FASTA_preprocessed allowed files prefixed by sample_names (#48)

* ci changes * FASTA_preprocessed by sample_names * fix test
qiita-spots · Jan 31, 2025 · 4a325e7 · 4a325e7
1 parent 508d124
commit 4a325e7
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Showing 4 changed files with 69 additions and 28 deletions.
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:
@@ -70,7 +70,7 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate qiita
-          pip install qiita-dev/ --no-binary redbiom
+          pip --quiet install qiita-dev/ --no-binary redbiom
           mkdir ~/.qiita_plugins
 
       - name: Install plugins
@@ -80,17 +80,17 @@ jobs:
           conda create -q --yes -n qtp-sequencing python=3.9 pip pigz quast fqtools
           conda activate qtp-sequencing
 
-          export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.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 install -U pip
           pip install .
-          configure_qtp_sequencing --env-script "source /home/runner/.profile; conda activate qtp-sequencing" --server-cert $QIITA_SERVER_CERT
+          configure_qtp_sequencing --env-script "source /home/runner/.profile; conda activate qtp-sequencing" --ca-cert $QIITA_ROOTCA_CERT
 
       - name: Starting services
         shell: bash -l {0}
         run: |
           conda activate qiita
-          export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.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}
 
@@ -123,7 +123,7 @@ jobs:
           COVER_PACKAGE: ${{ matrix.cover_package }}
         run: |
           conda activate qtp-sequencing
-          export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.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
 
           nosetests --with-doctest --with-coverage -v --cover-package=qtp_sequencing
@@ -135,21 +135,21 @@ jobs:
 
       - uses: codecov/codecov-action@v1
         with:
-         token: ${{ secrets.CODECOV_TOKEN }}
-         file: codecov.yml
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: codecov.yml
 
   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 qtp_sequencing setup.py scripts/*
+      - 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 qtp_sequencing setup.py scripts/*
diff --git a/qtp_sequencing/tests/test_validate.py b/qtp_sequencing/tests/test_validate.py
@@ -728,6 +728,33 @@ def test_validate_FASTA_preprocessed(self):
         exp = [ArtifactInfo(None, atype, files)]
         self.assertEqual(obs_ainfo, exp)
 
+    def test_validate_FASTA_preprocessed_samplename(self):
+        prep_info = {"1.SKB2.640194": {"run_prefix": "s1"},
+                     "1.SKM4.640180": {"run_prefix": "s2"},
+                     "1.SKB3.640195": {"run_prefix": "s3"},
+                     "1.SKB6.640176": {"run_prefix": "s4"}}
+
+        files = {'preprocessed_fasta': [
+            '/path/to/1.SKB2.640194.fna', '/path/to/1.SKM4.640180.fna',
+            '/path/to/1.SKB3.640195.fna', '/path/to/1.SKB6.640176.fna']}
+
+        out_dir = mkdtemp()
+        self._clean_up_files.append(out_dir)
+
+        atype = 'FASTA_preprocessed'
+        job_id, _ = self._create_template_and_job(prep_info, files, atype)
+        obs_success, obs_ainfo, obs_error = _validate_multiple(
+            self.qclient, job_id, prep_info, files, atype, True)
+        self.assertEqual(obs_error, "")
+        self.assertTrue(obs_success)
+
+        files = [('/path/to/1.SKB2.640194.fna.gz', 'preprocessed_fasta'),
+                 ('/path/to/1.SKM4.640180.fna.gz', 'preprocessed_fasta'),
+                 ('/path/to/1.SKB3.640195.fna.gz', 'preprocessed_fasta'),
+                 ('/path/to/1.SKB6.640176.fna.gz', 'preprocessed_fasta')]
+        exp = [ArtifactInfo(None, atype, files)]
+        self.assertEqual(obs_ainfo, exp)
+
 
 FASTQ_SEQS = """@{s1}_1 orig_bc=abc new_bc=abc bc_diffs=0
 xyz

diff --git a/qtp_sequencing/validate.py b/qtp_sequencing/validate.py
@@ -128,6 +128,7 @@ def _validate_multiple(qclient, job_id, prep_info, files, atype, test=False):
         # the run_prefix column
         run_prefixes = set(v['run_prefix'] for k, v in prep_info.items())
         num_prefixes = len(run_prefixes)
+        sample_names = prep_info.keys()
 
         # Check those filepath types that are required
         for ftype, t_files in files.items():
@@ -150,9 +151,22 @@ def _validate_multiple(qclient, job_id, prep_info, files, atype, test=False):
                     else:
                         fps.append(bn)
                 if fps:
-                    offending[ftype] = (
-                        "The provided files do not match the run prefix "
-                        "values in the prep information: %s" % ', '.join(fps))
+                    # let's check by sample_name
+                    fps_rp = fps
+                    rps, fps = [], []
+                    for fp in t_files:
+                        bn = basename(fp)
+                        found = [sn for sn in sample_names
+                                 if bn.startswith(sn)]
+                        if found:
+                            rps.extend(found)
+                        else:
+                            fps.append(bn)
+                    if fps:
+                        offending[ftype] = (
+                            "The provided files do not match the run prefix "
+                            "values in the prep information: %s" % ', '.join(
+                                fps_rp))
                 else:
                     rps = run_prefixes - set(rps)
                     if rps:

diff --git a/scripts/configure_qtp_sequencing b/scripts/configure_qtp_sequencing
@@ -16,13 +16,13 @@ from qtp_sequencing import plugin
 @click.command()
 @click.option('--env-script', prompt='Environment script',
               default='conda activate qtp-sequencing')
-@click.option('--server-cert', prompt='Server certificate', default='None')
-def config(env_script, server_cert):
+@click.option('--ca-cert', prompt='Server certificate', default='None')
+def config(env_script, ca_cert):
     """Generates the Qiita configuration files"""
-    if server_cert == 'None':
-        server_cert = None
+    if ca_cert == 'None':
+        ca_cert = None
     plugin.generate_config(env_script, 'start_qtp_sequencing',
-                           server_cert=server_cert)
+                           ca_cert)
 
 
 if __name__ == '__main__':