names remapping: avoid clashes by using different dirs

src/runcrate/cli.py

@@ -58,7 +58,7 @@ def cli():
 )
 @click.option(
     "--remap-names",
-    help="remap file/dir names to the original ones (MAY LEAD TO CLASHES!)",
+    help="remap file/dir names to the original ones",
     is_flag=True
 )
 def convert(root, output, license, workflow_name, readme, remap_names):

src/runcrate/convert.py

@@ -55,7 +55,7 @@
     "null": None,
 }
 
-SCATTER_JOB_PATTERN = re.compile(r"^(.+)_\d+$")
+SCATTER_JOB_PATTERN = re.compile(r"^(.+)_(\d+)$")
 
 CWLPROV_NONE = "https://w3id.org/cwl/prov#None"
 
@@ -215,6 +215,7 @@ def __init__(self, root, workflow_name=None, license=None, readme=None,
         self.file_map = {}
         self.manifest = self._get_manifest()
         self.remap_names = remap_names
+        self.data_root = "data"
 
     @staticmethod
     def _get_step_maps(cwl_defs):
@@ -240,11 +241,13 @@ def _get_manifest(self):
     def _resolve_plan(self, activity):
         job_qname = activity.plan()
         plan = activity.provenance.entity(job_qname)
+        scatter_id = None
         if not plan:
             m = SCATTER_JOB_PATTERN.match(str(job_qname))
             if m:
                 plan = activity.provenance.entity(m.groups()[0])
-        return plan
+                scatter_id = m.groups()[1]
+        return plan, scatter_id
 
     def _get_hash(self, prov_param):
         k = prov_param.id.localpart
@@ -463,9 +466,11 @@ def add_action(self, crate, activity, parent_instrument=None):
             "@type": "CreateAction",
             "name": activity.label,
         }))
-        plan = self._resolve_plan(activity)
+        plan, scatter_id = self._resolve_plan(activity)
         plan_tag = plan.id.localpart
+        dest_base = Path(self.data_root)
         if plan_tag == "main":
+            dest_base = dest_base / "main"
             assert str(activity.type) == "wfprov:WorkflowRun"
             instrument = workflow
             self.roc_engine_run["result"] = action
@@ -480,6 +485,7 @@ def to_wf_p(k):
                 if parts[0] == "main":
                     parts[0] = parent_instrument_fragment
                     plan_tag = "/".join(parts)
+            dest_base = dest_base / (f"{plan_tag}_{scatter_id}" if scatter_id else f"{plan_tag}")
             tool_name = self.step_maps[parent_instrument_fragment][plan_tag]["tool"]
             instrument = crate.dereference(f"{workflow.id}#{tool_name}")
             control_action = self.control_actions.get(plan_tag)
@@ -503,12 +509,14 @@ def to_wf_p(k):
         action["instrument"] = instrument
         action["startTime"] = activity.start().time.isoformat()
         action["endTime"] = activity.end().time.isoformat()
-        action["object"] = self.add_action_params(crate, activity, to_wf_p, "usage")
-        action["result"] = self.add_action_params(crate, activity, to_wf_p, "generation")
+        action["object"] = self.add_action_params(crate, activity, to_wf_p, "usage",
+                                                  dest_base / "in" if self.remap_names else "")
+        action["result"] = self.add_action_params(crate, activity, to_wf_p, "generation",
+                                                  dest_base / "out" if self.remap_names else "")
         for job in activity.steps():
             self.add_action(crate, job, parent_instrument=instrument)
 
