Fix omerotools

src/imcflibs/imagej/omerotools.py

@@ -14,6 +14,8 @@
 [omero-insight]: https://github.com/ome/omero-insight
 """
 
+import os
+
 from fr.igred.omero import Client
 from fr.igred.omero.annotations import (
     MapAnnotationWrapper,
@@ -27,14 +29,77 @@
 from omero.gateway.model import TableData, TableDataColumn
 
 
+def parse_url_string(url_str):
+    """Extract IDs from an OMERO URL.
+
+    Info: URLs can only be of the same type (Dataset, Project, Images).
+    Returns tuple[empty list, ""] if input str (URL) is not an OMERO URL.
+
+    Parameters
+    ----------
+    url_str : str
+        OMERO URL, e.g. from the webclient.
+
+    Returns
+    -------
+    tuple[list[str], str]
+        - List of IDs extracted from the OMERO URL.
+        - Type of IDs (i.e. "project", "dataset", or "image")
+    """
+    omero_types = ["dataset-", "project-", "image-"]
+
+    for omero_type in omero_types:
+        omero_ids = extract_ids_from_string(url_str, omero_type)
+        if len(omero_ids) > 0:
+            return omero_ids, omero_type.strip("-")
+    # If no IDs identified
+    return [], ""
+
+
+def extract_ids_from_string(omero_str, omero_type):
+    """Extract IDs from an OMERO URL for a given OMERO type.
+
+    Parameters
+    ----------
+    omero_str : str
+        OMERO URL, e.g. from the webclient.
+    omero_type : str
+        OMERO type, i.e. "project", "Dataset", or "Image" # FIXME
+
+    Returns
+    -------
+    list[str]
+        List of IDs extracted from the OMERO URL.
+    """
+    omero_type = omero_type.lower().strip("-")
+    if omero_type not in ["project", "dataset", "image"]:
+        raise ValueError("Unknown OMERO type: {}".format(omero_type))
+
+    omero_ids = []
+    omero_type = omero_type + "-"
+    if omero_type in omero_str:
+        # If there are multiple types
+        if "|" in omero_str:
+            parts = omero_str.split("|")
+            for part in parts:
+                if omero_type in part:
+                    omero_id = part.split(omero_type)[1].split("/")[0]
+                    omero_ids.append(omero_id)
+        else:
+            # If there is only one dataset
+            omero_id = omero_str.split(omero_type)[1].split("/")[0]
+            omero_ids.append(omero_id)
+    return omero_ids
+
+
 def parse_url(client, omero_str):
     """Parse an OMERO URL / image IDs into the respective ImageWrapper objects.
 
     Assemble a list of ImageWrapper objects from one of the following inputs:
 
-    - An OMERO URL (as retrieved e.g. from OMERO.web).
+    - An OMERO URL for Dataset(s) or Image(s)
+        (as retrieved e.g. from OMERO.web).
     - One or more OMERO image IDs.
-    - An OMERO Dataset ID.
 
     Parameters
     ----------
@@ -63,62 +128,31 @@ def parse_url(client, omero_str):
     # Sanitize the string
     omero_str = omero_str.strip()
 
-    image_ids = []
-    dataset_ids = []
-    image_wpr_list = []
+    # Get a list of str IDs and their OMERO type
+    omero_ids, omero_type = parse_url_string(omero_str)
 
-    # Check if the url is a dataset
-    if "dataset-" in omero_str:
-        # If there are multiple datasets
-        if "|" in omero_str:
-            parts = omero_str.split("|")
-            for part in parts:
-                if "dataset-" in part:
-                    image_ids.extend(
-                        [
-                            image
-                            for image in client.getDataset(
-                                Long(part.split("dataset-")[1].split("/")[0])
-                            ).getImages()
-                        ]
-                    )
-                    dataset_id = Long(part.split("dataset-")[1].split("/")[0])
-                    dataset_ids.append(dataset_id)
-        else:
-            image_ids.extend(
-                [
-                    image
-                    for image in client.getDataset(
-                        Long(omero_str.split("dataset-")[1].split("/")[0])
-                    ).getImages()
-                ]
-            )
-            # If there is only one dataset
-            dataset_id = Long(omero_str.split("dataset-")[1].split("/")[0])
-            dataset_ids.append(dataset_id)
+    if omero_type == "project":
+        raise NotImplementedError(
+            "Getting Image IDs from Project(s) is not implemented."
+        )
 
-        # Get the images from the dataset
-        for dataset_id in dataset_ids:
-            dataset_wpr = client.getDataset(dataset_id)
+    elif omero_type == "dataset":
+        image_wpr_list = []
+        # Get the images from the dataset(s)
+        for omero_id in omero_ids:
+            dataset_wpr = client.getDataset(Long(omero_id))
             image_wpr_list.extend(dataset_wpr.getImages())
-
         return image_wpr_list
 
