Merge pull request #217 from chStaiger/develop

Improving the templates, adding docs (#216)

docs/getting-started.qmd

@@ -13,25 +13,39 @@ Please start **iBridges-Gui** by typing `ibridges-gui` on your terminal and hit
 
 ## Configuring iBridges-Gui
 
+To connect to the server you need a configuration file, a so-called `irods_environment.json`. 
+You can create one for yourself using templates, editing default settings we provide for you or simply create such a file.
+
+### Installing iRODS server templates
+We have created a plugin system to automatically create the environment file for you. 
+Please follow the [documentation](https://ibridges.readthedocs.io/en/latest/cli.html) how to set it up.
+
+### Creating an iRODS configuration file
+
 When you start iBridges you will find in the upper drop-down menu `Connect` and `Configure`.
 
 ![](screenshots/start_ibridges.png){width=50% fig-align="center"}
 
-Before we start iBridges for the first time let us check and create a valid configuration file; Click on `Configure -> Add Configuration`.
+Let us check or create a valid configuration file; Click on `Configure -> Add Configuration`.
 
 ![](screenshots/add_check_config.png){width=75% fig-align="center"}
 
-If you already stored an `irods_environment.json` in the directory `~/.irods` (Windows `C:\Users\<username>\.irods`) then you can use the drop-down menu (little downward arrow) to load the configuration.
+#### Existing configuration files
+In the drop-down menu you will find previously created iRODS environments, they start with `irods_environment` and end with `.json`. Select the one you want to check.
 
-If you do not have an iRODS configuration yet, click on the button `New Config`.
+#### Creating a configuration from a template
+If you do not have an iRODS configuration yet, and you installed a plugin (see above) you can select a configuration template from the drop-down menu.
+You will have to add your username and save as `irods_environment.json`.
 
+#### Creating a new configuration
+To create a new environment click on the button `New Config`.
 You should see now something like:
 
 ![](screenshots/add_new_config.png){width=75% fig-align="center"}
 
 Click the `Check` button to find out whether you can make a connection to the iRODS server. If you get error messages, adjust the contents accordingly. If you are unsure, please contact your iRODS service provider.
 
-Once the check runs through fine click the `Save` or `Save as` button. This will store the adjusted configuration in the correct directory on you laptop so that we can use it for the login (See Section below).
+Once the check runs through fine click the `Save` or `Save as` button. This will store the adjusted configuration in the correct directory on your laptop so that we can use it for the login (See Section below).
 
 ## Start an iRODS session
 

ibridgesgui/__main__.py

@@ -48,7 +48,7 @@ def __init__(self, app_name):
             "tabSync": self.init_sync_tab,
             "tabSearch": self.init_search_tab,
             "tabInfo": self.init_info_tab,
-            "tabLog": self.init_log_tab
+            "tabLog": self.init_log_tab,
         }
 
         self.session = None
@@ -61,7 +61,6 @@ def __init__(self, app_name):
         self.action_check_configuration.triggered.connect(self.inspect_env_file)
         self.tab_widget.setCurrentIndex(0)
 
-
     def disconnect(self):
         """Close iRODS session."""
         self.error_label.clear()

ibridgesgui/config.py

@@ -10,6 +10,7 @@
 from typing import Union
 
 from ibridges.session import Session
+from irods.auth.pam import PamLoginException
 from irods.connection import PlainTextPAMPasswordError
 from irods.exception import (
     CAT_INVALID_AUTHENTICATION,
@@ -204,6 +205,12 @@ def check_irods_config(ienv: Union[Path, dict]) -> str:
         return repr(err)
     except AttributeError as err:
         return repr(err)
+    except PamLoginException as err:
+        # irods4.3+ specific
+        return f'Adjust "irods_authentication_scheme" {err.args}'
+    except ModuleNotFoundError as err:
+        # irods4.3+ uses string in authenticationscheme as class
+        return f'"irods_authentication_scheme": "{err.name}" does not exist'
 
     except PlainTextPAMPasswordError:
         return (

ibridgesgui/login.py

@@ -68,6 +68,17 @@ def close(self):
         """Abort login."""
         self.done(0)
 
