Merge pull request #197 from chStaiger/develop

Merge to main

README.md

@@ -16,6 +16,7 @@
 The git repository contains a generic *iRODS* graphical user interface.  The iRODS functionality is based on [ibridges](https://github.com/UtrechtUniversity/iBridges) and works with any *iRODS* instance.  
 
 
+![](docs/screenshots/metadata.png)
 
 ## Highlights
 

ibridgesgui/browser.py

@@ -9,10 +9,10 @@
 import PyQt6.QtGui
 import PyQt6.QtWidgets
 import PyQt6.uic
-from ibridges import IrodsPath, download, get_collection, get_dataobject, upload
-from ibridges.data_operations import obj_replicas
+from ibridges import IrodsPath, download, upload
 from ibridges.meta import MetaData
 from ibridges.permissions import Permissions
+from ibridges.util import obj_replicas
 
 from ibridgesgui.gui_utils import (
     UI_FILE_DIR,
@@ -22,7 +22,7 @@
     populate_table,
     populate_textfield,
 )
-from ibridgesgui.popup_widgets import CreateCollection
+from ibridgesgui.popup_widgets import CreateCollection, Rename
 from ibridgesgui.ui_files.tabBrowser import Ui_tabBrowser
 
 
@@ -42,20 +42,20 @@ def __init__(self, session, app_name):
         self.info_tabs.setCurrentIndex(0)
         # iRODS default home
         if self.session.home is not None:
-            root_path = self.session.home
+            root_path = IrodsPath(self.session).absolute()
+        else:
+            root_path = IrodsPath(
+                self.session, f"/{self.session.zone}/home/{self.session.username}"
+            )
+
+        if root_path.collection_exists():
+            self.root_coll = IrodsPath(self.session, root_path).collection
+        elif IrodsPath(self.session, f"/{self.session.zone}/home").collection_exists():
+            self.root_coll = IrodsPath(self.session, f"/{self.session.zone}/home").collection
         else:
-            root_path = f"/{self.session.zone}/home/{self.session.username}"
-        try:
-            self.root_coll = get_collection(self.session, root_path)
-        except irods.exception.CollectionDoesNotExist:
-            self.root_coll = get_collection(self.session, f"/{self.session.zone}/home")
-        except irods.exception.NetworkException:
-            self.error_label.setText("iRODS NETWORK ERROR: No Connection, please check network")
-        except Exception as err:
             self.error_label.setText(
                 'Cannot set root collection. Set "irods_home" in your environment.json'
             )
-            self.logger.exception("Failed to set iRODS home: %s", err)
         self.reset_path()
         self.browse()
 
@@ -75,6 +75,7 @@ def browse(self):
         self.upload_dir_button.clicked.connect(self.folder_upload)
         self.download_button.clicked.connect(self.download)
         self.create_coll_button.clicked.connect(self.create_collection)
+        self.rename_button.clicked.connect(self.rename_item)
 
         # Browser table behaviour
         self.browser_table.doubleClicked.connect(self.update_path)
@@ -104,7 +105,6 @@ def set_parent(self):
         self.path_input.setText(str(current_path.parent))
         self.load_browser_table()
 
-    # @PyQt6.QtCore.pyqtSlot(PyQt6.QtCore.QModelIndex)
     def update_path(self, index):
         """Take path from path_input and loads browser table."""
         self.error_label.clear()
@@ -122,6 +122,20 @@ def create_collection(self):
         coll_widget.exec()
         self.load_browser_table()
 
+    def rename_item(self):
+        """Rename/move a collection or data object."""
+        self.error_label.clear()
+        if self.browser_table.currentRow() == -1:
+            self.error_label.setText("Please select a row from the table first!")
+            return
+        item_name = self.browser_table.item(self.browser_table.currentRow(), 1).text()
+        irods_path = IrodsPath(self.session, "/" + self.path_input.text().strip("/")).joinpath(
+            item_name
+        )
+        rename_widget = Rename(irods_path, self.logger)
+        rename_widget.exec()
+        self.load_browser_table()
+
     def folder_upload(self):
         """Select a folder and upload."""
         self.error_label.clear()
@@ -187,7 +201,7 @@ def load_browser_table(self):
         obj_path = IrodsPath(self.session, self.path_input.text())
         if obj_path.collection_exists():
             try:
-                coll = get_collection(self.session, obj_path)
+                coll = obj_path.collection
 