-    # Check if the url is an image
-    elif "image-" in omero_str:
-        image_ids = omero_str.split("image-")
-        image_ids.pop(0)
-        image_ids = [s.split("%")[0].replace("|", "") for s in image_ids]
+    elif omero_type == "image":
+        # omero_ids will be processed at the end
+        pass
+
     else:
-        image_ids = (
-            [s.split("%")[0].replace("|", "") for s in omero_str.split("image-")[1:]]
-            if "image-" in omero_str
-            else omero_str.split(",")
-        )
-        # If it is a list of IDs separated by commas
-        image_ids = omero_str.split(",")
+        # (omero_type == "") supposedly a list of IDs separated by commas
+        omero_ids = omero_str.split(",")
 
-    return [client.getImage(Long(image_id)) for image_id in image_ids]
+    return [client.getImage(Long(image_id)) for image_id in omero_ids]
 
 
 def connect(host, port, username, password):
@@ -190,6 +224,12 @@ def upload_image_to_omero(user_client, path, dataset_id):
     Long
         ID of the uploaded image
     """
+    if not os.path.exists(path):
+        try:
+            raise FileNotFoundError("Could not find file: {}".format(path))
+        except NameError:
+            raise IOError("Could not find file: {}".format(path))
+
     return user_client.getDataset(Long(dataset_id)).importImage(user_client, path)[0]
 
 
@@ -201,7 +241,7 @@ def add_keyvalue_annotation(client, repository_wpr, annotations, header):
     client : fr.igred.omero.Client
         The client object used to connect to the OMERO server.
     repository_wpr : fr.igred.omero.repositor.GenericRepositoryObjectWrapper
-        Wrapper to the object for the anotation.
+        Wrapper to the object for the annotation.
     annotations : dict
         Dictionary with the annotation to add.
     header : str
@@ -222,7 +262,7 @@ def delete_keyvalue_annotations(user_client, object_wrapper):
     user_client : fr.igred.omero.Client
         Client used for login to OMERO.
     object_wrapper : fr.igred.omero.repositor.GenericRepositoryObjectWrapper
-        Wrapper to the object for the anotation.
+        Wrapper to the object for the annotation.
 
     """
     kv_pairs = object_wrapper.getMapAnnotations(user_client)

tests/interactive-imagej/omerotools/parse_url/test_parse_url_01.py

@@ -0,0 +1,58 @@
+# @ String (label="OMERO HOST") host
+# @ Integer (label="OMERO PORT", value=4064) port
+# @ String (label="OMERO User") user
+# @ String (label="OMERO Password", style="password") pwd
+# @ String (label="Provide OMERO Project URL") url_project
+# @ String (label="Provide OMERO 'Dataset A' URL") url_dataset
+# @ String (label="Provide OMERO URL for ALL images in 'Dataset A'") url_images
+# Examples
+# url_project: https://omero.biozentrum.unibas.ch/webclient/?show=project-25155
+# url_dataset: https://omero.biozentrum.unibas.ch/webclient/?show=dataset-82170
+# url_images: https://omero.biozentrum.unibas.ch/webclient/?show=image-3454870|image-3454871|image-3454872|image-3454873|image-3454874
+
+
+from imcflibs.imagej import omerotools
+
+# Parse the url_images to get the IDs
+image_ids = []
+parts = url_images.split("|")
+for part in parts:
+    if "image-" in part:
+        image_id = part.split("image-")[1].split("/")[0]
+        image_ids.append(image_id)
+assert len(image_ids) > 0, "No image ids in image url!"
+
+# Test
+try:
+    user_client = omerotools.connect(host, port, user, pwd)
+
+    # Project URLs are not implemented
+    ids = None
+    try:
+        ids = omerotools.parse_url(user_client, url_project)
+    except NotImplementedError:
+        pass
+    assert ids is None
+
+    # Single Dataset
+    ids = omerotools.parse_url(user_client, url_dataset)
+    assert len(ids) == len(image_ids)
+
+    # Images url
+    ids = omerotools.parse_url(user_client, url_images)
+    assert len(ids) == len(image_ids)
+    for cur_id in ids:
+        cur_id = cur_id.getId()
+        assert str(cur_id) in image_ids
+
+    # Image IDs as comma-separated string
+    ids = omerotools.parse_url(user_client, ",".join(image_ids))
+    assert len(ids) == len(image_ids)
+    for cur_id in ids:
+        cur_id = cur_id.getId()
+        assert str(cur_id) in image_ids
+finally:
+    if user_client is not user_client:
+        user_client.disconnect()
+
+print("Test completed!")