+    def _check_home(self, session):
+        if not IrodsPath(session).collection_exists():
+            return False
+        return True
+
+    def _check_resource(self, session):
+        resc = Resources(session).get_resource(session.default_resc)
+        if resc.parent is not None:
+            return False
+        return True
+
     def login_function(self):
         """Connect to iRODS server with gathered info."""
         self.error_label.clear()
@@ -86,8 +97,17 @@ def login_function(self):
                 session.home,
             )
             session.write_pam_password()
-            self.session_dict["session"] = session
-            set_last_ienv_path(env_file.name)
+            if self._check_home(session) and self._check_resource(session):
+                self.session_dict["session"] = session
+                set_last_ienv_path(env_file.name)
+                self.close()
+            elif not self._check_home(session):
+                self.error_label.setText(f'"irods_home": "{session.home}" does not exist.')
+            elif not self._check_resource(session):
+                self.error_label.setText(
+                    f'"irods_default_resource": "{session.default_resc}" not writeable.'
+                )
+
         except LoginError:
             self.error_label.setText("irods_environment.json not setup correctly.")
             self.logger.error("irods_environment.json not setup correctly.")
@@ -99,35 +119,10 @@ def login_function(self):
                 "Cannot connect to server. Check Internet, host name and port."
             )
             self.logger.exception("Network error.")
+        except ResourceDoesNotExist:
+            self.error_label.setText('"irods_default_resource" does not exist.')
+            self.logger.exception("Default resource does not exist.")
         except Exception as err:
             log_path = Path("~/.ibridges")
             self.logger.exception("Failed to login: %s", repr(err))
             self.error_label.setText(f"Login failed, consult the log file(s) in {log_path}")
-
-        #check irods_home
-        fail_home = True
-        if not IrodsPath(self.session_dict["session"]).collection_exists():
-            self.error_label.setText(f'"irods_home": "{session.home}" does not exist.')
-            self.logger.error("irods_home does not exist.")
-        else:
-            fail_home = False
-
-        #check existance of default resource
-        fail_resc = True
-        try:
-            resc = Resources(self.session_dict["session"]).get_resource(session.default_resc)
-            if resc.parent is None:
-                fail_resc = False
-            else:
-                self.error_label.setText(f'"default_resource": "{session.default_resc}" not valid.')
-        except ResourceDoesNotExist:
-            self.error_label.setText(
-                f'"default_resource": "{session.default_resc}" does not exist.')
-            self.logger.error("Default resource does not exist.")
-        except AttributeError:
-            self.error_label.setText(f'"default_resource": "{session.default_resc}" not valid.')
-
-        if fail_resc or fail_home:
-            del self.session_dict["session"]
-        else:
-            self.close()

ibridgesgui/logviewer.py

@@ -25,7 +25,7 @@ def __init__(self, text_browser):
 
     def emit(self, record):
         """Emit when new logging accurs."""
-        msg = self.format(record)+"\n"
+        msg = self.format(record) + "\n"
         self.append_plain_text.emit(msg)
 
 
@@ -44,7 +44,7 @@ def __init__(self, logger):
         self.log_label.setText(str(CONFIG_DIR))
         self.log_text = QTextEditLogger(self.log_browser)
         self.log_text.setFormatter(
-        logging.Formatter(
-            '%(asctime)s %(levelname)s %(module)s %(funcName)s %(message)s'))
+            logging.Formatter("%(asctime)s %(levelname)s %(module)s %(funcName)s %(message)s")
+        )
         self.logger.addHandler(self.log_text)
         self.logger.setLevel(logging.DEBUG)

ibridgesgui/popup_widgets.py

@@ -140,11 +140,16 @@ def __init__(self, logger, env_path):
         self.logger = logger
         self.env_path = env_path
         self.setWindowTitle("Create, edit and inspect iRODS environment")
+
+        providers = get_environment_providers()
+        self.templates = {
+            f"Template - {key} ({descr})": key
+            for p in providers
+            for key, descr in p.descriptions.items()
+        }
         self._init_env_box()
-        self._init_template_box()
 
