pma-python 2.0.0.185__tar.gz → 2.0.0.186__tar.gz

{pma_python-2.0.0.185 → pma_python-2.0.0.186}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pma_python
-Version: 2.0.0.185
+Version: 2.0.0.186
 Summary: Universal viewing of digital microscopy, whole slide imaging and digital pathology data
 Home-page: https://github.com/pathomation/pma_python
 Author: Pathomation

{pma_python-2.0.0.185 → pma_python-2.0.0.186}/pma_python/core.py

@@ -1935,13 +1935,68 @@ def _is_upload_type(upload_type, *candidates) -> bool:
     return False
 
 
+def _companion_folders(slide_path: str) -> list[str]:
+    """
+    Folders that hold the image data of a multi-file slide, by vendor naming convention:
+    - "<name>/"   e.g. 3DHistech MRXS
+    - "_<name>_/" e.g. Olympus/Evident VSI
+    """
+    directory = os.path.dirname(slide_path)
+    stem = os.path.splitext(os.path.basename(slide_path))[0]
+    return [os.path.join(directory, stem), os.path.join(directory, f"_{stem}_")]
+
+
+def _pma_start_files_for_slide(slide_path: str) -> list[str]:
+    """
+    Ask PMA.start which local files belong to this slide (it knows every multi-file format).
+    Best effort: returns [] when PMA.start is not running or cannot answer.
+    """
+    try:
+        return list(get_files_for_slide(slide_path, _pma_pmacoreliteSessionID) or [])
+    except Exception:
+        if pma._pma_debug == True:
+            print("PMA.start could not enumerate the files for", slide_path)
+        return []
+
+
 def _collect_slide_package_files(slide_path: str):
+    """
+    All local files that make up a slide: the main file first, then its image data files.
+    Files are found both by vendor folder conventions (see _companion_folders) and by asking
+    PMA.start, so a multi-file slide is never uploaded without its image data.
+    Relative paths are relative to the folder that contains the main file.
+    """
     if not os.path.isfile(slide_path):
         raise ValueError(f"File not found: {slide_path}")
 
+    slide_path = os.path.abspath(slide_path)
+    base_dir = os.path.dirname(slide_path)
     main_name = os.path.basename(slide_path)
-    child_folder = os.path.splitext(main_name)[0]
-    stack_root = os.path.join(os.path.dirname(slide_path), child_folder)
+
+    def key(path):
+        return os.path.normcase(os.path.abspath(path))
+
+    extra = {}
+
+    def add(path):
+        path = os.path.abspath(path)
+        if key(path) == key(slide_path) or not os.path.isfile(path):
+            return
+        rel = os.path.relpath(path, base_dir)
+        if rel.startswith(os.pardir) or os.path.isabs(rel):
+            # never upload files from outside the slide's own folder
+            return
+        extra.setdefault(key(path), (path, rel.replace("\\", "/")))
+
+    for folder in _companion_folders(slide_path):
+        if os.path.isdir(folder):
+            for root, dirnames, filenames in os.walk(folder):
+                dirnames.sort()
+                for filename in sorted(filenames):
+                    add(os.path.join(root, filename))
+
+    for path in _pma_start_files_for_slide(slide_path):
+        add(path)
 
     package_files = [{
         "local_path": slide_path,
@@ -1949,20 +2004,13 @@ def _collect_slide_package_files(slide_path: str):
         "is_main": True,
         "size": os.stat(slide_path).st_size
     }]
-
-    if os.path.isdir(stack_root):
-        for root, dirnames, filenames in os.walk(stack_root):
-            dirnames.sort()
-            filenames.sort()
-            for filename in filenames:
-                local_path = os.path.join(root, filename)
-                rel_inside_stack = os.path.relpath(local_path, stack_root).replace("\\", "/")
-                package_files.append({
-                    "local_path": local_path,
-                    "relative_path": f"{child_folder}/{rel_inside_stack}",
-                    "is_main": False,
-                    "size": os.stat(local_path).st_size
-                })
+    for path, rel in sorted(extra.values(), key=lambda item: item[1].lower()):
+        package_files.append({
+            "local_path": path,
+            "relative_path": rel,
+            "is_main": False,
+            "size": os.stat(path).st_size
+        })
 
     return package_files
 

pma_python-2.0.0.186/pma_python/version.py

@@ -0,0 +1 @@
+__version__ = '2.0.0.186'