tests/interactive-imagej/omerotools/upload_image_to_omero/test_upload_image_to_omero_01.py

@@ -0,0 +1,19 @@
+from imcflibs.imagej import omerotools
+
+
+error_type = "FileNotFoundError"
+try:
+    FileNotFoundError
+except NameError:
+    FileNotFoundError = IOError
+    error_type = "IOError"
+
+path = "/usr/fancy/path/pony-with-one-horn.tiff"
+
+try:
+    # No client needed. Only testing the exception
+    omerotools.upload_image_to_omero(None, path, None)
+except FileNotFoundError:
+    print("Got the expected {}".format(error_type))
+
+print("Test completed!")

tests/test_omerotools.py

@@ -0,0 +1,110 @@
+"""Tests for the imcflibs.imagej.omerotools module."""
+
+import pytest
+
+from imcflibs.imagej.omerotools import (
+    extract_ids_from_string,
+    parse_url,
+    parse_url_string,
+    upload_image_to_omero,
+)
+
+# Enusre Python 2.7 and 3.x compability
+try:
+    FileNotFoundError
+except NameError:
+    FileNotFoundError = IOError
+
+
+def test_upload_image_to_omero():
+    """Test `upload_image_to_omero()`.
+
+    Tests only the case for non-existing files.
+    """
+    path = "/usr/random/path/questionable/file.tiff"
+    with pytest.raises(FileNotFoundError, match=r"Could not find file"):
+        upload_image_to_omero(None, path, None)
+
+
+def test_extract_ids_from_string():
+    """Test `extract_ids_from_string()`."""
+
+    url_proj = "webclient/?show=project-25406"
+    # Expect error with wrong omero_type
+    with pytest.raises(ValueError, match=r"Unknown OMERO type"):
+        extract_ids_from_string(url_proj, "unicorn")
+
+    assert len(extract_ids_from_string(url_proj, "Project")) == 1
+    assert len(extract_ids_from_string(url_proj, "Project-")) == 1
+    assert len(extract_ids_from_string(url_proj, "Dataset")) == 0
+
+    url_dataset = "webclient/?show=dataset-82753"
+    assert len(extract_ids_from_string(url_dataset, "dataset")) == 1
+
+    url_image = "webclient/?show=image-3598144"
+    assert len(extract_ids_from_string(url_image, "image")) == 1
+
+    url_multi_image = (
+        "webclient/?show=image-3598144|image-3598145|image-3598146|image-3598147"
+    )
+    assert len(extract_ids_from_string(url_multi_image, "image-")) == 4
+    assert len(extract_ids_from_string(url_multi_image, "Project")) == 0
+
+    url_bad = "https://github.com/imcf/python-imcflibs"
+    assert len(extract_ids_from_string(url_bad, "image")) == 0
+
+
+def test_parse_url_string():
+    """Test `parse_url_string()`."""
+    url_proj = "webclient/?show=project-25406"
+    omero_ids, omero_type = parse_url_string(url_proj)
+    assert len(omero_ids) == 1
+    assert omero_type == "project"
+    assert "25406" in omero_ids
+
+    url_dataset = "webclient/?show=dataset-82753"
+    omero_ids, omero_type = parse_url_string(url_dataset)
+    assert len(omero_ids) == 1
+    assert omero_type == "dataset"
+    assert "82753" in omero_ids
+
+    url_image = "webclient/?show=image-3598144"
+    omero_ids, omero_type = parse_url_string(url_image)
+    assert len(omero_ids) == 1
+    assert omero_type == "image"
+    assert "3598144" in omero_ids
+
+    url_multi_image = (
+        "webclient/?show=image-3598144|image-3598145|image-3598146|image-3598147"
+    )
+    omero_ids, omero_type = parse_url_string(url_multi_image)
+    assert len(omero_ids) == 4
+    assert omero_type == "image"
+    assert "3598144" in omero_ids
+    assert "3598145" in omero_ids
+    assert "3598146" in omero_ids
+    assert "3598147" in omero_ids
+
+    url_bad = "https://github.com/imcf/python-imcflibs"
+    omero_ids, omero_type = parse_url_string(url_bad)
+    assert len(omero_ids) == 0
+    assert omero_type == ""
+
+
+def test_parse_url():
+    """Test `parse_url()`.
+
+    Only tests the first part of the function
+    (NotImplementedError on Project-URLs).
+    Since the reset of the function depends on OMERO libraries.
+    """
+    url_empty = ""
+    with pytest.raises(ValueError, match=r"No OMERO link or image ID prov"):
+        parse_url(None, url_empty)
+
+    url_proj = "webclient/?show=project-25406"
+    with pytest.raises(
+        NotImplementedError,
+        match=r"Getting Image IDs from Project",
+    ):
+        parse_url(None, url_proj)