Merge pull request #280 from iBridges-for-iRODS/develop

v1.2.0

.github/workflows/main.yml

@@ -18,7 +18,7 @@ jobs:
       fail-fast: true
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
         include:
           - os: windows-latest
             python-version: "3.12"
@@ -29,16 +29,13 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-
-      - name: Clone the repository
-        uses: actions/checkout@v4
+          cache: 'pip'
 
       - name: Install dependencies
         run: |
-          pip install --upgrade pip
           pip install ".[test]"
 
       - name: Test with pytest
@@ -59,11 +56,14 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: "pip"
+
 
       - name: Install dependencies
         run: |
-          pip install --upgrade pip
           pip install ".[test]"
 
       - name: Lint with Ruff

docker/README.md

@@ -10,7 +10,7 @@ Dockerised integration tests of iBridges with iRODS
 1. Clone iBridges
 
    ```sh
-   git clone --branch develop https://github.com/UtrechtUniversity/iBridges.git
+   git clone --branch develop https://github.com/iBridges-for-iRODS/iBridges.git
    ```
 
 Execute the following commands in the root ibridges directory:

docker/irods_client/tests/test_search.py

@@ -1,3 +1,4 @@
+import pytest
 from pytest import mark
 
 from ibridges import IrodsPath, search_data, upload
@@ -58,3 +59,30 @@ def test_find_meta(session, item_name, request, metadata, is_found):
 
     res = _found(search_data(session, metadata=metadata), ipath)
     assert res == is_found
+
+@mark.parametrize("metadata,is_found", [
+    (MetaSearch("author", "Ben"), True),
+    (MetaSearch(units="KG"), True)
+])
+@mark.parametrize("item_name", ["collection", "dataobject"])
+def test_find_case_ins_meta(session, item_name, request, metadata, is_found):
+    item = request.getfixturevalue(item_name)
+    ipath = IrodsPath(session, item.path)
+    ipath.meta.clear()
+    ipath.meta.add("Author", "Ben")
+    ipath.meta.add("Mass", "10", "kg")
+
+    res = _found(search_data(session, metadata=metadata), ipath)
+    assert res == is_found
+    res = _found(search_data(session, metadata=metadata, case_sensitive=True), ipath)
+    with pytest.raises(AssertionError):
+        assert res == is_found
+
+
+@mark.parametrize("item_name", ["collection", "dataobject"])
+def test_find_case_ins_path(session, item_name, request):
+    item = request.getfixturevalue(item_name)
+    ipath = IrodsPath(session, item.path)
+    assert _found(search_data(session, path_pattern=item.name.upper()), item.path)
+    with pytest.raises(AssertionError):
+        assert _found(search_data(session, path_pattern=item.name.upper(), case_sensitive=True), item.path)

docs/source/cli.rst

@@ -36,7 +36,7 @@ create the environment file for you. Below are the currently (known) plugins, se
     * - Organization
       - Link
     * - Utrecht University
-      - https://github.com/UtrechtUniversity/ibridges-servers-uu
+      - https://github.com/iBridges-for-iRODS/ibridges-servers-uu
 
 After installation, you will be able to create an `irods_environment.json` by simply answering questions such as which email-address
 you have. First find the server name with:

docs/source/faq.rst

@@ -18,15 +18,15 @@ An advantage compared to the iCommands is that iBridges also works on Mac OS and
 
 **I found a bug or have a feature request, where do I go?**
 ------------------------------------------------------------------------
-Our development is done on `GitHub <https://github.com/UtrechtUniversity/iBridges>`__ Look under the `Issues` section
+Our development is done on `GitHub <https://github.com/iBridges-for-iRODS/iBridges>`__ Look under the `Issues` section
 whether the bug or feature request has already been reported. If not, we heartily welcome creating a new issue. We
 try to get back to you as soon as possible, at least within a few days.
 
 
 **I want to contribute to iBridges, where do I go?**
 ----------------------------------------------------
 
-Our development is done on `GitHub <https://github.com/UtrechtUniversity/iBridges>`__ We are welcoming contributions
+Our development is done on `GitHub <https://github.com/iBridges-for-iRODS/iBridges>`__ We are welcoming contributions
 by pull requests. You can also ask for new features/ideas in our issue tracker.
 
 
@@ -85,10 +85,23 @@ Warnings can also be switched off through python's `warnings` package:
 
 .. code-block:: python
 
-   import warnings
-   warnings.filterwarnings("ignore")
+	import warnings
+	warnings.filterwarnings("ignore")
+
 
 **My metadata with keys starting with `org_` do not show up in the iBridges metadata.**
 ---------------------------------------------------------------------------------------
 
