adding lefse tests

mmeds/resources/lefse_config.yaml

@@ -1,3 +1,7 @@
-class: class_col
-subclass: subclass_col
-subjects: subjects_col
+tables:
+  - taxa_table_L6
+classes:
+  - Sex
+  - Group
+subclasses:
+  - Group

mmeds/tests/unit/test_analysis.py

@@ -4,7 +4,6 @@
 from time import sleep
 
 from mmeds.util import run_analysis, load_config, upload_sequencing_run_local
-from mmeds.summary import summarize_qiime
 from mmeds.spawn import Watcher
 from mmeds.logging import Logger
 from mmeds.tools.analysis import Analysis
@@ -24,9 +23,11 @@ def setUpClass(self):
         self.watcher.connect()
         self.queue = self.watcher.get_queue()
         self.config = load_config(fig.DEFAULT_CONFIG, fig.TEST_MIXED_METADATA, 'standard_pipeline')
+        self.config_lefse = load_config(fig.DEFAULT_CONFIG_LEFSE, fig.TEST_MIXED_METADATA, 'lefse')
         self.analysis = []
         with Database(owner=fig.TEST_USER_0, testing=True) as db:
-            self.analysis_code = db.create_access_code()
+            self.analysis_code_0 = db.create_access_code()
+            self.analysis_code_1 = db.create_access_code()
 
     def test_a_upload_sequencing_run(self):
         """ Upload sequencing run for analysis """
@@ -41,30 +42,36 @@ def test_b_analysis_init(self):
         """ Test analysis object """
         with Database(owner=fig.TEST_USER_0, testing=True) as db:
             self.runs = db.get_sequencing_run_locations(fig.TEST_MIXED_METADATA, fig.TEST_USER_0)
-        self.analysis += [Analysis(self.queue, fig.TEST_USER_0, self.analysis_code, fig.TEST_CODE_MIXED,
+        self.analysis += [Analysis(self.queue, fig.TEST_USER_0, self.analysis_code_0, fig.TEST_CODE_MIXED,
                                 'standard_pipeline', 'default', 'test_init', self.config, True, self.runs, False, threads=2)]
+        self.analysis += [Analysis(self.queue, fig.TEST_USER_0, self.analysis_code_1, fig.TEST_CODE_MIXED,
+                                'lefse', 'default', 'test_lefse', self.config_lefse, True, {}, False, threads=2)]
 
 
-    def test_b_standard_pipeline(self):
+    def test_c_standard_pipeline(self):
         """ Test running a standard analysis """
         # run_analysis() executes analyses synchronously rather than submitting as a job
         run_analysis(self.test_study, 'standard_pipeline', testing=True)
-        """
-        summarize_qiime(f'{self.test_study}/Qiime2_0', 'standard_pipeline', testing=True)
 
-         check for summary pdf, also gets uploaded as an artifact in github actions for inspection
-        pdf_output = Path(f'{self.test_study}/Qiime2_0/summary/[email protected]')
-        self.assertTrue(pdf_output.exists())
-        """
-
-    def test_c_analysis_class(self):
-        """ Test the analysis object """
+    def test_d_analysis_class(self):
+        """ Test the analysis objects """
         analysis = self.analysis[0]
         analysis.run()
 
         info = analysis.get_info()
+        table = Path(info['path']) / 'tables' / 'taxa_table_L6.qza'
+        table.touch()
+
+        self.assertEquals(info['owner'], fig.TEST_USER_0)
+        self.assertEquals(info['analysis_code'], self.analysis_code_0)
+
+    def test_e_lefse_analysis_class(self):
+        lefse_analysis = self.analysis[1]
+        lefse_analysis.run()
+
+        info = lefse_analysis.get_info()
         self.assertEquals(info['owner'], fig.TEST_USER_0)
-        self.assertEquals(info['analysis_code'], self.analysis_code)
+        self.assertEquals(info['analysis_code'], self.analysis_code_1)
 
     def test_d_analysis_utils(self):
         """ Test that adding files to the tool object works properly """

mmeds/tools/analysis.py

@@ -227,32 +227,6 @@ def create_snakemake_file(self):
         with open(snakefile, "wt") as f:
             f.write(workflow_text)
 
-    def summary(self):
-        """ Setup script to create summary. """
-        self.add_path('summary')
-        if self.testing:
-            self.jobtext.append('module load mmeds-stable;')
-        else:
-            self.jobtext.append(
-                'conda deactivate; source activate /hpc/users/mmedsadmin/.admin_modules/jupyter; ml texlive/2018')
-        # Make sure the kernel is up to date
-        self.jobtext.append('python -m ipykernel install --user --name jupyter --display-name "Jupyter"')
-        cmd = [
-            'summarize.py ',
-            '--path "{}"'.format(self.run_dir),
-            '--workflow_type {};'.format(self.doc.workflow_type)
-        ]
-        self.jobtext.append(' '.join(cmd))
-
-    def zip(self):
-        """
-        Create a zip of the whole analyis directory.
-        This way a user can download the whole thing
-        if they are so inclined.
-        """
-        cmd = f'zip -r {self.run_dir}.zip {self.run_dir};'
-        self.jobtext.append(cmd)
-
     def copy_taxonomic_database(self):
         """ Copy in the database (e.g. greengenes, silva) to be used for classification"""
         database_file = TAXONOMIC_DATABASES[self.config["taxonomic_database"]]
@@ -373,10 +347,6 @@ def setup_analysis(self, summary=False):
         self.jobtext.append(f"snakemake --use-conda --cores {self.num_jobs} --default-resource tmpdir=\"tmp_dir\"")
         self.jobtext.append('echo "MMEDS_FINISHED"')
 
-        Logger.debug("adding summary")
-        if summary:
-            self.summary()
-
         submitfile = self.path / 'submitfile'
         self.add_path(submitfile, '.sh', 'submitfile')
         # Define the job and error files