205 freeze (#209)

* Adding more logging information

* Fix while loop

* Update docs to new pypi package

* Ruff

* Ruff format

* add output to irods_tree_model

* more infowq

* bug info

* Fix double listing of the iRODS root

* fix README

* filter out root from subcollections efficiently

* Do not try to delete key "" if not present

* Remove print statements

---------

Co-authored-by: Staiger, Christine <christine.staiger@wur.nl>

README.md

@@ -30,11 +30,18 @@ The git repository contains a generic *iRODS* graphical user interface.  The iRO
 - Safe default options when working with your data.
 
 ## Installation
-- As python package
+- The python package 
 
   ```bash
   pip install ibridgesgui
   ```
+
+- A specific branch of the git repository (testers, developers)
+
+  ```bash
+  pip install git+https://github.com/chStaiger/iBridges-Gui.git@branch-name
+  ```
+
 - Locally from code (for developers)
 
   ```bash

docs/getting-started.qmd

@@ -4,8 +4,7 @@
 ## Install iBridges-gui
 
 ```
-pip install ibridges==0.1.6
-pip install pip install git+https://github.com/chStaiger/iBridges-Gui.git@main
+pip install ibridgesgui
 ```
 
 ## Start the program

ibridgesgui/__main__.py

@@ -82,13 +82,16 @@ def connect(self):
         login_window = Login(self.session_dict, self.app_name)
         login_window.exec()
         # Trick to get the session object from the QDialog
+
         if "session" in self.session_dict:
             self.session = self.session_dict["session"]
             try:
                 self.setup_tabs()
             except:
                 self.session = None
                 raise
+        else:
+            self.logger.exception("No session created. %s", self.session_dict)
 
     def exit(self):
         """Quit program."""

ibridgesgui/gui_utils.py

@@ -18,6 +18,7 @@
 UI_FILE_DIR = files(__package__) / "ui_files"
 LOGO_DIR = files(__package__) / "icons"
 
+
 # Widget utils
 def populate_table(table_widget, rows: int, data_by_row: list):
     """Populate a table-like pyqt widget with data."""

ibridgesgui/irods_tree_model.py

@@ -105,9 +105,12 @@ def add_subtree(self, tree_item, tree_item_data: list):
         _, level, _, _, _, abs_irods_path = tree_item_data
         parent_coll = IrodsPath(self.session, abs_irods_path).collection
 
+        # the irods root also contains the irods root as subcollection
+        subcolls = [c for c in parent_coll.subcollections if c.path != "/"]
+        dataobjs = parent_coll.data_objects
         # we assume that tree_item has no children yet.
         new_nodes = {}
-        for item in parent_coll.subcollections + parent_coll.data_objects:
+        for item in subcolls + dataobjs:
             row = self._tree_row_from_irods_item(item, parent_coll.id, int(level))
             tree_item.appendRow(row)
             new_nodes[item.id] = tree_item.child(tree_item.rowCount() - 1)

ibridgesgui/login.py

@@ -89,12 +89,15 @@ def login_function(self):
             self.close()
         except LoginError:
             self.error_label.setText("irods_environment.json not setup correctly.")
+            self.logger.error("irods_environment.json not setup correctly.")
         except PasswordError:
             self.error_label.setText("Wrong password!")
+            self.logger.error("Wrong password provided.")
         except ConnectionError:
             self.error_label.setText(
                 "Cannot connect to server. Check Internet, host name and port."
             )
+            self.logger.exception("Network error.")
         except Exception as err:
             log_path = Path("~/.ibridges")
             self.logger.exception("Failed to login: %s", repr(err))

ibridgesgui/search.py

@@ -184,7 +184,8 @@ def _validate_search_params(self) -> tuple[str, dict, str, str]:
                 key.text(): "%" if val.text() == "" else val.text()
                 for key, val in zip(self.keys, self.vals)
             }
-            del key_vals[""]
+            if "" in key_vals:
+                del key_vals[""]
 
         path = self.path_field.text() if self.path_field.text() != "" else None
         checksum = self.checksum_field.text() if self.checksum_field.text() != "" else None

ibridgesgui/sync.py

@@ -89,7 +89,7 @@ def _init_irods_tree(self):
     def irods_root(self):
         """Retrieve lowest visible level in the iRODS tree for the user."""
         lowest = IrodsPath(self.session).absolute()
-        while lowest.parent.exists():
+        while lowest.parent.exists() and str(lowest) != "/":
             lowest = lowest.parent
         return lowest
 
@@ -276,10 +276,12 @@ def _sync_diff_end(self, thread_output: dict):
             return
 
         self.error_label.clear()
-        table_data = [(ipath, lpath, ipath.size)
-                      for ipath, lpath in thread_output["result"]["download"]] + \
-                     [(lpath, ipath, lpath.stat().st_size)
-                      for lpath, ipath in thread_output["result"]["upload"]]
+        table_data = [
+            (ipath, lpath, ipath.size) for ipath, lpath in thread_output["result"]["download"]
+        ] + [
+            (lpath, ipath, lpath.stat().st_size)
+            for lpath, ipath in thread_output["result"]["upload"]
+        ]
         populate_table(self.diff_table, len(table_data), table_data)
         if len(table_data) == 0:
             self.error_label.setText("Data is already synchronised.")

ibridgesgui/welcome.py

@@ -1,4 +1,5 @@
 """Welcome tab."""
+
 import sys
 
 import PyQt6.QtCore
@@ -37,6 +38,6 @@ def __init__(self):
         self.grid.addWidget(self.tag, 2, 1)
         self.setLayout(self.grid)
 
-        self.setGeometry(150,150,300,300)
+        self.setGeometry(150, 150, 300, 300)
 
         self.show()