New release

.github/pull_request_template.md

@@ -1,79 +1,94 @@
-## Before submitting this PR
+## Read this before submitting the PR
 
-1. **Description:** _Add a summary of the changes in this PR and the related issue._
-2. **Jira task / GitHub issue:** _Link to the github issue or add the Jira task ID here._
-3. **How to test:** _Add information on how someone could manually test this functionality. As detailed as possible._
-4. **Type of change:** [_Check the relevant boxes in the section below_](#what-type-of-changes-does-the-pr-contain)
-5. **Add docstrings and comments to code**, _even if_ you personally think it's obvious.
+1. Always create a Draft PR first
+2. Go through sections 1-5 below, fill them in and check all the boxes
+3. Make sure that the branch is updated; if there's an "Update branch" button at the bottom of the PR, rebase or update branch.
+4. When all boxes are checked, information is filled in, and the branch is updated: mark as Ready For Review and tag reviewers (top right)
+5. Once there is a submitted review, implement the suggestions (if reasonable, otherwise discuss) and request an new review.
 
-## What _type of change(s)_ does the PR contain?
+If there is a field which you are unsure about, enter the edit mode of this description or go to the [PR template](https://github.com/ScilifelabDataCentre/dds_cli/blob/dev/.github/pull_request_template.md); There are invisible comments providing descriptions which may be of help.
 
-<!--
-- "Breaking": The change will cause existing functionality to not work as expected.
-- Workflow: E.g. a new github action or changes to this PR template. Anything that alters our or the codes workflow.
--->
+## 1. Description / Summary
+
+_Add a summary of the changes in this PR and the related issue._
+
+## 2. Jira task / GitHub issue
+
+_Link to the github issue or add the Jira task ID here._
+
+## 3. Type of change
+
+What _type of change(s)_ does the PR contain?
+
+**Check the relevant boxes below. For an explanation of the different sections, enter edit mode of this PR description template.**
 
