Merge pull request #287 from iBridges-for-iRODS/develop

v1.3.0

.github/workflows/linter.yml

@@ -8,22 +8,31 @@ on:
   push:
     branches:
       - develop
+    paths-ignore:
+      - 'docs/**'
+      - 'README.md'
+      - '_quarto.yml'
+      - 'index.qmd'
+
   pull_request:
-    branches:
-      - develop
+    paths-ignore:
+      - 'docs/**'
+      - 'README.md'
+      - '_quarto.yml'
+      - 'index.qmd'
 
 jobs:
   build:
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
         include:
           - os: windows-latest
-            python-version: "3.11"
+            python-version: "3.12"
           - os: macos-latest
-            python-version: "3.11"
+            python-version: "3.12"
     runs-on: ${{ matrix.os }}
 
     steps:

README.md

@@ -1,15 +1,16 @@
-# iBridges GUI <img src="https://github.com/chStaiger/iBridges-Gui/blob/develop/ibridgesgui/icons/logo.png?raw=true" width="150" align="right">  
+# iBridges GUI <img src="https://github.com/iBridges-for-iRods/iBridges-GUI/blob/3395dedf2c7b919e108356a3289eb2c2fc66af6d/ibridgesgui/icons/logo.png" width="150" align="right">  
+
 
 <p align="center">
   <p align="center">
-    <a href="https://chstaiger.github.io/iBridges-Gui/"><strong> Documentation »</strong></a> .
-    <a href="https://github.com/chStaiger/iBridges-Gui/issues">Report Bug or Request Feature</a>
+    <a href="https://ibridges-for-irods.github.io/iBridges-GUI/"><strong> Documentation »</strong></a> .
+    <a href="https://github.com/iBridges-for-iRods/iBridges-GUI/issues">Report Bug or Request Feature</a>
     .
   </p>
 </p>
 
-[![Python package](https://github.com/chStaiger/iBridges-Gui/actions/workflows/linter.yml/badge.svg)](https://github.com/chStaiger/iBridges-Gui/actions/workflows/linter.yml)
-[![Quarto Publish](https://github.com/chStaiger/iBridges-Gui/actions/workflows/publish.yml/badge.svg)](https://github.com/chStaiger/iBridges-Gui/actions/workflows/publish.yml)
+[![Python package](https://github.com/iBridges-for-iRods/iBridges-GUI/actions/workflows/linter.yml/badge.svg)](https://github.com/iBridges-for-iRods/iBridges-GUI/actions/workflows/linter.yml)
+[![Quarto Publish](https://github.com/iBridges-for-iRods/iBridges-GUI/actions/workflows/publish.yml/badge.svg)](https://github.com/iBridges-for-iRods/iBridges-GUI/actions/workflows/publish.yml)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12583957.svg)](https://doi.org/10.5281/zenodo.12583957)
 
 
@@ -86,7 +87,7 @@ The git repository contains a generic *iRODS* graphical user interface.  The iRO
 
 ## Contributing
 ### Code
-Instructions on how to extend the GUI or contribute to the code base can be found in the [documentation](https://chstaiger.github.io/iBridges-Gui/).
+Instructions on how to extend the GUI or contribute to the code base can be found in the [documentation](https://ibridges-for-irods.github.io/iBridges-GUI/).
 
 ## License
 This project is licensed under the GPL-v3 license.

ibridgesgui/browser.py

@@ -2,14 +2,14 @@
 
 import logging
 import sys
+from typing import Union
 
 import irods.exception
 import PyQt6.QtCore
 import PyQt6.QtGui
 import PyQt6.QtWidgets
 import PyQt6.uic
 from ibridges import IrodsPath
-from ibridges.meta import MetaData
 from ibridges.permissions import Permissions
 from ibridges.util import obj_replicas
 
@@ -26,7 +26,7 @@
 class Browser(PyQt6.QtWidgets.QWidget, Ui_tabBrowser):
     """Browser view for iRODS session."""
 
