dds-cli 2.12.0__tar.gz → 2.13.0__tar.gz

{dds_cli-2.12.0 → dds_cli-2.13.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dds_cli
-Version: 2.12.0
+Version: 2.13.0
 Summary: A command line tool to manage data and projects in the SciLifeLab Data Delivery System.
 Home-page: https://github.com/ScilifelabDataCentre/dds_cli
 Author: SciLifeLab Data Centre
@@ -18,7 +18,7 @@ Requires-Dist: boto3==1.24.73
 Requires-Dist: botocore==1.27.73
 Requires-Dist: click==8.1.3
 Requires-Dist: click-pathlib==2020.3.13.0
-Requires-Dist: cryptography==42.0.4
+Requires-Dist: cryptography==44.0.1
 Requires-Dist: immutabledict==2.2.1
 Requires-Dist: jwcrypto==1.5.6
 Requires-Dist: prettytable==3.7.0
@@ -27,7 +27,7 @@ Requires-Dist: PyNaCl==1.5.0
 Requires-Dist: pytz==2022.2.1
 Requires-Dist: PyYAML==6.0.2
 Requires-Dist: questionary==1.10.0
-Requires-Dist: requests==2.32.2
+Requires-Dist: requests==2.32.4
 Requires-Dist: rich==13.6.0
 Requires-Dist: rich-click==1.5.2
 Requires-Dist: simplejson==3.17.6

{dds_cli-2.12.0 → dds_cli-2.13.0}/dds_cli/__init__.py

@@ -44,7 +44,7 @@ DDS_DIR_REQUIRED_METHODS = ["put", "get"]
 DDS_KEYS_REQUIRED_METHODS = ["put", "get"]
 
 # Token related variables
-TOKEN_FILE = pathlib.Path(os.path.expanduser("~/.dds_cli_token"))
+TOKEN_FILE = pathlib.Path.home() / ".dds_cli_token"
 TOKEN_EXPIRATION_WARNING_THRESHOLD = datetime.timedelta(hours=6)
 
 

dds_cli-2.13.0/dds_cli/constants.py

@@ -0,0 +1,14 @@
+"""Shared constants used in the DDS CLI.
+
+Using this will avoid e.g. circular imports and 
+make it easier to maintain.
+
+TODO: Move other constants here from __init__.py.
+"""
+
+# Timeout settings for upload and download
+READ_TIMEOUT = 300
+CONNECT_TIMEOUT = 60
+
+# Import these constants when using '*'
+__all__ = ["READ_TIMEOUT", "CONNECT_TIMEOUT"]

{dds_cli-2.12.0 → dds_cli-2.13.0}/dds_cli/data_getter.py

@@ -14,6 +14,7 @@ from rich.markup import escape
 from rich.progress import Progress, SpinnerColumn
 
 # Own modules
+from dds_cli import constants
 from dds_cli import DDSEndpoint, FileSegment
 from dds_cli import file_handler_remote as fhr
 from dds_cli import data_remover as dr
@@ -235,8 +236,11 @@ class DataGetter(base.DDSBaseClass):
         file_remote = self.filehandler.data[file]["url"]
 
         try:
-            # TODO: Set timeout? (pylint)
-            with requests.get(file_remote, stream=True) as req:
+            with requests.get(
+                file_remote,
+                stream=True,
+                timeout=(constants.CONNECT_TIMEOUT, constants.READ_TIMEOUT),
+            ) as req:
                 req.raise_for_status()
                 with file_local.open(mode="wb") as new_file:
                     for chunk in req.iter_content(chunk_size=FileSegment.SEGMENT_SIZE_CIPHER):

{dds_cli-2.12.0 → dds_cli-2.13.0}/dds_cli/dds_gui/app.py

@@ -1,6 +1,6 @@
 """GUI Application for DDS CLI."""
 