-        self.envbox.activated.connect(self.load_env)
-        self.template_box.activated.connect(self.load_template)
+        self.envbox.activated.connect(self.load)
         self.new_button.clicked.connect(self.create_env)
         self.check_button.clicked.connect(self.check_env)
         self.save_button.clicked.connect(self.save_env)
@@ -156,36 +161,30 @@ def _init_env_box(self):
         env_jsons = [""] + [path.name for path in self.env_path.glob("irods_environment*json")]
         if len(env_jsons) != 0:
             self.envbox.addItems(env_jsons)
-            self.envbox.setCurrentIndex(0)
-
-    def _init_template_box(self):
-        self.template_box.clear()
-        providers = get_environment_providers()
-
-        if len(providers) == 0:
-            self.template_box.hide()
-            return
+        self.envbox.addItems(self.templates.keys())
+        self.envbox.setCurrentIndex(0)
 
-        templates = [key+":    "+descr for p in providers
-                                     for key, descr in p.descriptions.items()]
-        if len(templates) > 0:
-            self.template_box.addItems(templates)
-            self.template_box.setCurrentIndex(0)
+    def load(self):
+        """Decide whether load template or irods env."""
+        selected = self.envbox.currentText()
+        if selected.startswith("Template - "):
+            self.load_template(self.templates[selected])
+        else:
+            self.load_env(self.env_path.joinpath(selected))
 
-    def load_template(self):
+    def load_template(self, template_key):
         """Load environment template into text field."""
         self.error_label.clear()
-        template = self.template_box.currentText()
-        key = template.split(":    ")[0]
-        env_json = find_environment_provider(get_environment_providers(), key).\
-                                             environment_json(key, "USERNAME").split("\n")
+        provider = find_environment_provider(get_environment_providers(), template_key)
+        env_json = provider.environment_json(
+            template_key, *[q.upper() for q in provider.questions]
+        ).split("\n")
         populate_textfield(self.env_field, env_json)
         self.error_label.setText("Please fill in your user name.")
 
-    def load_env(self):
+    def load_env(self, env_file):
         """Load json into text field."""
         self.error_label.clear()
-        env_file = self.env_path.joinpath(self.envbox.currentText())
         try:
             content = json.dumps(
                 _read_json(env_file), sort_keys=True, indent=4, separators=(",", ": ")

ibridgesgui/ui_files/configCheck.py

@@ -1,6 +1,6 @@
 # Form implementation generated from reading ui file 'ibridgesgui/ui_files/configCheck.ui'
 #
-# Created by: PyQt6 UI code generator 6.4.2
+# Created by: PyQt6 UI code generator 6.6.1
 #
 # WARNING: Any manual changes made to this file will be lost when pyuic6 is
 # run again.  Do not edit this file unless you know what you are doing.
@@ -56,10 +56,6 @@ def setupUi(self, Dialog):
         self.envbox = QtWidgets.QComboBox(parent=Dialog)
         self.envbox.setObjectName("envbox")
         self.horizontalLayout.addWidget(self.envbox)
-        self.template_box = QtWidgets.QComboBox(parent=Dialog)
-        self.template_box.setObjectName("template_box")
-        self.template_box.addItem("")
-        self.horizontalLayout.addWidget(self.template_box)
         self.new_button = QtWidgets.QPushButton(parent=Dialog)
         self.new_button.setObjectName("new_button")
         self.horizontalLayout.addWidget(self.new_button)
@@ -105,7 +101,6 @@ def setupUi(self, Dialog):
     def retranslateUi(self, Dialog):
         _translate = QtCore.QCoreApplication.translate
         Dialog.setWindowTitle(_translate("Dialog", "Dialog"))
-        self.template_box.setItemText(0, _translate("Dialog", "Server Templates"))
         self.new_button.setText(_translate("Dialog", "New Config"))
         self.check_button.setText(_translate("Dialog", "Check"))
         self.save_button.setText(_translate("Dialog", "Save"))

ibridgesgui/ui_files/configCheck.ui

@@ -57,15 +57,6 @@ QTabWidget#info_tabs
      <item>
       <widget class="QComboBox" name="envbox"/>
      </item>
-     <item>
-      <widget class="QComboBox" name="template_box">
-       <item>
-        <property name="text">
-         <string>Server Templates</string>
-        </property>
-       </item>
-      </widget>
-     </item>
      <item>
       <widget class="QPushButton" name="new_button">
        <property name="text">