-    def add_action_params(self, crate, activity, to_wf_p, ptype="usage"):
+    def add_action_params(self, crate, activity, to_wf_p, ptype="usage", dest_base=""):
         action_params = []
         all_roles = set()
         for rel in getattr(activity, ptype)():
@@ -528,7 +536,7 @@ def add_action_params(self, crate, activity, to_wf_p, ptype="usage"):
             wf_p = crate.dereference(to_wf_p(k))
             k = get_fragment(k)
             v = rel.entity()
-            value = self.convert_param(v, crate)
+            value = self.convert_param(v, crate, dest_base=dest_base)
             if value is None:
                 continue  # param is optional with no default and was not set
             if {"ro:Folder", "wf4ever:File"} & set(str(_) for _ in v.types()):
@@ -565,7 +573,7 @@ def _set_alternate_name(prov_param, action_p, parent=None):
         if "alternateName" in parent:
             action_p["alternateName"] = (Path(parent["alternateName"]) / basename).as_posix()
 
-    def convert_param(self, prov_param, crate, convert_secondary=True, parent=None):
+    def convert_param(self, prov_param, crate, convert_secondary=True, parent=None, dest_base=""):
         type_names = frozenset(str(_) for _ in prov_param.types())
         secondary_files = [_.generated_entity() for _ in prov_param.derivations()
                            if str(_.type) == "cwlprov:SecondaryFile"]
@@ -589,7 +597,7 @@ def convert_param(self, prov_param, crate, convert_secondary=True, parent=None):
                 basename = getattr(prov_param, "basename", hash_)
             else:
                 basename = hash_
-            dest = Path(parent.id if parent else "") / basename
+            dest = Path(parent.id if parent else dest_base) / basename
             action_p = crate.dereference(dest.as_posix())
             if not action_p:
                 source = self.manifest[hash_]
@@ -610,7 +618,7 @@ def convert_param(self, prov_param, crate, convert_secondary=True, parent=None):
                 basename = getattr(prov_param, "basename", hash_)
             else:
                 basename = hash_
-            dest = Path(parent.id if parent else "") / basename
+            dest = Path(parent.id if parent else dest_base) / basename
             action_p = crate.dereference(dest.as_posix())
             if not action_p:
                 action_p = crate.add_directory(dest_path=dest)

tests/test_cli.py

@@ -101,8 +101,8 @@ def test_cli_convert_remap_names(data_dir, tmpdir):
     args = ["convert", str(root), "-o", str(crate_dir), "--remap-names"]
     assert runner.invoke(cli, args).exit_code == 0
     crate = ROCrate(crate_dir)
-    assert crate.get("grepucase_in/")
-    assert (crate_dir / "grepucase_in").is_dir()
+    assert crate.get("data/main/in/grepucase_in/")
+    assert (crate_dir / "data" / "main" / "in" / "grepucase_in").is_dir()
 
 
 def test_cli_report_provenance_minimal(data_dir, caplog):