-from textual.app import App, ComposeResult
+from textual.app import ComposeResult
 from textual.binding import Binding
 from textual.widgets import Header
 from textual.theme import Theme
@@ -33,7 +33,7 @@ theme = Theme(
 )
 
 
-class DDSApp(App, DDSStateManager):
+class DDSApp(DDSStateManager):  ### Moved Textual App class to State Manager to access notifications
     """Textual App for DDS CLI."""
 
     def __init__(self, token_path: str):

dds_cli-2.13.0/dds_cli/dds_gui/dds_state_manager.py

@@ -0,0 +1,165 @@
+"""DDS State Manager"""
+
+import pathlib
+from typing import List
+from textual.app import App
+from textual import work
+from textual.reactive import reactive
+
+import dds_cli.auth
+import dds_cli.data_lister
+import dds_cli.exceptions
+import dds_cli.project_info
+
+from dds_cli.dds_gui.models.project import ProjectContentData
+from dds_cli.dds_gui.models.project_information import ProjectInformationData
+
+
+class DDSStateManager(App):
+    """
+    State manager for the DDS CLI. Consists of reactive states available app wide.
+
+    Reactive attributes are used to update the UI, fetch data, set new states, etc.
+    Reactive attributes are recomposed when the state changes,
+    triggering re-renders and re-computations of the derived states.
+
+    Derived states are attributes computed based on the reactive attributes.
+    When the reactive attributes are updated, the derived states are automatically updated.
+
+    Setters are used to avoid pylint warnings about attribute-defined-outside-init.
+    Functionally, the reactive attributes can be set in the child classes,
+    but are set here for consistence over the app, instead of ignoring the pylint warnings.
+    """
+
+    #### TOKEN PATH #########################################################
+
+    # Default token path for CLI authentication token
+    token_path = str(pathlib.Path.home() / ".dds_cli_token")
+
+    #### AUTH ################################################################
+
+    auth: reactive[dds_cli.auth.Auth] = reactive(
+        dds_cli.auth.Auth(authenticate=False, token_path=token_path), recompose=True
+    )
+    auth_status: reactive[bool] = reactive(False, recompose=True)
+
+    def set_auth_status(self, new_auth_status: bool) -> None:
+        """Set the auth status."""
+        self.auth_status = new_auth_status
+
+    #### PROJECT LISTING ####################################################
+
+    project_list: reactive[List[dict]] = reactive(None, recompose=True)
+    selected_project_id: reactive[str] = reactive(None, recompose=True)
+
+    def fetch_projects(self) -> List[str]:
+        """Fetch the projects and automatically compute project_ids via reactive watcher."""
+        self.project_list: List[dict] = dds_cli.data_lister.DataLister(json=True).list_projects()
+
+    def set_selected_project_id(self, project_id: str) -> None:
+        """Set the selected project id."""
+        self.selected_project_id = project_id
+
+    #### PROJECT CONTENT #####################################################
+
+    project_content: reactive[ProjectContentData] = reactive(None, recompose=True)
+    is_loading: reactive[bool] = reactive(False, recompose=True)
+
+    @work(exclusive=True, thread=True)
+    def load_project_content(self, project_id: str) -> None:
+        """Background worker to fetch project content for a project id.
+        This solution was proposed to avoid unnecessary re-renders of the project
+        content widget while still keeping the label reactive.
+        Reference: https://textual.textualize.io/guide/workers/
+        """
+        try:
+            project_content = dds_cli.data_lister.DataLister(
+                json=True, project=project_id
+            ).list_recursive()
+        except (
+            dds_cli.exceptions.ApiRequestError,
+            dds_cli.exceptions.ApiResponseError,
