Add check, report, destroy, and table to tests, add returning debug …

…values for table #464

looper/cli_looper.py

@@ -761,13 +761,13 @@ def main(test_args=None):
         )
         if args.command == "table":
             if use_pipestat:
-                Tabulator(prj)(args)
+                return Tabulator(prj)(args)
             else:
                 raise PipestatConfigurationException("table")
 
         if args.command == "report":
             if use_pipestat:
-                Reporter(prj)(args)
+                return Reporter(prj)(args)
             else:
                 raise PipestatConfigurationException("report")
 

looper/looper.py

@@ -545,6 +545,7 @@ class Reporter(Executor):
 
     def __call__(self, args):
         # initialize the report builder
+        self.debug = {}
         p = self.prj
         project_level = args.project
 
@@ -559,6 +560,8 @@ def __call__(self, args):
                     looper_samples=self.prj.samples, portable=portable
                 )
                 print(f"Report directory: {report_directory}")
+                self.debug["report_directory"] = report_directory
+            return self.debug
         else:
             for piface_source_samples in self.prj._samples_by_piface(
                 self.prj.piface_key
@@ -576,6 +579,8 @@ def __call__(self, args):
                         looper_samples=self.prj.samples, portable=portable
                     )
                     print(f"Report directory: {report_directory}")
+                    self.debug["report_directory"] = report_directory
+            return self.debug
 
 
 class Linker(Executor):
@@ -614,7 +619,6 @@ class Tabulator(Executor):
     """
 
     def __call__(self, args):
-        # p = self.prj
         project_level = args.project
         results = []
         if project_level:

tests/test_comprehensive.py

@@ -10,6 +10,7 @@
 from tests.smoketests.test_run import is_connected
 from tempfile import TemporaryDirectory
 from git import Repo
+from pipestat import PipestatManager
 
 from yaml import dump, safe_load
 
@@ -68,4 +69,65 @@ def test_comprehensive_looper_pipestat():
         except Exception:
             raise pytest.fail("DID RAISE {0}".format(Exception))
 
+        # TODO TEST PROJECT LEVEL RUN
+        # Must add this to hello_looper for pipestat example
+
+        # TEST LOOPER CHECK
+
+        # looper cannot create flags, the pipeline or pipestat does that
+        # if you do not specify flag dir, pipestat places them in the same dir as config file
+        path_to_pipestat_config = os.path.join(
+            pipestat_dir, "looper_pipestat_config.yaml"
+        )
+        psm = PipestatManager(config_file=path_to_pipestat_config)
+        psm.set_status(record_identifier="frog_1", status_identifier="completed")
+        psm.set_status(record_identifier="frog_2", status_identifier="completed")
+
+        # Now use looper check to get statuses
+        x = ["check", "--looper-config", path_to_looper_config]
+
+        try:
+            result = main(test_args=x)
+            assert result["example_pipestat_pipeline"]["frog_1"] == "completed"
+        except Exception:
+            raise pytest.fail("DID RAISE {0}".format(Exception))
+
+        # TEST LOOPER REPORT
+
+        x = ["report", "--looper-config", path_to_looper_config]
+
+        try:
+            result = main(test_args=x)
+            assert "report_directory" in result
+        except Exception:
+            raise pytest.fail("DID RAISE {0}".format(Exception))
+
+        # TEST LOOPER Table
+
+        x = ["table", "--looper-config", path_to_looper_config]
+
+        try:
+            result = main(test_args=x)
+            assert "example_pipestat_pipeline_stats_summary.tsv" in result[0]
+        except Exception:
+            raise pytest.fail("DID RAISE {0}".format(Exception))
+
+        # TEST LOOPER DESTROY
+        # TODO add destroying individual samples via pipestat
+
+        x = [
+            "destroy",
+            "--looper-config",
+            path_to_looper_config,
+            "--force-yes",
+        ]  # Must force yes or pytest will throw an exception "OSError: pytest: reading from stdin while output is captured!"
+
+        try:
+            result = main(test_args=x)
+            # assert "report_directory" in result
+        except Exception:
+            raise pytest.fail("DID RAISE {0}".format(Exception))
+
+        # TODO TEST LOOPER INSPECT  -> I believe this moved to Eido?
+
         print(result)