 - [ ] New feature
-  - [ ] Breaking: _Please describe the reason for the break and how we can fix it._
-  - [ ] Non-breaking
-- [ ] Bug fix
-  - [ ] Breaking: _Please describe the reason for the break and how we can fix it._
-  - [ ] Non-breaking
-- [ ] Security Alert fix
-- [ ] Documentation
-- [ ] Tests **(only)**
-- [ ] Workflow
-
-## Checklist
-
-- [Sprintlog](../SPRINTLOG.md)
-  - [ ] Added
-  - [ ] Not needed (E.g. PR contains _only_ tests)
-- Rebase / Update / Merge _from_ base branch (the branch from which the current is forked)
-  - [ ] Done
-  - [ ] Not needed
-- Blocking PRs
-  - [ ] Merged
-  - [ ] No blocking PRs
-- PR to `master` branch
-  - [ ] Yes: Read [the release instructions](../docs/procedures/new_release.md)
-    - [ ] I have followed steps 1-7.
-  - [ ] No
-
-## Actions / Scans
-
-<!-- Go through all checkboxes. All actions must pass before merging is allowed.-->
-
-- **Black**: Python code formatter. Does not execute. Only tests.
-  Run `black .` locally to execute formatting.
-  - [ ] Passed
-- **Pylint**: Python code linter. Does not execute. Only tests.
-  Fix code producing warnings. Code must get 10/10.
-  - [ ] Warnings fixed
-  - [ ] Passed
-- **Prettier**: General code formatter. Our use case: MD and yaml mainly.
-  Run `npx prettier --write .` locally to execute formatting.
-  - [ ] Passed
-- **Yamllint**: Linting of yaml files.
-  - [ ] Passed
-- **Tests**: Pytest to verify that functionality works as expected.
-  - [ ] New tests added
-  - [ ] No new tests
-  - [ ] Passed
-- **TestPyPi**: Build CLI and publish to TestPyPi in order to verify before release.
-  - [ ] Passed
-- **CodeQL**: Scan for security vulnerabilities, bugs, errors
-  - [ ] New alerts: _Go through them and either fix, dismiss och ignore. Add reasoning in items below._
-  - [ ] Alerts fixed: _What?_
-  - [ ] Alerts ignored / dismissed: _Why?_
-  - [ ] Passed
-- **Trivy**: Security scanner
-  - [ ] New alerts: _Go through them and either fix, dismiss och ignore. Add reasoning in items below._
-  - [ ] Alerts fixed: _What?_
-  - [ ] Alerts ignored / dismissed: _Why?_
-  - [ ] Passed
-- **Snyk**: Security scanner
-  - [ ] New alerts: _Go through them and either fix, dismiss och ignore. Add reasoning in items below._
-  - [ ] Alerts fixed: _What?_
-  - [ ] Alerts ignored / dismissed: _Why?_
-  - [ ] Passed
+  - [ ] Breaking: _Why / How? Add info here._ <!-- Should be checked if the changes in this PR will cause existing functionality to not work as expected. E.g. with the master branch of the `dds_cli` -->
+  - [ ] Non-breaking <!-- Should be checked if the changes will not cause existing functionality to fail. "Non-breaking" is just an addition of a new feature. -->
+- [ ] Database change: _Remember the to include a new migration version, **or** explain here why it's not needed._ <!-- Should be checked when you've changed something in `models.py`. For a guide on how to add the a new migration version, look at the "Database changes" section in the README.md. -->
+- [ ] Bug fix <!-- Should be checked when a bug is fixed in existing functionality. If the bug fix also is a breaking change (see above), add info about that beside this check box. -->
+- [ ] Security Alert fix <!-- Should be checked if the PR attempts to solve a security vulnerability, e.g. reported by the "Security" tab in the repo. -->
+- [ ] Documentation <!-- Should be checked if the PR adds or updates the CLI documentation -- anything in docs/ directory. -->
+- [ ] Workflow <!-- Should be checked if the PR includes a change in e.g. the github actions files (dds_cli/.github/*) or another type of workflow change. Anything that alters our or the codes workflow. -->
+- [ ] Tests **only** <!-- Should only be checked if the PR only contains tests, none of the other types of changes listed above. -->
+
+## 4. Additional information
+
+- [ ] [Sprintlog](https://github.com/ScilifelabDataCentre/dds_cli/blob/dev/SPRINTLOG.md) <!-- Add a row at the bottom of the SPRINTLOG.md file (not needed if PR contains only tests). Follow the format of previous rows. If the PR is the first in a new sprint, add a new sprint header row (follow the format of previous sprints). -->
+- [ ] Blocking PRs <!-- Should be checked if there are blocking PRs or other tasks that need to be merged prior to this. Add link to PR or Jira card if this is the case. -->
+  - [ ] Merged <!-- Should be checked if the "Blocking PRs" box was checked AND all blocking PRs have been merged / fixed. -->
+- [ ] PR to `master` branch: _If checked, read [the release instructions](https://github.com/ScilifelabDataCentre/dds_cli/blob/dev/docs/procedures/new_release.md)_ <!-- Check this if the PR is made to the `master` branch. Only the `dev` branch should be doing this. -->
+  - [ ] I have followed steps 1-8. <!-- Should be checked if the "PR to `master` branch" box is checked AND the specified steps in the release instructions have been followed. -->
+
+## 5. Actions / Scans
+
+_Check the boxes when the specified checks have passed._
+
+**For information on what the different checks do and how to fix it if they're failing, enter edit mode of this description or go to the [PR template](https://github.com/ScilifelabDataCentre/dds_cli/blob/dev/.github/pull_request_template.md).**
+
+- [ ] **Black**
+<!--
+  What: Python code formatter.
+  How to fix: Run `black .` locally to execute formatting.
+-->
+- [ ] **Pylint**
+<!--
+  What: Python code linter.
+  How to fix: Manually fix the code producing warnings. Code must get 10/10.
+-->
+- [ ] **Prettier**
+<!--
+  What: General code formatter. Our use case: MD and yaml mainly.
+  How to fix: Run npx prettier --write . locally to execute formatting.
+-->
+- [ ] **Yamllint**
+<!--
+  What: Linting of yaml files.
+  How to fix: Manually fix any errors locally.
+-->
+- [ ] **Tests**
+<!--
+  What: Pytest to verify that functionality works as expected.
+  How to fix: Manually fix any errors locally. Follow the instructions in the "Run tests" section of the README.md to run the tests locally.
+  Additional info: The PR should ALWAYS include new tests or fixed tests when there are code changes. When pytest action has finished, it will post a codecov report; Look at this report and verify the files you have changed are listed. "90% <100.00%> (+0.8%)" means "Tests cover 90% of the changed file, <100 % of this PR's code changes are tested>, and (the code changes and added tests increased the overall test coverage with 0.8%)
+-->
+- [ ] **TestPyPI**
+<!--
+  What: Builds the CLI and publishes to TestPyPI in order to verify before release.
+  How to fix: Check the action logs and fix potential issues manually.
+-->
+- [ ] **CodeQL**
+<!--
+  What: Scan for security vulnerabilities, bugs, errors.
+  How to fix: Go through the alerts and either manually fix, dismiss or ignore. Add info on ignored or dismissed alerts.
+-->
+- [ ] **Trivy**
+<!--
+  What: Security scanner.
+  How to fix: Go through the alerts and either manually fix, dismiss or ignore. Add info on ignored or dismissed alerts.
+-->
+- [ ] **Snyk**
+<!--
+  What: Security scanner.
+  How to fix: Go through the alerts and either manually fix, dismiss or ignore. Add info on ignored or dismissed alerts.
+-->