                 coll_data = [
                     (
@@ -422,7 +436,7 @@ def _fill_replicas_tab(self, irods_path):
         """
         self.replica_table.setRowCount(0)
         if irods_path.dataobject_exists():
-            obj = get_dataobject(self.session, irods_path)
+            obj = irods_path.dataobject
             populate_table(self.replica_table, len(obj_replicas(obj)), obj_replicas(obj))
             self.replica_table.setRowCount(len(obj.replicas))
         self.replica_table.resizeColumnsToContents()
@@ -442,10 +456,10 @@ def _fill_acls_tab(self, irods_path):
         self.acl_box.setCurrentText("")
         obj = None
         if irods_path.collection_exists():
-            obj = get_collection(self.session, irods_path)
+            obj = irods_path.collection
             inheritance = f"{obj.inheritance}"
         elif irods_path.dataobject_exists():
-            obj = get_dataobject(self.session, irods_path)
+            obj = irods_path.dataobject
             inheritance = ""
         if obj is not None:
             acls = Permissions(self.session, obj)
@@ -468,9 +482,9 @@ def _fill_metadata_tab(self, irods_path):
         self.meta_units_field.clear()
         item = None
         if irods_path.collection_exists():
-            item = get_collection(self.session, irods_path)
+            item = irods_path.collection
         elif irods_path.dataobject_exists():
-            item = get_dataobject(self.session, irods_path)
+            item = irods_path.dataobject
         if item is not None:
             meta = MetaData(item)
             populate_table(self.meta_table, len(list(meta)), meta)
@@ -486,14 +500,14 @@ def _fill_preview_tab(self, irods_path):
 
         """
         if irods_path.collection_exists():
-            obj = get_collection(self.session, irods_path)
+            obj = irods_path.collection
             content = ["Collections:", "-----------------"]
             content.extend([sc.name for sc in obj.subcollections])
             content.extend(["\n", "DataObjects:", "-----------------"])
             content.extend([do.name for do in obj.data_objects])
         elif irods_path.dataobject_exists():
             file_type = ""
-            obj = get_dataobject(self.session, irods_path)
+            obj = irods_path.dataobject
             if "." in irods_path.parts[-1]:
                 file_type = irods_path.parts[-1].split(".")[1]
             if file_type in ["txt", "json", "csv"]:

ibridgesgui/config.py

@@ -10,7 +10,13 @@
 from typing import Union
 
 from ibridges.session import Session
-from irods.exception import CAT_INVALID_USER, PAM_AUTH_PASSWORD_FAILED, NetworkException
+from irods.connection import PlainTextPAMPasswordError
+from irods.exception import (
+    CAT_INVALID_AUTHENTICATION,
+    CAT_INVALID_USER,
+    PAM_AUTH_PASSWORD_FAILED,
+    NetworkException,
+)
 from irods.session import iRODSSession
 
 LOG_LEVEL = {
@@ -133,7 +139,6 @@ def is_session_from_config(session: Session) -> Union[Session, None]:
     ienv_path = Path("~").expanduser().joinpath(".irods", get_last_ienv_path())
     try:
         env = _read_json(ienv_path)
-        print(env)
     except Exception:
         return False
 
@@ -170,7 +175,8 @@ def check_irods_config(ienv: Union[Path, dict]) -> str:
         except FileNotFoundError:
             return f"{ienv} not found."
         except JSONDecodeError as err:
-            return f"{ienv} not well formatted.\n{err.msg}"
+            print(repr(err))
+            return f"{ienv} not well formatted.\n {err.msg} at position {err.pos}."
     else:
         env = ienv
     # check host and port and connectivity
@@ -199,10 +205,22 @@ def check_irods_config(ienv: Union[Path, dict]) -> str:
     except AttributeError as err:
         return repr(err)
 
+    except PlainTextPAMPasswordError:
+        return (
+            'Value of "irods_client_server_negotiation" needs to be'
+            + ' "request_server_negotiation".'
+        )
+
+    except CAT_INVALID_AUTHENTICATION:
+        return 'Wrong "irods_authentication_scheme".'
+    except ValueError as err:
+        if "scheme" in err.args[0]:
+            return 'Value of "irods_authentication_scheme" not recognised.'
+        return f"{err.args}"
+
     # password incorrect but rest is fine
-    except (ValueError, CAT_INVALID_USER, PAM_AUTH_PASSWORD_FAILED):
+    except (CAT_INVALID_USER, PAM_AUTH_PASSWORD_FAILED):
         return "All checks passed successfully."
-
     # all tests passed
     return "All checks passed successfully."
 

ibridgesgui/gui_utils.py

@@ -1,13 +1,19 @@
 """Handy and reusable functions for the GUI."""
 