-iBridges **does not show** metadata that contain a key starting with the prefix `org_`. This is due to data security reasons on `Yoda systems <https://github.com/UtrechtUniversity/yoda>`__.
+By default, iBridges **does not show** metadata that contain a key starting with the prefix `org_`. This is due to data security reasons on `Yoda systems <https://github.com/UtrechtUniversity/yoda>`__.
+
+You can omit this by the following code:
+
+.. code-block:: python
+
+    from ibridges.meta import MetaData
+    
+    # collections
+    meta = MetaData(IrodsPath(session, "~", "my_coll").collection, blacklist=None)
+    # data objects
+    meta = MetaData(IrodsPath(session, "~", "my_obj").dataobject, blacklist=None)
+    print(meta)

docs/source/index.rst

@@ -6,20 +6,20 @@
 Welcome to the iBridges documentation!
 ======================================
 
-`iBridges <https://github.com/UtrechtUniversity/iBridges>`__ is a Python library to connect to iRODS servers in a simplified and safe manner.
+`iBridges <https://github.com/iBridges-for-iRODS/iBridges>`__ is a Python library to connect to iRODS servers in a simplified and safe manner.
 iBridges consists of three major components: a Python API for Python programmers, a Command Line Interface and a Graphical user interface.
 The documentation presented here is for the Python API and Command Line Interface. The documentation for the Graphical User Interface is
 located on a separate `page <https://chstaiger.github.io/iBridges-Gui/>`__.
 
 .. note::
-   The project is in active development, current features are stable and the documentation is complete. However, we are still actively developing new features and improving the existing ones. We appreciate help, suggestions, issues and bug reports in our issue tracker on `GitHub <https://github.com/UtrechtUniversity/iBridges>`__.
+   The project is in active development, current features are stable and the documentation is complete. However, we are still actively developing new features and improving the existing ones. We appreciate help, suggestions, issues and bug reports in our issue tracker on `GitHub <https://github.com/iBridges-for-iRODS/iBridges>`__.
 
 
 iBridges is a wrapper around the `python-irodsclient <https://github.com/irods/python-irodsclient>`__. While the
 python-irodsclient is very powerful and feature rich, we aim to provide an easier API for users (mainly researchers)
 that do not have any technical knowledge of iRods.
 
-We provide extensive tutorials on how to work with data in iRODS. Please consult our `tutorials <https://github.com/UtrechtUniversity/iBridges/tree/main/tutorials>`__ page.
+We provide extensive tutorials on how to work with data in iRODS. Please consult our `tutorials <https://github.com/iBridges-for-iRODS/iBridges/tree/main/tutorials>`__ page.
 
 .. toctree::
    :hidden:

docs/source/ipath.rst

@@ -14,7 +14,7 @@ We strongly recommend using :class:`IrodsPath` over using strings for the follow
 - :class:`IrodsPath` is **more convenient** since there are many methods and attributes available such as: the name, size and parent of the iRODS path.
 - The string representation of the :class:`IrodsPath` is available through :code:`str(ipath)`.
 
-A complete tutorial on iRODS paths can be followed `here <https://github.com/UtrechtUniversity/iBridges/tree/main/tutorials>`__. For an overview of
+A complete tutorial on iRODS paths can be followed `here <https://github.com/iBridges-for-iRODS/iBridges/tree/main/tutorials>`__. For an overview of
 all functionality connected to the :class:`IrodsPath`, see the :doc:`API documentation <api/generated/ibridges.path.IrodsPath>`. 
 
 IrodsPath

ibridges/__main__.py

@@ -7,7 +7,7 @@
 import sys
 from argparse import RawTextHelpFormatter
 from pathlib import Path
-from typing import Optional, Union
+from typing import Literal, Optional, Union
 
 from ibridges.data_operations import download, sync, upload
 from ibridges.interactive import DEFAULT_IENV_PATH, DEFAULT_IRODSA_PATH, interactive_auth
@@ -278,7 +278,7 @@ def ibridges_setup():
         if len(env_providers) == 0:
             print(
                 "No server information was found. To use this function, please install a plugin"
-                " such as:\n\nhttps://github.com/UtrechtUniversity/ibridges-servers-uu"
+                " such as:\n\nhttps://github.com/iBridges-for-iRODS/ibridges-servers-uu"
                 "\n\nAlternatively create an irods_environment.json by yourself or with the help "
                 "of your iRODS administrator."
             )
@@ -374,9 +374,11 @@ def _parse_remote(remote_path: Union[None, str], session: Session) -> IrodsPath:
         return IrodsPath(session, remote_path[7:])
     return IrodsPath(session, remote_path[6:])
 
+
 def _get_metadata_path(args, ipath: IrodsPath, lpath: Union[str, Path],
                        mode: str) -> Union[None, str, Path]:
-    metadata = False if not hasattr(args, "metadata") else args.metadata
+    metadata: Union[Literal[False], Path, None
+                    ] = False if not hasattr(args, "metadata") else args.metadata
     if ipath.dataobject_exists() and metadata is None:
         raise ValueError("Supply metadata path for downloading metadata of data objects.")
     if mode == "download":
@@ -385,8 +387,10 @@ def _get_metadata_path(args, ipath: IrodsPath, lpath: Union[str, Path],
         default_meta_path = Path(lpath, ".ibridges_metadata.json")
     else:
         raise ValueError("Internal error, contact the iBridges team.")
-    metadata = metadata if metadata is not None else default_meta_path
-    metadata = None if metadata is False else metadata
+    if metadata is None:
+        return default_meta_path
+    if metadata is False:
+        return None
     return metadata
 
