plexora 0.0.20__tar.gz → 0.0.22__tar.gz

{plexora-0.0.20/plexora.egg-info → plexora-0.0.22}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: plexora
-Version: 0.0.20
+Version: 0.0.22
 Summary: OpenSeadragon-based cellular image viewing and analysis tool.
 License-Expression: LicenseRef-Plexora-Academic-1.0
 Requires-Python: <3.14,>=3.12
@@ -191,12 +191,31 @@ plexora.configure_project("sample2", data="sample2.csv", cell_id="CellID")
 plexora.project_manifest("sample2")   # what it has, and what is still open
 ```
 
+Files do not all have to be on the same machine. `node` names a data node you
+are connected to, and any field can say otherwise for itself -- so a cohort
+whose slides sit on a cluster and whose quantification sits on your laptop is
+one document:
+
+```python
+plexora.create_dataset("Melanoma Cohort", node="hms-o2", projects=[
+    {"image": "/n/scratch/reg/sample1.ome.tif",
+     "segmentation": "/n/scratch/seg/sample1.tif",
+     "data": {"path": "C:/quant/sample1.csv", "node": None}},
+    {"image": "/n/scratch/reg/sample2.ome.tif"},
+])
+```
+
+The projects are registered here, so they appear in the Samples page like any
+other; the bytes stay where they are and are read through the node.
+
 The same options exist as flags:
 
 ```bash
 plexora project create slide.ome.tif --data cells.csv --cell-id CellID \
     --markers CD3 CD8 --dataset melanoma_cohort
 plexora project show slide            # every question, and whether it is answered
+
+plexora dataset create "Melanoma Cohort" --from projects.json --node hms-o2
 ```
 
 ### Shared projects

{plexora-0.0.20 → plexora-0.0.22}/README.md

@@ -140,12 +140,31 @@ plexora.configure_project("sample2", data="sample2.csv", cell_id="CellID")
 plexora.project_manifest("sample2")   # what it has, and what is still open
 ```
 
+Files do not all have to be on the same machine. `node` names a data node you
+are connected to, and any field can say otherwise for itself -- so a cohort
+whose slides sit on a cluster and whose quantification sits on your laptop is
+one document:
+
+```python
+plexora.create_dataset("Melanoma Cohort", node="hms-o2", projects=[
+    {"image": "/n/scratch/reg/sample1.ome.tif",
+     "segmentation": "/n/scratch/seg/sample1.tif",
+     "data": {"path": "C:/quant/sample1.csv", "node": None}},
+    {"image": "/n/scratch/reg/sample2.ome.tif"},
+])
+```
+
+The projects are registered here, so they appear in the Samples page like any
+other; the bytes stay where they are and are read through the node.
+
 The same options exist as flags:
 
 ```bash
 plexora project create slide.ome.tif --data cells.csv --cell-id CellID \
     --markers CD3 CD8 --dataset melanoma_cohort
 plexora project show slide            # every question, and whether it is answered
+
+plexora dataset create "Melanoma Cohort" --from projects.json --node hms-o2
 ```
 
 ### Shared projects

{plexora-0.0.20 → plexora-0.0.22}/plexora/cli.py

@@ -719,6 +719,11 @@ _PROJECT_OPTIONS = (
                       "help": "Override how the image is read."}),
     ("--copy", {"action": "store_true",
                 "help": "Copy the files into the project directory."}),
+    ("--node", {"metavar": "NAME",
+                "help": "The data node the files are on, for any path that "
+                        "does not say for itself. In a spec file, "
+                        '{"path": ..., "node": null} keeps one file on this '
+                        "machine."}),
 )
 
 
@@ -751,6 +756,11 @@ def _build_dataset_parser():
                              "or a bare list of project specs. Command-line "
                              "arguments win over what is in it.")
     create.add_argument("--description", default="")
+    create.add_argument("--node", metavar="NAME",
+                        help="The data node these files are on. Every path "
+                             "that does not say otherwise is a path over "
+                             "there, and the projects address it rather than "
+                             "copying anything here.")
     create.add_argument("--exist-ok", action="store_true",
                         help="Add to the dataset if it already exists.")
     create.add_argument("--json", action="store_true",
@@ -1549,6 +1559,7 @@ def _run_dataset(args):
                 images=images or None,
                 projects=projects or None if not images else None,
                 description=args.description or document.get("description", ""),
+                node=args.node,
                 exist_ok=args.exist_ok,
             )
             if args.json:
@@ -1558,6 +1569,7 @@ def _run_dataset(args):
                       f"{len(dataset)} project{'' if len(dataset) == 1 else 's'}")
                 for name in dataset.projects:
                     print(f"  {name}")
+                _say_what_is_converting(api, dataset.projects)
             return _said_where(args, mutating=True)
 
         if command == "list":
@@ -1656,12 +1668,15 @@ def _run_project(args):
 
     try:
         if command == "create":
-            paths = list(args.paths)
-            if _wants_detection(paths, args):
-                name = api.import_sample(*paths, name=args.name,
-                                         dataset=args.dataset)
+            # `given`, not `paths`: the module imported above answers
+            # `paths.DataRootError` in the handler below, and rebinding the
+            # name here made that an AttributeError on this one path.
+            given = list(args.paths)
+            if _wants_detection(given, args):
+                name = api.import_sample(*given, name=args.name,
+                                         dataset=args.dataset, node=args.node)
             else:
-                spec = _spec_from_args(args, image=paths[0], name=args.name)
+                spec = _spec_from_args(args, image=given[0], name=args.name)
                 if args.spec_file:
                     spec = {**_load_spec_file(args.spec_file), **spec}
                 spec["exist_ok"] = args.exist_ok
@@ -1671,6 +1686,7 @@ def _run_project(args):
             else:
                 print(name)
                 _print_manifest(api.project_manifest(name))
+                _say_what_is_converting(api, [name])
             return _said_where(args, mutating=True)
 
         if command == "show":
@@ -1714,6 +1730,37 @@ def _message(exc):
     return str(exc.args[0]) if exc.args else str(exc)
 
 
+def _say_what_is_converting(api, names):
+    """Name anything a node is still preparing for these projects.
+
+    A mask on a node has to be turned into a label pyramid before a tile can
+    be served, and that happens after registration returns -- the project is
+    valid and openable while it runs. Said here because a command line has no
+    progress bar: the viewer shows one, and somebody who was not told to look
+    sees an empty layer and assumes the import failed.
+
+    Human output only. The JSON is a payload other programs parse, and a line
+    about work in flight is not part of what was registered.
+
+    A conversion that has already FAILED is said too, with the node's reason.
+    The project is registered either way, but its mask cannot be drawn until
+    whatever the node names is fixed -- and silence here is how a mask in a
+    directory this account could not write went unnoticed until it drew wrong.
+    """
+    for row in api.pending_conversions(names):
+        count = row["count"]
+        what = row["kind"] + ("" if count == 1 else "s")
+        print(f"{count} {what} {'is' if count == 1 else 'are'} converting on "
+              f"{row['node']}; the viewer shows progress.")
+    for row in api.failed_conversions(names):
+        print(f"Could not prepare {row['kind']} {row['id']!r} on {row['node']}: "
+              f"{row['error']}")
+        print("  Opening the project in the viewer tries again; until then "
+              "the unconverted mask is drawn, more slowly.")
+    for row in api.conversion_warnings(names):
+        print(f"Note: {row['warning']}")
+
+
 def _print_manifest(record):
     """One line per question: what it is, where it stands, and the answer.