-    def __init__(self, session, app_name):
+    def __init__(self, session, app_name: str):
         """Initialize an iRODS browser view."""
         super().__init__()
         if getattr(sys, "frozen", False):
@@ -81,15 +81,15 @@ def init_browser(self):
         self.meta_table.clicked.connect(self.edit_metadata)
         self.add_meta_button.clicked.connect(self.add_icat_meta)
         self.add_meta_button.setToolTip("Add new metadata item.")
-        self.update_meta_button.clicked.connect(self.set_icat_meta)
-        self.update_meta_button.setToolTip("Set all entries with the same key to the new values.")
+        self.update_meta_button.clicked.connect(self.update_icat_meta)
+        self.update_meta_button.setToolTip("Update the metadata item.")
         self.delete_meta_button.clicked.connect(self.delete_icat_meta)
         self.delete_meta_button.setToolTip("Delete the metadata item.")
         # Manilpulate ACLs
         self.acl_table.clicked.connect(self.edit_permission)
         self.add_acl_button.clicked.connect(self.update_permission)
 
-    def update_input_path(self, irods_path):
+    def update_input_path(self, irods_path: Union[str, IrodsPath]):
         """Set the input path to a new path and loads the table."""
         self.input_path.setText(str(irods_path))
         # reset the params to load info tabs
@@ -253,10 +253,10 @@ def fill_info_tab_content(self):
                 self.logger.exception("Error loading %s of %s .", tab_name, irods_path)
                 self.error_label.setText(f"Error loading {tab_name} of {irods_path}: {repr(err)}")
 
-    def set_icat_meta(self):
+    def update_icat_meta(self):
         """Button metadata set."""
         try:
-            self._metadata_edits("set")
+            self._metadata_edits("update")
         except Exception as error:
             self.error_label.setText(repr(error))
 
@@ -275,7 +275,7 @@ def delete_icat_meta(self):
             self.error_label.setText(repr(error))
 
     # @PyQt6.QtCore.pyqtSlot(PyQt6.QtCore.QModelIndex)
-    def edit_metadata(self, index):
+    def edit_metadata(self, index: PyQt6.QtCore.QModelIndex):
         """Load selected metadata info edit fields."""
         self.error_label.clear()
         self.meta_key_field.clear()
@@ -293,7 +293,7 @@ def edit_metadata(self, index):
         self.meta_units_field.setText(units)
 
     # @PyQt6.QtCore.pyqtSlot(PyQt6.QtCore.QModelIndex)
-    def edit_permission(self, index):
+    def edit_permission(self, index: PyQt6.QtCore.QModelIndex):
         """Load selected acl into editing fields."""
         self.error_label.clear()
         self.acl_user_field.clear()
@@ -317,10 +317,10 @@ def update_permission(self):
         acc_name = self.acl_box.currentText()
 
         perm_lables_to_acl = {
-                "Newly added items to collection will inherit permissions": "inherit",
-                "Remove inhertiance.": "noinherit",
-                "delete": "null"
-                }
+            "Newly added items to collection will inherit permissions": "inherit",
+            "Remove inhertiance.": "noinherit",
+            "delete": "null",
+        }
 
         if perm_lables_to_acl.get(acc_name, acc_name) in ("inherit", "noinherit"):
             if irods_path.dataobject_exists():
@@ -335,19 +335,29 @@ def update_permission(self):
         recursive = self.recursive_box.currentText() == "True"
         try:
             perm = Permissions(self.session, get_irods_item(irods_path))
-            perm.set(perm=perm_lables_to_acl.get(acc_name, acc_name),
-                     user=user_name, zone=user_zone, recursive=recursive)
+            perm.set(
+                perm=perm_lables_to_acl.get(acc_name, acc_name),
+                user=user_name,
+                zone=user_zone,
+                recursive=recursive,
+            )
             if perm_lables_to_acl.get(acc_name, acc_name) == "null":
                 self.logger.info(
                     "Delete access (%s, %s, %s, %s) for %s",
                     perm_lables_to_acl.get(acc_name, acc_name),
-                    user_name, user_zone, str(recursive), str(irods_path)
+                    user_name,
+                    user_zone,
+                    str(recursive),
+                    str(irods_path),
                 )
             else:
                 self.logger.info(
                     "Add/change access of %s to (%s, %s, %s, %s)",
-                    str(irods_path), perm_lables_to_acl.get(acc_name, acc_name),
-                    user_name, user_zone, str(recursive)
+                    str(irods_path),
+                    perm_lables_to_acl.get(acc_name, acc_name),
+                    user_name,
+                    user_zone,
+                    str(recursive),
                 )
             self._fill_acls_tab(irods_path)
         except (irods.exception.CAT_INVALID_USER, irods.exception.SYS_NOT_ALLOWED):
@@ -367,7 +377,7 @@ def _clear_info_tabs(self):
         self.preview_browser.clear()
         self.no_meta_label.clear()
 
