7 @@ jobs:
 
           conda activate klp
 
-          export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/server.crt
+          export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
           export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
           pip --quiet install -U pip
 
@@ -95,8 +95,8 @@ jobs:
 
           export QP_KLP_CONFIG_FP=`pwd`/configuration.json
 
-          configure_qtp_job_output_folder --env-script "source /home/runner/.profile; conda activate klp" --server-cert $QIITA_SERVER_CERT
-          configure_klp --env-script "source /home/runner/.profile; export QP_KLP_CONFIG_FP=$QP_KLP_CONFIG_FP; conda activate klp" --server-cert $QIITA_SERVER_CERT
+          configure_qtp_job_output_folder --env-script "source /home/runner/.profile; conda activate klp" --ca-cert $QIITA_ROOTCA_CERT
+          configure_klp --env-script "source /home/runner/.profile; export QP_KLP_CONFIG_FP=$QP_KLP_CONFIG_FP; conda activate klp" --ca-cert $QIITA_ROOTCA_CERT
 
           echo "Available Qiita plugins"
           ls ~/.qiita_plugins/
@@ -105,7 +105,7 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate qiita
-          export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/server.crt
+          export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
           export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
           sed "s#/home/runner/work/qiita/qiita#${PWD}/qiita-dev/#g" `pwd`/qiita-dev/qiita_core/support_files/config_test.cfg > ${QIITA_CONFIG_FP}
 
@@ -137,28 +137,27 @@ jobs:
           COVER_PACKAGE: ${{ matrix.cover_package }}
         run: |
           conda activate klp
-          export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/server.crt
+          export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
           export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
           export QP_KLP_CONFIG_FP=`pwd`/configuration.json
           export PYTHONWARNINGS="ignore:Certificate for localhost has no \`subjectAltName\`"
           nosetests --with-doctest --with-coverage -v --cover-package=qp_klp
       - uses: codecov/codecov-action@v3
         with:
-         token: ${{ secrets.CODECOV_TOKEN }}
+          token: ${{ secrets.CODECOV_TOKEN }}
 
   lint:
     runs-on: ubuntu-latest
     steps:
-    - name: flake8
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.9
-    - name: install dependencies
-      run: python -m pip install --upgrade pip
-    - name: Check out repository code
-      uses: actions/checkout@v2
-    - name: lint
-      run: |
-        pip install -q flake8
-        flake8 qp_klp
-
+      - name: flake8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+      - name: install dependencies
+        run: python -m pip install --upgrade pip
+      - name: Check out repository code
+        uses: actions/checkout@v2
+      - name: lint
+        run: |
+          pip install -q flake8
+          flake8 qp_klp
diff --git a/.gitignore b/.gitignore
@@ -127,3 +127,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# ignore local changes
+qp_klp/tests/data/sample-sheets/*/*/*.csv
diff --git a/qp_klp/Assays.py b/qp_klp/Assays.py
@@ -521,11 +521,6 @@ def load_preps_into_qiita(self):
 
         return df
 
-
-class Metagenomic(MetaOmic):
-    METAGENOMIC_TYPE = 'Metagenomic'
-    assay_type = ASSAY_NAME_METAGENOMIC
-
     def execute_pipeline(self):
         '''
         Executes steps of pipeline in proper sequence.
@@ -632,6 +627,11 @@ def execute_pipeline(self):
             self.execute_commands()
 
 
+class Metagenomic(MetaOmic):
+    METAGENOMIC_TYPE = 'Metagenomic'
+    assay_type = ASSAY_NAME_METAGENOMIC
+
+
 class Metatranscriptomic(MetaOmic):
     METATRANSCRIPTOMIC_TYPE = 'Metatranscriptomic'
     assay_type = ASSAY_NAME_METATRANSCRIPTOMIC
diff --git a/qp_klp/scripts/configure_klp.py b/qp_klp/scripts/configure_klp.py
@@ -16,13 +16,13 @@
 @click.command()
 @click.option('--env-script', prompt='Environment script', required=True,
               default='source activate qp-klp')
-@click.option('--server-cert', prompt='Server certificate', required=False,
+@click.option('--ca-cert', prompt='Server certificate', required=False,
               default='None', show_default=True)
-def config(env_script, server_cert):
+def config(env_script, ca_cert):
     """Generates the Qiita configuration files"""
-    if server_cert == 'None':
-        server_cert = None
-    plugin.generate_config(env_script, 'start_klp', server_cert=server_cert)
+    if ca_cert == 'None':
+        ca_cert = None
+    plugin.generate_config(env_script, 'start_klp', ca_cert)
 
