begin work on looper link #72

looper/cli_looper.py

@@ -118,6 +118,7 @@ def add_subparser(cmd):
         inspect_subparser = add_subparser("inspect")
         init_subparser = add_subparser("init")
         init_piface = add_subparser("init-piface")
+        #link_subparser = add_subparser("link")
 
         # Flag arguments
         ####################################################################
@@ -314,6 +315,58 @@ def add_subparser(cmd):
             action="store_true",
             default=False,
         )
+        #
+        # link_subparser.add_argument(
+        #     "-o",
+        #     "--output-dir",
+        #     dest="output_dir",
+        #     metavar="DIR",
+        #     default=None,
+        #     type=str,
+        # )
+        #
+        # link_subparser.add_argument(
+        #         "--looper-config",
+        #         required=False,
+        #         default=None,
+        #         type=str,
+        #         help="Looper configuration file (YAML)",
+        #
+        # )
+        #
+        # link_subparser.add_argument(
+        #     "config_file",
+        #     nargs="?",
+        #     default=None,
+        #     help="Project configuration file (YAML) or pephub registry path.",
+        #
+        # )
+        # link_subparser.add_argument(
+        # "-a",
+        # "--amend",
+        # nargs = "+",
+        # metavar = "A",
+        # help = "List of amendments to activate",
+        # )
+        # link_subparser.add_argument(
+        #     f"--{SAMPLE_SELECTION_ATTRIBUTE_OPTNAME}",
+        #     default="toggle",
+        #     metavar="ATTR",
+        #     help="Attribute for sample exclusion OR inclusion",
+        # )
+        # #protocols = fetch_samples_group.add_mutually_exclusive_group()
+        # link_subparser.add_argument(
+        #     f"--{SAMPLE_EXCLUSION_OPTNAME}",
+        #     nargs="*",
+        #     metavar="E",
+        #     help="Exclude samples with these values",
+        # )
+        # link_subparser.add_argument(
+        #     f"--{SAMPLE_INCLUSION_OPTNAME}",
+        #     nargs="*",
+        #     metavar="I",
+        #     help="Include only samples with these values",
+        # )
 
         # Common arguments
         for subparser in [
@@ -724,6 +777,12 @@ def main(test_args=None):
             else:
                 raise PipestatConfigurationException("report")
 
+        if args.command == "link":
+            if use_pipestat:
+                Linker(prj)(args)
+            else:
+                raise PipestatConfigurationException("link")
+
         if args.command == "check":
             if use_pipestat:
                 return Checker(prj)(args)

looper/const.py

@@ -258,4 +258,5 @@ def _get_apperance_dict(type, templ=APPEARANCE_BY_FLAG):
     "inspect": "Print information about a project.",
     "init": "Initialize looper config file.",
     "init-piface": "Initialize generic pipeline interface.",
+    "link": "Create directory of symlinks for reported results."
 }

looper/looper.py

@@ -565,6 +565,32 @@ def __call__(self, args):
                     psm.summarize()
 
 
+class Linker(Executor):
+    """Create symlinks for reported results. Requires pipestat to be configured."""
+
+    def __call__(self, args):
+        # initialize the report builder
+        p = self.prj
+        project_level = args.project
+        link_dir = args.output_dir
+
+        if project_level:
+            psms = self.prj.get_pipestat_managers(project_level=True)
+            for name, psm in psms.items():
+                psm.link(link_dir=link_dir)
+        else:
+            for piface_source_samples in self.prj._samples_by_piface(
+                self.prj.piface_key
+            ).values():
+                # For each piface_key, we have a list of samples, but we only need one sample from the list to
+                # call the related pipestat manager object which will pull ALL samples when using psm.summarize
+                first_sample_name = list(piface_source_samples)[0]
+                psms = self.prj.get_pipestat_managers(
+                    sample_name=first_sample_name, project_level=False
+                )
+                for name, psm in psms.items():
+                    psm.link(link_dir=link_dir)
+
 class Tabulator(Executor):
     """Project/Sample statistics and table output generator