 import pathlib
-from importlib.resources import files
 from typing import Union
 
 import irods
 import PyQt6
-from ibridges import get_collection, get_dataobject
-from ibridges.path import IrodsPath
+from ibridges import IrodsPath, download
+
+from ibridgesgui.config import get_last_ienv_path, is_session_from_config
+
+try:
+    from importlib.resources import files
+except ImportError:
+    from importlib_resources import files
+
 
 UI_FILE_DIR = files(__package__) / "ui_files"
 
@@ -35,10 +41,10 @@ def populate_textfield(text_widget, text_by_row: Union[str, list]):
 # iBridges/iRODS utils
 def get_irods_item(irods_path: IrodsPath):
     """Get the item behind an iRODS path."""
-    try:
-        item = get_collection(irods_path.session, irods_path)
-    except ValueError:
-        item = get_dataobject(irods_path.session, irods_path)
+    if irods_path.collection_exists():
+        item = irods_path.collection
+    else:
+        item = irods_path.dataobject
     return item
 
 
@@ -62,6 +68,37 @@ def get_coll_dict(root_coll: irods.collection.iRODSCollection) -> dict:
     }
 
 
+def prep_session_for_copy(session, error_label) -> pathlib.Path:
+    """Either return a save path to create a new session from or sets message in error label."""
+    if is_session_from_config(session):
+        return pathlib.Path.home().joinpath(".irods", get_last_ienv_path())
+
+    text = "The ibridges config changed during the session."
+    text += "Please reset or restart the session."
+    error_label.setText(text)
+    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
+
+
 # OS utils
 def get_downloads_dir() -> pathlib.Path:
     """Find the platform-dependent 'Downloads' directory.
@@ -73,9 +110,9 @@ def get_downloads_dir() -> pathlib.Path:
 
     """
     # Linux and Mac Download folders
-    if pathlib.Path("~", "Downloads").expanduser().is_dir():
-        return pathlib.Path("~", "Downloads").expanduser()
+    if pathlib.Path.home().joinpath("Downloads").is_dir():
+        return pathlib.Path.home().joinpath("Downloads")
 
     # Try to create Downloads
-    pathlib.Path("~", "Downloads").expanduser().mkdir(parents=True)
-    return pathlib.Path("~", "Downloads").expanduser()
+    pathlib.Path.home().joinpath("Downloads").mkdir(parents=True)
+    return pathlib.Path.home().joinpath("Downloads")

ibridgesgui/irods_tree_model.py

@@ -11,7 +11,7 @@
 import PyQt6.QtCore
 import PyQt6.QtGui
 import PyQt6.QtWidgets
-from ibridges import IrodsPath, get_collection
+from ibridges import IrodsPath
 
 
 class IrodsTreeModel(PyQt6.QtGui.QStandardItemModel):
@@ -70,15 +70,14 @@ def init_tree(self):
         root = self.invisibleRootItem()
 
         # Start the tree, add the highest level to the invisible root
-        root_coll = get_collection(self.session, self.irods_root_path)
+        root_coll = IrodsPath(self.session, self.irods_root_path).collection
         root_row = self._tree_row_from_irods_item(root_coll, -1, -1, True)
         root.appendRow(root_row)
 
         new_node = root.child(root.rowCount() - 1)
 
         # insert a dummy child to get the link to open the collection
-        if len(root_coll.subcollections + root_coll.data_objects) > 0:
-            new_node.appendRow(None)
+        new_node.appendRow(None)
 
     def delete_subtree(self, tree_item):
         """Delete subtree.
@@ -104,8 +103,7 @@ def add_subtree(self, tree_item, tree_item_data: list):
 
         """
         _, level, _, _, _, abs_irods_path = tree_item_data
-        # _tree_row_from_irods_item(self, item, parent_id, level, display_path = False)
-        parent_coll = get_collection(self.session, abs_irods_path)
+        parent_coll = IrodsPath(self.session, abs_irods_path).collection
 
         # we assume that tree_item has no children yet.
         new_nodes = {}
@@ -114,9 +112,8 @@ def add_subtree(self, tree_item, tree_item_data: list):
             tree_item.appendRow(row)
             new_nodes[item.id] = tree_item.child(tree_item.rowCount() - 1)
             if isinstance(item, irods.collection.iRODSCollection):
-                if len(item.subcollections + item.data_objects) > 0:
-                    # insert a dummy child to get the link to open the collection
-                    new_nodes[item.id].appendRow(None)
+                # insert a dummy child to get the link to open the collection
+                new_nodes[item.id].appendRow(None)
 
     def refresh_subtree(self, position):
         """Refresh the tree view.