tests/test_cwlprov_crate_builder.py

@@ -1174,48 +1174,73 @@ def test_remap_names(data_dir, tmpdir):
     assert len(wf_objects) == 2
     assert len(wf_results) == 1
     wf_objects_map = {_.id: _ for _ in wf_objects}
-    wf_input_dir = wf_objects_map.get("grepucase_in/")
+    wf_input_dir = wf_objects_map.get("data/main/in/grepucase_in/")
     assert wf_input_dir
     wf_output_dir = wf_results[0]
-    assert wf_output_dir.id == "ucase_out/"
+    assert wf_output_dir.id == "data/main/out/ucase_out/"
     assert set(_.id for _ in wf_input_dir["hasPart"]) == {
-        "grepucase_in/bar", "grepucase_in/foo"
+        "data/main/in/grepucase_in/bar", "data/main/in/grepucase_in/foo"
     }
     assert set(_.id for _ in wf_output_dir["hasPart"]) == {
-        "ucase_out/bar.out/", "ucase_out/foo.out/"
+        "data/main/out/ucase_out/bar.out/", "data/main/out/ucase_out/foo.out/"
     }
     for d in wf_output_dir["hasPart"]:
-        if d.id == "ucase_out/bar.out/":
-            assert d["hasPart"][0].id == "ucase_out/bar.out/bar.out.out"
+        if d.id == "data/main/out/ucase_out/bar.out/":
+            assert d["hasPart"][0].id == "data/main/out/ucase_out/bar.out/bar.out.out"
         else:
-            assert d["hasPart"][0].id == "ucase_out/foo.out/foo.out.out"
+            assert d["hasPart"][0].id == "data/main/out/ucase_out/foo.out/foo.out.out"
     greptool_action = action_map["packed.cwl#greptool.cwl"]
     greptool_objects = greptool_action["object"]
     greptool_results = greptool_action["result"]
     assert len(greptool_objects) == 2
     assert len(greptool_results) == 1
     greptool_objects_map = {_.id: _ for _ in greptool_objects}
-    greptool_input_dir = greptool_objects_map.get("grepucase_in/")
-    assert greptool_input_dir is wf_input_dir
+    greptool_input_dir = greptool_objects_map.get("data/main/grep/in/grepucase_in/")
+    assert greptool_input_dir
+    assert set(_.id for _ in greptool_input_dir["hasPart"]) == {
+        "data/main/grep/in/grepucase_in/bar", "data/main/grep/in/grepucase_in/foo"
+    }
     greptool_output_dir = greptool_results[0]
-    assert greptool_output_dir.id == "grep_out/"
+    assert greptool_output_dir.id == "data/main/grep/out/grep_out/"
+    assert set(_.id for _ in greptool_output_dir["hasPart"]) == {
+        "data/main/grep/out/grep_out/bar.out", "data/main/grep/out/grep_out/foo.out"
+    }
     ucasetool_action = action_map["packed.cwl#ucasetool.cwl"]
     ucasetool_objects = ucasetool_action["object"]
     ucasetool_results = ucasetool_action["result"]
     assert len(ucasetool_objects) == 1
     assert len(ucasetool_results) == 1
     ucasetool_input_dir = ucasetool_objects[0]
-    assert ucasetool_input_dir is greptool_output_dir
+    assert ucasetool_input_dir.id == "data/main/ucase/in/grep_out/"
+    assert set(_.id for _ in ucasetool_input_dir["hasPart"]) == {
+        "data/main/ucase/in/grep_out/bar.out", "data/main/ucase/in/grep_out/foo.out"
+    }
     ucasetool_output_dir = ucasetool_results[0]
-    assert ucasetool_output_dir is wf_output_dir
+    assert ucasetool_output_dir.id == "data/main/ucase/out/ucase_out/"
+    assert set(_.id for _ in ucasetool_output_dir["hasPart"]) == {
+        "data/main/ucase/out/ucase_out/bar.out/", "data/main/ucase/out/ucase_out/foo.out/"
+    }
+
+    for d in ucasetool_output_dir["hasPart"]:
+        if d.id == "data/main/ucase/out/ucase_out/bar.out/":
+            assert d["hasPart"][0].id == "data/main/ucase/out/ucase_out/bar.out/bar.out.out"
+        else:
+            assert d["hasPart"][0].id == "data/main/ucase/out/ucase_out/foo.out/foo.out.out"
+
     for e in crate.data_entities:
         assert "alternateName" not in e
     for p in (
-            "grepucase_in/bar",
-            "grepucase_in/foo",
-            "grep_out/bar.out",
-            "grep_out/foo.out",
-            "ucase_out/bar.out/bar.out.out",
-            "ucase_out/foo.out/foo.out.out",
+            "data/main/in/grepucase_in/bar",
+            "data/main/in/grepucase_in/foo",
+            "data/main/out/ucase_out/bar.out/bar.out.out",
+            "data/main/out/ucase_out/foo.out/foo.out.out",
+            "data/main/grep/in/grepucase_in/bar",
+            "data/main/grep/in/grepucase_in/foo",
+            "data/main/grep/out/grep_out/bar.out",
+            "data/main/grep/out/grep_out/foo.out",
+            "data/main/ucase/in/grep_out/bar.out",
+            "data/main/ucase/in/grep_out/foo.out",
+            "data/main/ucase/out/ucase_out/bar.out/bar.out.out",
+            "data/main/ucase/out/ucase_out/foo.out/foo.out.out",
     ):
         assert (output / p).is_file()