Merge pull request #247 from chStaiger/develop

v1.0.4

.github/workflows/pypi_release.yml

@@ -33,7 +33,7 @@ jobs:
     - name: Build package
       run: python -m build
     - name: Publish package
-      uses: pypa/gh-action-pypi-publish@7eb3b701d11256e583f5b49899c5e7203deab573
+      uses: pypa/gh-action-pypi-publish@v1.9.0
       with:
         user: __token__
         password: ${{ secrets.PYPI_API_TOKEN }}

docs/userdoc.qmd

@@ -30,9 +30,11 @@ You can **navigate to another part of the iRODS collection tree** by editing thi
 
 - The `Create Collection` button will create a collection in the path shown in the navigation field above.
 
-- The buttons `Upload File` and `Upload Folder` open a file dialog to select data to upload. The destination will be the path shown in the navigation field.
+- The `Upload` button opens a new popup window to select data to upload. The destination will be the path shown in the navigation field.
 
-- The `Download` button will download data to your `Downloads` folder. To download data you will need to select an item in the table below.
+- The `Download` button opens a popup window to select the destination on your computer. You will also be able to export the metadata and store it in a separate file along your download. To download data you will need to select an item in the table below.
+
+- With the `Delete` button you can delete the selected collection or data object in the table. **Note, The data will be deleted completely from the iRODS instance.**
 
 ### Listing
 

ibridgesgui/__main__.py

@@ -119,6 +119,7 @@ def setup_tabs(self):
         for tab_fun in self.ui_tabs_lookup.values():
             tab_fun()
             # self.ui_tabs_lookup[tab_name]()
+        self.tab_widget.setCurrentIndex(1)
 
     def welcome_tab(self):
         """Create first tab."""

ibridgesgui/config.py

@@ -31,7 +31,7 @@
 
 CONFIG_DIR = Path("~", ".ibridges").expanduser()
 CONFIG_FILE = CONFIG_DIR.joinpath("ibridges_gui.json")
-
+IRODSA = Path.home() / ".irods" / ".irodsA"
 
 def ensure_log_config_location():
     """Ensure the location for logs and config files."""
@@ -131,6 +131,23 @@ def _get_config() -> Union[None, dict]:
         print(f"CANNOT START APP: {CONFIG_FILE} incorrectly formatted.")
         sys.exit(1)
 
+def save_current_settings(env_path_name: Path):
+    """Store the environment with the currently scrambled password in irodsA."""
+    with open(IRODSA, "r", encoding="utf-8") as f:
+        pw = f.read()
+    config = _get_config()
+    if config is not None:
+        if "settings" not in config:
+            config["settings"] = {}
+        config["settings"][str(env_path_name)] = pw
+        _save_config(config)
+
+def get_prev_settings():
+    """Extract the settings from the configuration."""
+    config = _get_config()
+    if config is None:
+        return {}
+    return config.get("settings", {})
 
 # irods config functions
 

ibridgesgui/gui_utils.py

@@ -5,7 +5,8 @@
 
 import irods
 import PyQt6
-from ibridges import IrodsPath, download
+from ibridges import IrodsPath
+from ibridges.executor import Operations
 
 from ibridgesgui.config import get_last_ienv_path, is_session_from_config
 
@@ -82,25 +83,16 @@ def prep_session_for_copy(session, error_label) -> pathlib.Path:
     return None
 
 
-def combine_diffs(session, sources: list, destination: Union[IrodsPath, pathlib.Path]) -> dict:
-    """Combine the diffs of several upload or download dry-runs."""
-    combined_diffs = {
-        "create_dir": set(),
-        "create_collection": set(),
-        "upload": [],
-        "download": [],
-        "resc_name": "",
-        "options": None,
-    }
-    if isinstance(destination, pathlib.Path):
-        for ipath in sources:
-            diff = download(session, ipath, destination, dry_run=True, overwrite=True)
-            combined_diffs["download"].extend(diff["download"])
-            combined_diffs["create_dir"] = combined_diffs["create_dir"].union(diff["create_dir"])
-    elif isinstance(destination, IrodsPath):
-        print("not implemented yet")
-    return combined_diffs
+def combine_operations(operations: list[Operations]) -> Operations:
+    """Combine the operations of several upload or download dry-runs."""
+    ops = operations[0]
+    ops.create_dir = set().union(*[o.create_dir for o in operations])
+    ops.create_collection = set().union(*[o.create_collection for o in operations])
+    for op in operations[1:]:
+        ops.download.extend(op.download)
+        ops.upload.extend(op.upload)
 
+    return ops
 
 # OS utils
 def get_downloads_dir() -> pathlib.Path:

ibridgesgui/login.py

@@ -11,7 +11,13 @@
 from PyQt6.QtWidgets import QDialog, QLineEdit
 from PyQt6.uic import loadUi
 
-from ibridgesgui.config import get_last_ienv_path, set_last_ienv_path
+from ibridgesgui.config import (
+    IRODSA,
+    get_last_ienv_path,
+    get_prev_settings,
+    save_current_settings,
+    set_last_ienv_path,
+)
 from ibridgesgui.gui_utils import UI_FILE_DIR
 from ibridgesgui.ui_files.irodsLogin import Ui_irodsLogin
 
@@ -32,6 +38,7 @@ def __init__(self, session_dict, app_name):
 
         self.session_dict = session_dict
         self._init_envbox()
+        self.prev_settings = get_prev_settings()
         self.cached_pw = self._init_password()
         self._load_gui()
         self.setWindowTitle("Connect to iRODS server")
@@ -40,6 +47,7 @@ def _load_gui(self):
         self.connect_button.clicked.connect(self.login_function)
         self.cancel_button.clicked.connect(self.close)
         self.password_field.setEchoMode(QLineEdit.EchoMode.Password)
+        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")]
@@ -57,11 +65,12 @@ def _init_envbox(self):
             self.envbox.setCurrentIndex(0)
 
     def _init_password(self):
-        # Check if there is a cached password
-        passwd_file = self.irods_config_dir.joinpath(".irodsA")
-        if passwd_file.is_file():
+        # Check if there is a cached password in the ibridges_gui config file
+        env_file = self.irods_config_dir.joinpath(self.envbox.currentText())
+        if str(env_file) in self.prev_settings:
             self.password_field.setText("***********")
             return True
+        self.password_field.clear()
         return False
 
     def close(self):
@@ -86,6 +95,9 @@ 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:
+                    f.write(self.prev_settings[str(env_file)])
+
                 session = Session(irods_env=env_file)
             else:
                 session = Session(irods_env=env_file, password=self.password_field.text())
@@ -97,6 +109,7 @@ def login_function(self):
                 session.home,
             )
             session.write_pam_password()
+            save_current_settings(env_file)
             if self._check_home(session) and self._check_resource(session):
                 self.session_dict["session"] = session
                 set_last_ienv_path(env_file.name)