continue looper link, now functional #72

pepkit · Oct 13, 2023 · 6523e4b · 6523e4b
1 parent 2935a23
commit 6523e4b
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Showing 3 changed files with 6 additions and 54 deletions.
diff --git a/looper/cli_looper.py b/looper/cli_looper.py
@@ -118,7 +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")
+        link_subparser = add_subparser("link")
 
         # Flag arguments
         ####################################################################
@@ -315,58 +315,6 @@ 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 [
@@ -379,6 +327,7 @@ def add_subparser(cmd):
             clean_subparser,
             collate_subparser,
             inspect_subparser,
+            link_subparser,
         ]:
             subparser.add_argument(
                 "config_file",
@@ -455,6 +404,7 @@ def add_subparser(cmd):
             clean_subparser,
             collate_subparser,
             inspect_subparser,
+            link_subparser,
         ]:
             fetch_samples_group = subparser.add_argument_group(
                 "sample selection arguments",
@@ -508,6 +458,7 @@ def add_subparser(cmd):
             table_subparser,
             check_subparser,
             destroy_subparser,
+            link_subparser,
         ]:
             subparser.add_argument(
                 "--project",

diff --git a/looper/const.py b/looper/const.py
@@ -258,5 +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."
+    "link": "Create directory of symlinks for reported results.",
 }
diff --git a/looper/looper.py b/looper/looper.py
@@ -591,6 +591,7 @@ def __call__(self, args):
                 for name, psm in psms.items():
                     psm.link(link_dir=link_dir)
 
+
 class Tabulator(Executor):
     """Project/Sample statistics and table output generator