Merge pull request #409 from pepkit/pipestat_polish

Pipestat compatibility and move table function to pipestat
pepkit · Aug 25, 2023 · 8703d23 · 8703d23
2 parents 9c7e20a + 7e1ed55
commit 8703d23
Show file tree

Hide file tree

Showing 16 changed files with 429 additions and 2,704 deletions.
diff --git a/looper/cli_looper.py b/looper/cli_looper.py
@@ -449,7 +449,12 @@ def add_subparser(cmd):
                 metavar="A",
                 help="List of amendments to activate",
             )
-        for subparser in [report_subparser, table_subparser, check_subparser]:
+        for subparser in [
+            report_subparser,
+            table_subparser,
+            check_subparser,
+            destroy_subparser,
+        ]:
             subparser.add_argument(
                 "--project",
                 help="Process project-level pipelines",
@@ -697,29 +702,32 @@ def main(test_args=None):
         # with no pipestat reporting would not be compatible with
         # commands: table, report and check. Therefore we plan maintain
         # the old implementations for a couple of releases.
-        if hasattr(args, "project"):
-            use_pipestat = (
-                prj.pipestat_configured_project
-                if args.project
-                else prj.pipestat_configured
-            )
+        # if hasattr(args, "project"):
+        #     use_pipestat = (
+        #         prj.pipestat_configured_project
+        #         if args.project
+        #         else prj.pipestat_configured
+        #     )
+        use_pipestat = (
+            prj.pipestat_configured_project if args.project else prj.pipestat_configured
+        )
         if args.command == "table":
             if use_pipestat:
                 Tabulator(prj)(args)
             else:
-                TableOld(prj)()
+                raise PipestatConfigurationException("table")
 
         if args.command == "report":
             if use_pipestat:
                 Reporter(prj)(args)
             else:
-                ReportOld(prj)(args)
+                raise PipestatConfigurationException("report")
 
         if args.command == "check":
             if use_pipestat:
-                Checker(prj)(args)
+                return Checker(prj)(args)
             else:
-                CheckerOld(prj)(flags=args.flags)
+                raise PipestatConfigurationException("check")
 
         if args.command == "clean":
             return Cleaner(prj)(args)

diff --git a/looper/conductor.py b/looper/conductor.py
@@ -708,10 +708,15 @@ def write_script(self, pool, size):
                 namespaces.update({"sample": sample})
             else:
                 namespaces.update({"samples": self.prj.samples})
-            pipestat_namespace = self._set_pipestat_namespace(
-                sample_name=sample.sample_name if sample else None
-            )
-            namespaces.update({"pipestat": pipestat_namespace})
+            if self.prj.pipestat_configured:
+                pipestat_namespace = self._set_pipestat_namespace(
+                    sample_name=sample.sample_name if sample else None
+                )
+                namespaces.update({"pipestat": pipestat_namespace})
+            else:
+                # Pipestat isn't configured, simply place empty YAMLConfigManager object instead.
+                pipestat_namespace = YAMLConfigManager()
+                namespaces.update({"pipestat": pipestat_namespace})
             res_pkg = self.pl_iface.choose_resource_package(
                 namespaces, size or 0
             )  # config

diff --git a/looper/const.py b/looper/const.py
@@ -187,7 +187,7 @@ def _get_apperance_dict(type, templ=APPEARANCE_BY_FLAG):
 DEFAULT_PIPESTAT_RESULTS_FILE_ATTR = "pipestat_results_file"
 PIPESTAT_NAMESPACE_ATTR_KEY = "namespace_attribute"
 PIPESTAT_CONFIG_ATTR_KEY = "config_attribute"
-PIPESTAT_RESULTS_FILE_ATTR_KEY = "results_file_attribute"
+PIPESTAT_RESULTS_FILE_ATTR_KEY = "results_file_path"
 
 PIPE_ARGS_SECTION = "pipeline_args"
 CLI_KEY = "cli"
@@ -224,6 +224,7 @@ def _get_apperance_dict(type, templ=APPEARANCE_BY_FLAG):
     DRY_RUN_KEY,
     FILE_CHECKS_KEY,
     SAMPLE_PL_ARG,
+    PIPESTAT_KEY,
 ]
 
 # resource package TSV-related consts

diff --git a/looper/exceptions.py b/looper/exceptions.py
@@ -60,6 +60,17 @@ def __init__(self, sub_cmd, script):
         super(JobSubmissionException, self).__init__(reason)
 
 
+class PipestatConfigurationException(LooperError):
+    """Error type for when command fails due to missing pipestat config"""
+
+    def __init__(
+        self,
+        sub_cmd,
+    ):
+        reason = "Pipestat must be configured for command {}".format(sub_cmd)
+        super(PipestatConfigurationException, self).__init__(reason)
+
+
 class MissingPipelineConfigurationException(LooperError):
     """A selected pipeline needs configuration data."""