 

ibridges/meta.py

@@ -58,8 +58,9 @@ def __iter__(self) -> Iterator:
         """Iterate over all metadata key/value/units triplets."""
         if self.blacklist is None:
             yield from self.item.metadata.items()
+            return
         for meta in self.item.metadata.items():
-            if re.match(self.blacklist, meta.name) is None:
+            if self.blacklist and re.match(self.blacklist, meta.name) is None:
                 yield meta
             else:
                 warnings.warn(f"Ignoring metadata entry with value {meta.name}, because it matches "
@@ -148,6 +149,9 @@ def add(self, key: str, value: str, units: Optional[str] = None):
         try:
             if (key, value, units) in self:
                 raise ValueError("ADD META: Metadata already present")
+            if self.blacklist:
+                if re.match(self.blacklist, key):
+                    raise ValueError(f"ADD META: Key must not start with {self.blacklist}.")
             self.item.metadata.add(key, value, units)
         except irods.exception.CAT_NO_ACCESS_PERMISSION as error:
             raise PermissionError("UPDATE META: no permissions") from error

ibridges/search.py

@@ -43,6 +43,7 @@ def search_data(  # pylint: disable=too-many-branches
     checksum: Optional[str] = None,
     metadata: Union[None, MetaSearch, list[MetaSearch], list[tuple]] = None,
     item_type: Optional[str] = None,
+    case_sensitive: bool = False
 ) -> list[IrodsPath]:
     """Search for collections, data objects and metadata.
 
@@ -72,6 +73,8 @@ def search_data(  # pylint: disable=too-many-branches
     item_type:
         Type of the item to search for, by default None indicating both data objects and collections
         are returned. Set to "data_object" for data objects and "collection" for collections.
+    case_sensitive:
+        Case sensitive search for Paths and metadata. Default: False
 
     Raises
     ------
@@ -148,17 +151,21 @@ def search_data(  # pylint: disable=too-many-branches
     queries = []
     if item_type != "data_object" and checksum is None:
         # create the query for collections; we only want to return the collection name
-        coll_query = session.irods_session.query(icat.COLL_NAME)
+        coll_query = session.irods_session.query(icat.COLL_NAME, case_sensitive=case_sensitive)
         coll_query = coll_query.filter(icat.LIKE(icat.COLL_NAME, _postfix_wildcard(path)))
         queries.append((coll_query, "collection"))
     if item_type != "collection":
         # create the query for data objects; we need the collection name, the data name and checksum
-        data_query = session.irods_session.query(icat.COLL_NAME, icat.DATA_NAME, icat.DATA_CHECKSUM)
+        data_query = session.irods_session.query(icat.COLL_NAME,
+                                                 icat.DATA_NAME,
+                                                 icat.DATA_CHECKSUM,
+                                                 case_sensitive=case_sensitive)
         data_query = data_query.filter(icat.LIKE(icat.COLL_NAME, _postfix_wildcard(path)))
         queries.append((data_query, "data_object"))
 
         data_name_query = session.irods_session.query(icat.COLL_NAME, icat.DATA_NAME,
-                                                    icat.DATA_CHECKSUM)
+                                                      icat.DATA_CHECKSUM,
+                                                      case_sensitive=case_sensitive)
         data_name_query.filter(icat.LIKE(icat.COLL_NAME, f"{path}"))
         queries.append((data_name_query, "data_object"))
 

ibridges/session.py

@@ -273,9 +273,13 @@ def write_pam_password(self):
         connection = self.irods_session.pool.get_connection()
         pam_passwords = self.irods_session.pam_pw_negotiated
         if len(pam_passwords):
+            actual_password = pam_passwords[0]
+        else:
+            actual_password = self._password
+        if actual_password:
             irods_auth_file = self.irods_session.get_irods_password_file()
             with open(irods_auth_file, "w", encoding="utf-8") as authfd:
-                authfd.write(irods.password_obfuscation.encode(pam_passwords[0]))
+                authfd.write(irods.password_obfuscation.encode(actual_password))
         else:
             warnings.warn("WARNING -- unable to cache obfuscated password locally")
         connection.release()

pyproject.toml

@@ -34,8 +34,8 @@ dependencies = [
 dynamic = ["version"]
 
 [project.urls]
-GitHub = "https://github.com/UtrechtUniversity/iBridges"
-documentation = "https://github.com/UtrechtUniversity/iBridges"
+GitHub = "https://github.com/iBridges-for-iRODS/iBridges"
+documentation = "https://github.com/iBridges-for-iRODS/iBridges"
 
 [project.optional-dependencies]
 test = [
@@ -47,7 +47,7 @@ test = [
     "types-tqdm",
 ]
 docs = [
-    "sphinx<8",
+    "sphinx<9",
     "sphinx-rtd-theme",
     "sphinxcontrib-napoleon",
     "sphinx-autodoc-typehints",