+            dds_cli.exceptions.DDSCLIException,
+        ) as err:
+            self.call_from_thread(self._on_project_content_error, project_id, str(err), "error")
+            return
+        except dds_cli.exceptions.NoDataError as data_err:
+            self.call_from_thread(
+                self._on_project_content_error, project_id, str(data_err), "warning"
+            )
+            return
+
+        content = ProjectContentData.from_dict(project_content, project_name=project_id)
+        self.call_from_thread(self._on_project_content_loaded, content)
+
+    def _on_project_content_loaded(self, content: ProjectContentData) -> None:
+        """Handle successful content load on the main thread."""
+        self.is_loading = False
+        self.project_content = content
+
+    def _on_project_content_error(self, project_id: str, message: str, severity: str) -> None:
+        """Handle content load error on the main thread."""
+        self.is_loading = False
+        if severity == "warning":
+            self.notify(f"No data found for project {project_id}: {message}", severity="warning")
+        else:
+            self.notify(f"Failed to fetch project content: {message}", severity="error")
+        if self.selected_project_id == project_id:
+            self.project_content = None
+
+    #### PROJECT INFORMATION #################################################
+
+    project_information: reactive[ProjectInformationData] = reactive(None, recompose=True)
+
+    def fetch_project_information(self, project_id: str) -> None:
+        """Fetch the project information for a project id."""
+        try:
+            self.project_information = ProjectInformationData.from_dict(
+                dds_cli.project_info.ProjectInfoManager(project=project_id).get_project_info()
+            )
+        except (
+            dds_cli.exceptions.ApiRequestError,
+            dds_cli.exceptions.ApiResponseError,
+            dds_cli.exceptions.DDSCLIException,
+        ) as err:
+            self.notify(f"Failed to fetch project information: {err}", severity="error")
+            self.project_information = None
+
+    #### WATCHERS ###########################################################
+
+    def watch_auth_status(self, auth_status: bool) -> None:
+        """Watch the auth status."""
+        if auth_status:
+            # Fetch the projects when the auth status is True.
+            # This is to ensure that the projects are fetched when the user is authenticated only.
+            # If called without auth status, recursion error occurs and/or the base class
+            #  will try to authenticate in the CLI.
+            try:
+                self.fetch_projects()
+            except (
+                dds_cli.exceptions.ApiRequestError,
+                dds_cli.exceptions.ApiResponseError,
+                dds_cli.exceptions.DDSCLIException,
+            ) as err:
+                self.notify(f"Failed to fetch projects: {err}", severity="error")
+                self.project_list = None  # This triggers watch_projects to clear project_ids
+        else:
+            self.project_list = None  # This triggers watch_projects to clear project_ids
+            self.selected_project_id = None
+
+    def watch_selected_project_id(self, selected_project_id: str) -> None:
+        """Start loading project content when the selected project changes."""
+        # Clear current content and information when switching projects
+        self.project_information = None
+        self.project_content = None
+
+        if not selected_project_id:
+            self.is_loading = False
+            return
+
+        # Get project information
+        self.fetch_project_information(selected_project_id)
+
+        # Start loading project content
+        self.is_loading = True
+        self.load_project_content(selected_project_id)