{pma_python-2.0.0.185 → pma_python-2.0.0.186}/pma_python.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pma_python
-Version: 2.0.0.185
+Version: 2.0.0.186
 Summary: Universal viewing of digital microscopy, whole slide imaging and digital pathology data
 Home-page: https://github.com/pathomation/pma_python
 Author: Pathomation

{pma_python-2.0.0.185 → pma_python-2.0.0.186}/pma_python.egg-info/SOURCES.txt

@@ -13,4 +13,5 @@ pma_python.egg-info/SOURCES.txt
 pma_python.egg-info/dependency_links.txt
 pma_python.egg-info/not-zip-safe
 pma_python.egg-info/requires.txt
-pma_python.egg-info/top_level.txt
+pma_python.egg-info/top_level.txt
+tests/test_slide_package.py

pma_python-2.0.0.186/tests/test_slide_package.py

@@ -0,0 +1,143 @@
+"""Tests for _collect_slide_package_files: multi-file slides must be uploaded with their image data."""
+import asyncio
+import os
+import shutil
+import tempfile
+import unittest
+from unittest import mock
+
+from pma_python import core
+
+REAL_PMA_START_HELPER = core._pma_start_files_for_slide
+
+
+def write(path, size):
+    os.makedirs(os.path.dirname(path), exist_ok=True)
+    with open(path, "wb") as f:
+        f.write(b"x" * size)
+    return path
+
+
+class CollectSlidePackageFiles(unittest.TestCase):
+    def setUp(self):
+        self.dir = tempfile.mkdtemp()
+        # by default PMA.start is not running
+        p = mock.patch.object(core, "_pma_start_files_for_slide", return_value=[])
+        p.start()
+        self.addCleanup(p.stop)
+
+    def tearDown(self):
+        shutil.rmtree(self.dir, ignore_errors=True)
+
+    def rel(self, files):
+        return [f["relative_path"] for f in files]
+
+    def test_olympus_vsi_underscore_folder(self):
+        vsi = write(os.path.join(self.dir, "VL1_Name, A_1AH&E.vsi"), 100)
+        write(os.path.join(self.dir, "_VL1_Name, A_1AH&E_", "stack1", "frame_t.ets"), 5000)
+        write(os.path.join(self.dir, "_VL1_Name, A_1AH&E_", "stack10001", "frame_t.ets"), 300)
+        files = core._collect_slide_package_files(vsi)
+        self.assertEqual(self.rel(files), [
+            "VL1_Name, A_1AH&E.vsi",
+            "_VL1_Name, A_1AH&E_/stack1/frame_t.ets",
+            "_VL1_Name, A_1AH&E_/stack10001/frame_t.ets",
+        ])
+        self.assertTrue(files[0]["is_main"])
+        self.assertFalse(any(f["is_main"] for f in files[1:]))
+        self.assertEqual(core._get_slide_package_size(vsi), (5400, 5000))
+
+    def test_mrxs_same_name_folder(self):
+        mrxs = write(os.path.join(self.dir, "slide.mrxs"), 10)
+        write(os.path.join(self.dir, "slide", "Data0000.dat"), 700)
+        write(os.path.join(self.dir, "slide", "Slidedat.ini"), 20)
+        self.assertEqual(self.rel(core._collect_slide_package_files(mrxs)),
+                         ["slide.mrxs", "slide/Data0000.dat", "slide/Slidedat.ini"])
+
+    def test_single_file_slide(self):
+        svs = write(os.path.join(self.dir, "single.svs"), 42)
+        write(os.path.join(self.dir, "other.svs"), 42)          # unrelated neighbour
+        files = core._collect_slide_package_files(svs)
+        self.assertEqual(self.rel(files), ["single.svs"])
+        self.assertEqual(core._get_slide_package_size(svs), (42, 42))
+
+    def test_pma_start_list_is_merged_without_duplicates(self):
+        vsi = write(os.path.join(self.dir, "a.vsi"), 1)
+        ets = write(os.path.join(self.dir, "_a_", "stack1", "frame_t.ets"), 9)
+        extra = write(os.path.join(self.dir, "a_extra", "x.bin"), 3)   # a convention we do not know
+        outside = write(os.path.join(tempfile.mkdtemp(), "elsewhere.bin"), 3)
+        with mock.patch.object(core, "_pma_start_files_for_slide", return_value=[vsi, ets, extra, outside]):