-    def _get_item_path(self, row):
+    def _get_item_path(self, row: int):
         item_name = self.browser_table.item(row, 1).text()
         return IrodsPath(self.session, "/", *self.input_path.text().split("/"), item_name)
 
@@ -386,7 +396,7 @@ def _update_last_selected_row(self):
         # fill currently selected tab with info
         self.fill_info_tab_content()
 
-    def _fill_replicas_tab(self, irods_path):
+    def _fill_replicas_tab(self, irods_path: Union[IrodsPath, str]):
         """Populate the table in the Replicas tab.
 
         Parameters
@@ -402,7 +412,7 @@ def _fill_replicas_tab(self, irods_path):
             self.replica_table.setRowCount(len(obj.replicas))
         self.replica_table.resizeColumnsToContents()
 
-    def _fill_acls_tab(self, irods_path):
+    def _fill_acls_tab(self, irods_path: Union[IrodsPath, str]):
         """Populate the table in the ACLs tab.
 
         Parameters
@@ -420,7 +430,9 @@ def _fill_acls_tab(self, irods_path):
         obj = None
         obj_acl_box_items = ["read", "write", "own", "delete"]
         coll_acl_box_items = obj_acl_box_items + [
-                "Newly added items to collection will inherit permissions", "Remove inheritance."]
+            "Newly added items to collection will inherit permissions",
+            "Remove inheritance.",
+        ]
 
         if irods_path.collection_exists():
             obj = irods_path.collection
@@ -439,7 +451,7 @@ def _fill_acls_tab(self, irods_path):
         self.acl_table.resizeColumnsToContents()
         self.owner_label.setText(f"{obj.owner_name}")
 
-    def _fill_metadata_tab(self, irods_path):
+    def _fill_metadata_tab(self, irods_path: Union[IrodsPath, str]):
         """Populate the table in the metadata tab.
 
         Parameters
@@ -452,19 +464,13 @@ def _fill_metadata_tab(self, irods_path):
         self.meta_value_field.clear()
         self.meta_units_field.clear()
         self.no_meta_label.clear()
-        item = None
-        if irods_path.collection_exists():
-            item = irods_path.collection
-        elif irods_path.dataobject_exists():
-            item = irods_path.dataobject
-        if item is not None:
-            meta = MetaData(item)
-            populate_table(self.meta_table, len(list(meta)), meta)
-        if len(list(meta)) == 0:
+        if irods_path.exists():
+            populate_table(self.meta_table, len(list(irods_path.meta)), irods_path.meta)
+        if len(irods_path.meta) == 0:
             self.no_meta_label.setText(f"Metadata for {str(irods_path)} is empty.")
         self.meta_table.resizeColumnsToContents()
 
-    def _fill_preview_tab(self, irods_path):
+    def _fill_preview_tab(self, irods_path: Union[IrodsPath, str]):
         """Populate the table in the metadata tab.
 
         Parameters
@@ -501,7 +507,7 @@ def _fill_preview_tab(self, irods_path):
         populate_textfield(self.preview_browser, content)
         self.preview_browser.verticalScrollBar().setValue(0)
 