{dds_cli-2.12.0 → dds_cli-2.13.0}/dds_cli/dds_gui/pages/authentication/authentication_form.py

@@ -48,8 +48,8 @@ class AuthenticationForm(Container):
     def on_button_pressed(self, event: events.Click) -> None:
         """Handle button presses."""
         if event.button.id == "send-2fa-code":
-            self.authenticate_user_credentials()
-            if self.auth:
+            success = self.authenticate_user_credentials()
+            if success:
                 self.query_one("#dds-auth-form").remove()
                 self.query_one("#dds-auth-form-container").mount(
                     TwoFactorFormFields(id="dds-2fa-form")
@@ -57,25 +57,36 @@ class AuthenticationForm(Container):
         if event.button.id == "login":
             self.confirm_2factor_code()
 
-    def authenticate_user_credentials(self) -> None:
+    def authenticate_user_credentials(self) -> bool:
         """Authenticate the user credentials."""
         username = self.query_one("#username").value
         password = self.query_one("#password").value
 
+        if not username or not password:
+            self.notify("Error: Username and password are required.", severity="error", timeout=10)
+            return False
+
         try:
             self.partial_auth_token, self.secondfactor_method = self.auth.login(username, password)
             self.notify("Two factor code sent to email.")
         except (
             dds_cli.exceptions.AuthenticationError,
             dds_cli.exceptions.ApiRequestError,
+            dds_cli.exceptions.ApiResponseError,
+            dds_cli.exceptions.DDSCLIException,
         ) as error:
             self.notify(f"Error: {error}", severity="error")
-            self.auth = None
+            return False
+        return True
 
     def confirm_2factor_code(self) -> None:
         """Confirm the 2FA code."""
         code = self.query_one("#code").value
 
+        if not code:
+            self.notify("Error: 2FA code is required.", severity="error", timeout=10)
+            return
+
         try:
             self.auth.confirm_twofactor(
                 partial_auth_token=self.partial_auth_token,
@@ -84,7 +95,12 @@ class AuthenticationForm(Container):
             )
             self.notify("Successfully authenticated.")
             self.app.set_auth_status(True)
-        except dds_cli.exceptions.AuthenticationError as error:
+        except (
+            dds_cli.exceptions.AuthenticationError,
+            dds_cli.exceptions.ApiRequestError,
+            dds_cli.exceptions.ApiResponseError,
+            dds_cli.exceptions.DDSCLIException,
+        ) as error:
             self.notify(f"Error: {error}", severity="error", timeout=10)
         self.close_modal()
 

{dds_cli-2.12.0 → dds_cli-2.13.0}/dds_cli/dds_gui/pages/project_view.py

@@ -1,13 +1,16 @@
 """DDS Project View Page"""
 
 from typing import Any
-
 from textual.app import ComposeResult
 from textual.containers import Vertical, Horizontal
 from textual.widget import Widget
 from textual.widgets import Placeholder
+
 from dds_cli.dds_gui.pages.authentication.authentication import Authentication
+from dds_cli.dds_gui.pages.project_content.project_content import ProjectContent
+from dds_cli.dds_gui.pages.project_list.project_list import ProjectList
 from dds_cli.dds_gui.pages.important_information.important_information import ImportantInformation
+from dds_cli.dds_gui.pages.project_information.project_information import ProjectInformation
 
 
 class ProjectView(Widget):
@@ -51,21 +54,15 @@ class ProjectView(Widget):
     def compose(self) -> ComposeResult:
         with Horizontal():
             with Vertical(id="left-container"):
-                yield Placeholder(
-                    id="project-list"
-                )  # ProjectList(title="Projects", id="project-list")
+                yield ProjectList(title="Projects", id="project-list")
                 yield ImportantInformation(
                     title="Important Information", id="important-information"
                 )  # ImportantInformation(title="Important Information", id="important-information")
                 yield Authentication(title="Authentication", id="auth-menu")
             with Vertical(id="right-container"):
                 with Horizontal(id="top-container"):
-                    yield Placeholder(
-                        id="project-content"
-                    )  # ProjectContent(title="Project Content", id="project-content")
-                    yield Placeholder(
-                        id="project-information"
-                    )  # ProjectInformation(title="Project Information", id="project-information")
+                    yield ProjectContent(title="Project Content", id="project-content")
+                    yield ProjectInformation(title="Project Information", id="project-information")
                 with Horizontal(id="bottom-container"):
                     yield Placeholder(
                         id="project-actions"

{dds_cli-2.12.0 → dds_cli-2.13.0}/dds_cli/project_status.py

@@ -234,7 +234,7 @@ class ProjectStatusManager(base.DDSBaseClass):
             f"\nThe new deadline for project {project_id} will be: [b][blue]{new_deadline_date}[/b][/blue]"
             "\n\n[b][blue]Are you sure [/b][/blue]you want to perform this operation? "
             "\nYou can only extend the data availability a maximum of "
-            "[b][blue]3 times[/b][/blue], this consumes one of those times."
+            "[b][blue]2 times[/b][/blue], this consumes one of those times."
         )
 
         if not rich.prompt.Confirm.ask(prompt_question):