+            files = core._collect_slide_package_files(vsi)
+        self.assertEqual(self.rel(files), ["a.vsi", "_a_/stack1/frame_t.ets", "a_extra/x.bin"])
+        shutil.rmtree(os.path.dirname(outside), ignore_errors=True)
+
+    def test_pma_start_unavailable_is_not_fatal(self):
+        vsi = write(os.path.join(self.dir, "b.vsi"), 1)
+        write(os.path.join(self.dir, "_b_", "stack1", "frame_t.ets"), 9)
+        with mock.patch.object(core, "get_files_for_slide", side_effect=ConnectionError("PMA.start down")), \
+             mock.patch.object(core, "_pma_start_files_for_slide", side_effect=REAL_PMA_START_HELPER):
+            files = core._collect_slide_package_files(vsi)
+        self.assertEqual(self.rel(files), ["b.vsi", "_b_/stack1/frame_t.ets"])
+
+    def test_missing_file(self):
+        with self.assertRaises(ValueError):
+            core._collect_slide_package_files(os.path.join(self.dir, "nope.vsi"))
+
+
+class RealPmaStartHelper(unittest.TestCase):
+    def test_returns_empty_list_when_pma_start_errors(self):
+        with mock.patch.object(core, "get_files_for_slide", side_effect=ConnectionError("down")):
+            self.assertEqual(core._pma_start_files_for_slide("C:/x.vsi"), [])
+
+    def test_returns_paths_from_pma_start(self):
+        with mock.patch.object(core, "get_files_for_slide", return_value={"C:/x.vsi": {}, "C:/_x_/s/f.ets": {}}):
+            self.assertEqual(sorted(core._pma_start_files_for_slide("C:/x.vsi")), ["C:/_x_/s/f.ets", "C:/x.vsi"])
+
+
+class CloudUploadSendsWholeSlide(unittest.TestCase):
+    """End to end through upload_file_on_cloud with a fake server: every file must be announced and sent."""
+
+    def test_vsi_upload_sends_image_data(self):
+        d = tempfile.mkdtemp()
+        self.addCleanup(shutil.rmtree, d, True)
+        vsi = write(os.path.join(d, "VL9_X, Y_1AH&E.vsi"), 100)
+        write(os.path.join(d, "_VL9_X, Y_1AH&E_", "stack1", "frame_t.ets"), 5000)
+
+        sent = []
+
+        class FakeResp:
+            id, upload_type, urls, multipart_files = 7, 2, ["u1", "u2"], []
+
+        class FakeClient:
+            server_url = "https://pma.example/"
+
+            def __init__(self, url):
+                pass
+
+            async def upload_header(self, header, session_id):
+                self.header = header
+                sent.append(("header", [(f.path, f.length, f.isMain) for f in header.files]))
+                return FakeResp()
+
+            async def upload_file(self, upload_id, upload_type, url, rel, stream, session_id, **kw):
+                sent.append(("file", rel, len(stream.read())))
+
+        class Ok:
+            status_code = 200
+
+        with mock.patch.object(core, "PmaCoreClient", FakeClient), \
+             mock.patch.object(core, "_pma_start_files_for_slide", return_value=[]), \
+             mock.patch.object(core.requests, "get", return_value=Ok()), \
+             mock.patch.object(core, "get_slide_info", return_value={}):
+            ok, err = asyncio.run(core.upload_file_on_cloud(
+                pma_core_url="https://pma.example/", session_id="S", slide_path=vsi,
+                upload_directory="Slides/Received"))
+
+        self.assertTrue(ok, err)
+        self.assertEqual(sent[0], ("header", [("VL9_X, Y_1AH&E.vsi", 100, True),
+                                              ("_VL9_X, Y_1AH&E_/stack1/frame_t.ets", 5000, False)]))
+        self.assertEqual(sent[1:], [("file", "VL9_X, Y_1AH&E.vsi", 100),
+                                    ("file", "_VL9_X, Y_1AH&E_/stack1/frame_t.ets", 5000)])
+
+
+if __name__ == "__main__":
+    unittest.main(verbosity=2)

pma_python-2.0.0.185/pma_python/version.py

@@ -1 +0,0 @@
-__version__ = '2.0.0.185'