Tests update

qiita-spots · May 15, 2024 · 8102d3b · 8102d3b
1 parent 933bdde
commit 8102d3b
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Showing 4 changed files with 47 additions and 50 deletions.
diff --git a/qiita_db/test/test_software.py b/qiita_db/test/test_software.py
@@ -494,8 +494,11 @@ def test_processing_jobs(self):
                     '6ad4d590-4fa3-44d3-9a8f-ddbb472b1b5f',
                     '063e553b-327c-4818-ab4a-adfe58e49860',
                     'ac653cb5-76a6-4a45-929e-eb9b2dee6b63']
-        exp = [qdb.processing_job.ProcessingJob(j) for j in exp_jids]
-        self.assertCountEqual(qdb.software.Command(1).processing_jobs, exp)
+
+        exp = set([qdb.processing_job.ProcessingJob(j) for j in exp_jids])
+        set_jobs = set(qdb.software.Command(1).processing_jobs)
+
+        self.assertEqual(len(set_jobs & exp), len(exp_jids))
 
         exp_jids = ['bcc7ebcd-39c1-43e4-af2d-822e3589f14d']
         exp = [qdb.processing_job.ProcessingJob(j) for j in exp_jids]

diff --git a/qiita_db/test/test_user.py b/qiita_db/test/test_user.py
@@ -491,17 +491,10 @@ def test_jobs(self):
             limit=1, ignore_status=ignore_status), [
                 PJ('b72369f9-a886-4193-8d3d-f7b504168e75')])
 
-        # no jobs
-        self.assertEqual(qdb.user.User('[email protected]').jobs(
-            ignore_status=ignore_status), [])
-
         # generates expected jobs
         jobs = qdb.user.User('[email protected]').jobs()
         self.assertEqual(jobs, [])
 
-        # no jobs
-        self.assertEqual(qdb.user.User('[email protected]').jobs(), [])
-
     def test_update_email(self):
         user = qdb.user.User('[email protected]')
         with self.assertRaisesRegex(IncorrectEmailError, 'Bad email given:'):

diff --git a/qiita_db/test/test_util.py b/qiita_db/test/test_util.py
@@ -1312,49 +1312,15 @@ def setUp(self):
         self.CNAME = "Split libraries FASTQ"
         self.SNAME = "QIIMEq2"
         self.col_name = 'samples * columns'
-        self.df = self.get_df()
-
-    def get_df(self):
-        with qdb.sql_connection.TRN:
-            sql = f"""
-                SELECT
-                    s.name AS sName,
-                    s.version AS sVersion,
-                    sc.command_id AS cID,
-                    sc.name AS cName,
-                    pr.processing_job_id AS processing_job_id,
-                    pr.command_parameters AS parameters,
-                    sra.samples AS samples,
-                    sra.columns AS columns,
-                    sra.input_size AS input_size,
-                    sra.extra_info AS extra_info,
-                    sra.memory_used AS memory_used,
-                    sra.walltime_used AS walltime_used
-                FROM
-                    qiita.processing_job pr
-                JOIN
-                    qiita.software_command sc ON pr.command_id = sc.command_id
-                JOIN
-                    qiita.software s ON sc.software_id = s.software_id
-                JOIN
-                    qiita.slurm_resource_allocations sra
-                    ON pr.processing_job_id = sra.processing_job_id
-                WHERE
-                    sc.name = '{self.CNAME}'
-                    AND s.name = '{self.SNAME}';
-                """
-
-            qdb.sql_connection.TRN.add(sql)
-            res = qdb.sql_connection.TRN.execute_fetchindex()
-            columns = [
-                "sName", "sVersion", "cID", "cName",
-                "processing_job_id", "parameters", "samples", "columns",
-                "input_size", "extra_info", "MaxRSSRaw", "ElapsedRaw"]
-            df = pd.DataFrame(res, columns=columns)
-            return df
+        self.columns = [
+                "sName", "sVersion", "cID", "cName", "processing_job_id",
+                "parameters", "samples", "columns", "input_size", "extra_info",
+                "MaxRSSRaw", "ElapsedRaw"]
+        self.df = pd.DataFrame(
+            qdb.util._retrieve_resource_data(self.CNAME, self.SNAME),
+            columns=self.columns)
 
     def test_plot_return(self):
-
         # check the plot returns correct objects
         fig1, axs1 = qdb.util.resource_allocation_plot(
             self.df, self.CNAME, self.SNAME, self.col_name)

diff --git a/qiita_db/util.py b/qiita_db/util.py
@@ -2380,6 +2380,41 @@ def resource_allocation_plot(df, cname, sname, col_name):
     return fig, axs
 
 
+def _retrieve_resource_data(cname, sname):
+    with qdb.sql_connection.TRN:
+        sql = """
+            SELECT
+                s.name AS sName,
+                s.version AS sVersion,
+                sc.command_id AS cID,
+                sc.name AS cName,
+                pr.processing_job_id AS processing_job_id,
+                pr.command_parameters AS parameters,
+                sra.samples AS samples,
+                sra.columns AS columns,
+                sra.input_size AS input_size,
+                sra.extra_info AS extra_info,
+                sra.memory_used AS memory_used,
+                sra.walltime_used AS walltime_used
+            FROM
+                qiita.processing_job pr
+            JOIN
+                qiita.software_command sc ON pr.command_id = sc.command_id
+            JOIN
+                qiita.software s ON sc.software_id = s.software_id
+            JOIN
+                qiita.slurm_resource_allocations sra
+                ON pr.processing_job_id = sra.processing_job_id
+            WHERE
+                sc.name = %s
+                AND s.name = %s;
+            """
+        qdb.sql_connection.TRN.add(sql, sql_args=[cname, sname])
+        res = qdb.sql_connection.TRN.execute_fetchindex()
+        return res
+    pass
+
+
 def _resource_allocation_plot_helper(
         df, ax, cname, sname, curr, models, col_name):
     """Helper function for resource allocation plot. Builds plot for MaxRSSRaw