{dds_cli-2.12.0 → dds_cli-2.13.0}/dds_cli/s3_connector.py

@@ -15,6 +15,7 @@ import botocore
 
 # Own modules
 import dds_cli.utils
+from dds_cli import constants
 from dds_cli import DDSEndpoint
 
 ###############################################################################
@@ -75,6 +76,14 @@ class S3Connector:
                 endpoint_url=self.url,
                 aws_access_key_id=self.keys["access_key"],
                 aws_secret_access_key=self.keys["secret_key"],
+                config=botocore.client.Config(
+                    read_timeout=constants.READ_TIMEOUT,
+                    connect_timeout=constants.CONNECT_TIMEOUT,
+                    retries={
+                        "max_attempts": 10,
+                        # TODO: Add retry strategy mode="standard" when boto3 version >= 1.26.0
+                    },
+                ),
             )
         except (boto3.exceptions.Boto3Error, botocore.exceptions.BotoCoreError) as err:
             LOG.warning("S3 connection failed: %s", err)

{dds_cli-2.12.0 → dds_cli-2.13.0}/dds_cli/user.py

@@ -76,7 +76,7 @@ class User:
         LOG.debug("Starting authentication on the API...")
 
         # If no username or password is provided, prompt for them
-        if not username and not password:
+        if not username or not password:
             if self.no_prompt:
                 raise exceptions.AuthenticationError(
                     message=(
@@ -88,12 +88,12 @@ class User:
             username = Prompt.ask("DDS username")
             password = getpass.getpass(prompt="DDS password: ")
 
-        if username == "":
+        if not username:
             raise exceptions.AuthenticationError(
                 message="Non-empty username needed to be able to authenticate."
             )
 
-        if password == "":
+        if not password:
             raise exceptions.AuthenticationError(
                 message="Non-empty password needed to be able to authenticate."
             )
@@ -289,7 +289,7 @@ class TokenFile:
         if token_path is None:
             self.token_file = dds_cli.TOKEN_FILE
         else:
-            self.token_file = pathlib.Path(os.path.expanduser(token_path))
+            self.token_file = pathlib.Path(token_path).expanduser()
 
     def read_token(self):
         """Attempts to fetch a valid token from the token file.

{dds_cli-2.12.0 → dds_cli-2.13.0}/dds_cli/version.py

@@ -2,4 +2,4 @@
 
 # Do not change bump the major version unless absolutely necessary - makes incompatible with API
 # If mid or minor version reaches 9, continue to 10, 11 etc.
-__version__ = "2.12.0"
+__version__ = "2.13.0"

{dds_cli-2.12.0 → dds_cli-2.13.0}/dds_cli.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dds_cli
-Version: 2.12.0
+Version: 2.13.0
 Summary: A command line tool to manage data and projects in the SciLifeLab Data Delivery System.
 Home-page: https://github.com/ScilifelabDataCentre/dds_cli
 Author: SciLifeLab Data Centre
@@ -18,7 +18,7 @@ Requires-Dist: boto3==1.24.73
 Requires-Dist: botocore==1.27.73
 Requires-Dist: click==8.1.3
 Requires-Dist: click-pathlib==2020.3.13.0
-Requires-Dist: cryptography==42.0.4
+Requires-Dist: cryptography==44.0.1
 Requires-Dist: immutabledict==2.2.1
 Requires-Dist: jwcrypto==1.5.6
 Requires-Dist: prettytable==3.7.0
@@ -27,7 +27,7 @@ Requires-Dist: PyNaCl==1.5.0
 Requires-Dist: pytz==2022.2.1
 Requires-Dist: PyYAML==6.0.2
 Requires-Dist: questionary==1.10.0
-Requires-Dist: requests==2.32.2
+Requires-Dist: requests==2.32.4
 Requires-Dist: rich==13.6.0
 Requires-Dist: rich-click==1.5.2
 Requires-Dist: simplejson==3.17.6