 
 if __name__ == '__main__':
diff --git a/qp_klp/tests/test_WorkflowFactory.py b/qp_klp/tests/test_WorkflowFactory.py
@@ -6,17 +6,19 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 from qp_klp.WorkflowFactory import WorkflowFactory
-from unittest import TestCase
+from unittest import main
 from os import makedirs
 from qp_klp.Protocol import (PROTOCOL_NAME_ILLUMINA,
                              PROTOCOL_NAME_TELLSEQ)
 from qp_klp.Assays import (ASSAY_NAME_METAGENOMIC,
                            ASSAY_NAME_METATRANSCRIPTOMIC,
                            ASSAY_NAME_AMPLICON)
 from shutil import rmtree
+from qiita_client.testing import PluginTestCase
+from qiita_client.exceptions import NotFoundError
 
 
-class WorkflowFactoryTests(TestCase):
+class WorkflowFactoryTests(PluginTestCase):
     def setUp(self):
         self.remove_these = []
 
@@ -100,7 +102,7 @@ def test_invalid_sample_sheets(self):
     def test_metagenomic_workflow_creation(self):
         kwargs = {"uif_path": "qp_klp/tests/data/sample-sheets/metagenomic/"
                   "illumina/good_sheet1.csv",
-                  "qclient": None,
+                  "qclient": self.qclient,
                   "lane_number": "1",
                   "config_fp": "qp_klp/tests/data/configuration.json",
                   "run_identifier": "211021_A00000_0000_SAMPLE",
@@ -117,10 +119,14 @@ def test_metagenomic_workflow_creation(self):
         self.assertEqual(wf.protocol_type, PROTOCOL_NAME_ILLUMINA)
         self.assertEqual(wf.assay_type, ASSAY_NAME_METAGENOMIC)
 
+        with self.assertRaisesRegex(
+                NotFoundError, '{"message": "Study not found"}'):
+            wf.execute_pipeline()
+
     def test_metatranscriptomic_workflow_creation(self):
         kwargs = {"uif_path": "qp_klp/tests/data/sample-sheets/"
                   "metatranscriptomic/illumina/good_sheet1.csv",
-                  "qclient": None,
+                  "qclient": self.qclient,
                   "lane_number": "1",
                   "config_fp": "qp_klp/tests/data/configuration.json",
                   "run_identifier": "211021_A00000_0000_SAMPLE",
@@ -137,9 +143,13 @@ def test_metatranscriptomic_workflow_creation(self):
         self.assertEqual(wf.protocol_type, PROTOCOL_NAME_ILLUMINA)
         self.assertEqual(wf.assay_type, ASSAY_NAME_METATRANSCRIPTOMIC)
 
+        with self.assertRaisesRegex(
+                NotFoundError, '{"message": "Study not found"}'):
+            wf.execute_pipeline()
+
     def test_amplicon_workflow_creation(self):
         kwargs = {"uif_path": "qp_klp/tests/data/pre-preps/good_pre_prep1.txt",
-                  "qclient": None,
+                  "qclient": self.qclient,
                   "config_fp": "qp_klp/tests/data/configuration.json",
                   "run_identifier": "211021_A00000_0000_SAMPLE",
                   "output_dir": "qp_klp/tests/test_output",
@@ -155,10 +165,14 @@ def test_amplicon_workflow_creation(self):
         self.assertEqual(wf.protocol_type, PROTOCOL_NAME_ILLUMINA)
         self.assertEqual(wf.assay_type, ASSAY_NAME_AMPLICON)
 
+        with self.assertRaisesRegex(
+                NotFoundError, '{"message": "Study not found"}'):
+            wf.execute_pipeline()
+
     def test_tellseq_workflow_creation(self):
         kwargs = {"uif_path": "qp_klp/tests/data/sample-sheets/metagenomic/"
                   "tellseq/good_sheet1.csv",
-                  "qclient": None,
+                  "qclient": self.qclient,
                   "config_fp": "qp_klp/tests/data/configuration.json",
                   "run_identifier": "211021_A00000_0000_SAMPLE",
                   "output_dir": "qp_klp/tests/test_output",
@@ -174,3 +188,11 @@ def test_tellseq_workflow_creation(self):
         # confirm that the proper type of workflow was generated.
         self.assertEqual(wf.protocol_type, PROTOCOL_NAME_TELLSEQ)
         self.assertEqual(wf.assay_type, ASSAY_NAME_METAGENOMIC)
+
+        with self.assertRaisesRegex(
+                NotFoundError, '{"message": "Study not found"}'):
+            wf.execute_pipeline()
+
+
+if __name__ == '__main__':
+    main()