-    def _metadata_edits(self, operation):
+    def _metadata_edits(self, operation: str):
         self.error_label.clear()
         if self._nothing_selected_error():
             return
@@ -510,23 +516,27 @@ def _metadata_edits(self, operation):
         new_key = self.meta_key_field.text()
         new_val = self.meta_value_field.text()
         new_units = self.meta_units_field.text()
-        if new_key != "" and new_val != "":
-            irods_path = self._get_item_path(self.browser_table.currentRow())
-            if operation == "add":
-                irods_path.meta.add(new_key, new_val, new_units)
-                self.logger.info(
-                    "Add metadata (%s, %s, %s) to %s", new_key, new_val, new_units, irods_path
-                )
-            elif operation == "set":
-                irods_path.meta.set(new_key, new_val, new_units)
-                self.logger.info(
-                    "Set all metadata with key %s to (%s, %s, %s) for %s",
-                    new_key, new_key, new_val, new_units, irods_path
+        irods_path = self._get_item_path(self.browser_table.currentRow())
+        if operation == "add":
+            irods_path.meta.add(new_key, new_val, new_units)
+            self.logger.info(
+                "Add metadata (%s, %s, %s) to %s", new_key, new_val, new_units, irods_path
+            )
+        elif operation == "update":
+            row = self.meta_table.currentRow()
+            old_key = self.meta_table.item(row, 0).text()
+            old_val = self.meta_table.item(row, 1).text()
+            old_units = self.meta_table.item(row, 2).text()
+            print(old_key, old_val, old_units)
+            self.logger.info(
+                "Update metadata of %s from (%s, %s, %s) to (%s, %s, %s)",
+                irods_path, old_key, old_val, old_units,
+                new_key, new_val, new_units,
                 )
-            elif operation == "delete":
-                irods_path.meta.delete(new_key, new_val, new_units)
-                self.logger.info(
-                    "Delete metadata (%s, %s, %s) from %s",
-                    new_key, new_val, new_units, irods_path
+            irods_path.meta[old_key, old_val, old_units] = [new_key, new_val, new_units]
+        elif operation == "delete":
+            irods_path.meta.delete(new_key, new_val, new_units)
+            self.logger.info(
+                "Delete metadata (%s, %s, %s) from %s", new_key, new_val, new_units, irods_path
                 )
-            self._fill_metadata_tab(irods_path)
+        self._fill_metadata_tab(irods_path)

ibridgesgui/config.py

@@ -35,13 +35,13 @@
 
 def ensure_log_config_location():
     """Ensure the location for logs and config files."""
-    CONFIG_DIR.mkdir(parents=True, exist_ok=True)
+    CONFIG_DIR.mkdir(parents=True, mode=0o700, exist_ok=True)
 
 
 def ensure_irods_location():
     """Ensure that .irods exists in user's home."""
     irods_loc = Path("~/.irods").expanduser()
-    irods_loc.mkdir(exist_ok=True)
+    irods_loc.mkdir(mode=0o700, exist_ok=True)
 
 # logging functions
 def init_logger(app_name: str, log_level: str) -> logging.Logger:
@@ -281,4 +281,4 @@ def _read_json(file_path: Path) -> dict:
 
 def _write_json(file_path: Path, content: dict):
     with open(file_path, "w", encoding="utf-8") as handle:
-        json.dump(content, handle)
+        json.dump(content, handle, indent=4)

ibridgesgui/login.py

@@ -1,6 +1,7 @@
 """Pop up Widget for Login."""
 
 import logging
+import os
 import sys
 from pathlib import Path
 
@@ -23,6 +24,10 @@
 from ibridgesgui.ui_files.irodsLogin import Ui_irodsLogin
 
 
+def strictwrite(path, flags, mode=0o600):
+    """Create opener for the standard open command to modify the umask."""
+    return os.open(path, flags, mode)
+
 class Login(QDialog, Ui_irodsLogin):
     """Definition and initialization of the iRODS login window."""
 
@@ -51,10 +56,10 @@ def _load_gui(self):
         self.envbox.currentTextChanged.connect(self._init_password)
 
     def _init_envbox(self):
-        env_jsons = [path.name for path in self.irods_config_dir.glob("irods_environment*json")]
+        env_jsons = [path.name for path in self.irods_config_dir.glob("*.json")]
         if len(env_jsons) == 0:
             self.error_label.setText(
-                f"ERROR: no irods_environment*json files found in {self.irods_config_dir}"
+                f"ERROR: no .json files found in {self.irods_config_dir}"
             )
 
         self.envbox.clear()
@@ -105,7 +110,7 @@ def login_function(self):
         try:
             if self.cached_pw is True and self.password_field.text() == "***********":
                 self.logger.debug("Login with %s and cached password.", env_file)
-                with open(IRODSA, "w",  encoding="utf-8") as f:
+                with open(IRODSA, "w",  encoding="utf-8", opener=strictwrite) as f:
                     f.write(self.prev_settings[str(env_file)])
 
                 session = Session(irods_env=env_file)