{dds_cli-2.12.0 → dds_cli-2.13.0}/dds_cli.egg-info/SOURCES.txt

@@ -7,6 +7,7 @@ dds_cli/__main__.py
 dds_cli/account_manager.py
 dds_cli/auth.py
 dds_cli/base.py
+dds_cli/constants.py
 dds_cli/custom_decorators.py
 dds_cli/data_getter.py
 dds_cli/data_lister.py
@@ -54,7 +55,6 @@ dds_cli/dds_gui/components/dds_modal.py
 dds_cli/dds_gui/components/dds_select.py
 dds_cli/dds_gui/components/dds_status_chip.py
 dds_cli/dds_gui/components/dds_text_item.py
-dds_cli/dds_gui/components/dds_tree_view.py
 dds_cli/dds_gui/pages/__init__.py
 dds_cli/dds_gui/pages/project_view.py
 dds_cli/dds_gui/pages/authentication/__init__.py
@@ -66,9 +66,6 @@ dds_cli/dds_gui/pages/authentication/modals/logout_modal.py
 dds_cli/dds_gui/pages/authentication/modals/reauthenticate_modal.py
 dds_cli/dds_gui/pages/project_view_mode/__init__.py
 dds_cli/dds_gui/pages/project_view_mode/project_actions.py
-dds_cli/dds_gui/pages/project_view_mode/project_content.py
-dds_cli/dds_gui/pages/project_view_mode/project_information.py
-dds_cli/dds_gui/pages/project_view_mode/project_list.py
 dds_cli/dds_gui/pages/project_view_mode/project_actions_tabs/__init__.py
 dds_cli/dds_gui/pages/project_view_mode/project_actions_tabs/download_data.py
 dds_cli/dds_gui/pages/project_view_mode/project_actions_tabs/user_access.py
@@ -81,15 +78,20 @@ tests/__init__.py
 tests/test_account_manager.py
 tests/test_auth.py
 tests/test_base.py
+tests/test_data_getter.py
 tests/test_data_remover.py
 tests/test_file_compressor.py
 tests/test_file_encryptor.py
 tests/test_file_handler_local.py
 tests/test_motd_manager.py
 tests/test_project_status.py
+tests/test_s3_connector.py
 tests/test_superadmin_helper.py
 tests/test_user.py
 tests/test_utils.py
 tests/gui_tests/__init__.py
 tests/gui_tests/test_authentication.py
-tests/gui_tests/test_important_information.py
+tests/gui_tests/test_important_information.py
+tests/gui_tests/test_project_content.py
+tests/gui_tests/test_project_information.py
+tests/gui_tests/test_project_list.py

{dds_cli-2.12.0 → dds_cli-2.13.0}/dds_cli.egg-info/requires.txt

@@ -2,7 +2,7 @@ boto3==1.24.73
 botocore==1.27.73
 click==8.1.3
 click-pathlib==2020.3.13.0
-cryptography==42.0.4
+cryptography==44.0.1
 immutabledict==2.2.1
 jwcrypto==1.5.6
 prettytable==3.7.0
@@ -11,7 +11,7 @@ PyNaCl==1.5.0
 pytz==2022.2.1
 PyYAML==6.0.2
 questionary==1.10.0
-requests==2.32.2
+requests==2.32.4
 rich==13.6.0
 rich-click==1.5.2
 simplejson==3.17.6

{dds_cli-2.12.0 → dds_cli-2.13.0}/gui_build/gui_standalone.py

@@ -2,8 +2,10 @@
 This file is used to run the DDS GUI standalone for the executable.
 """
 
+import pathlib
+
 from dds_cli.dds_gui.app import DDSApp
 
 if __name__ == "__main__":
-    app = DDSApp(token_path="~/.dds_cli_token")
+    app = DDSApp(token_path=pathlib.Path.home() / ".dds_cli_token")
     app.run()