CHANGELOG.rst

@@ -1,6 +1,15 @@
 Changelog
 ==========
 
+.. _2.5.2:
+
+2.5.2 - 2023-10-25
+~~~~~~~~~~~~~~~~~~~
+
+- Updated command: `dds project status delete/archive` now prints project information and asks for confirmation from user.
+- "Checksum verification successful" is not printed when file integrity is verified (unless `-v` option is used); Only prints if there is an error.
+- New command `dds project status extend`: Unit Admins / Personnel can extend the project deadline prior to the project expiring.
+
 .. _2.5.1:
 
 2.5.1 - 2023-09-25

SPRINTLOG.md

@@ -300,4 +300,11 @@ _Nothing merged in CLI during this sprint_
 
 # 2023-09-18 - 2023-09-29
 
-- GitHub Actions to generate the documentation fixed ([#1473])(https://scilifelab.atlassian.net/jira/software/projects/DDS/boards/13?selectedIssue=DDS-1473)
+- GitHub Actions to generate the documentation fixed ([#650](https://github.com/ScilifelabDataCentre/dds_cli/pull/650))
+- Print project information and ask user for confirmation when deleting or archiving projects ([#655](https://github.com/ScilifelabDataCentre/dds_cli/pull/655))
+
+# 2023-10-16 - 2023-10-27
+
+- Change "Checksum verification successful. File integrity verified." logging level from INFO to DEBUG in order to not print for all files ([#662](https://github.com/ScilifelabDataCentre/dds_cli/pull/662)
+- New command `dds project status extend` to allow extension of project deadline ([#661](https://github.com/ScilifelabDataCentre/dds_cli/pull/661)
+- New version: 2.5.2 ([#660](https://github.com/ScilifelabDataCentre/dds_cli/pull/660))

dds_cli/__main__.py

@@ -1196,28 +1196,22 @@ def archive_project(click_ctx, project: str, abort: bool = False):
 
     Use the `--abort` flag to indicate that something has gone wrong in the project.
     """
-    proceed_deletion = (
-        True
-        if click_ctx.get("NO_PROMPT", False)
-        else dds_cli.utils.get_deletion_confirmation(action="archive", project=project)
-    )
-    if proceed_deletion:
-        try:
-            with dds_cli.project_status.ProjectStatusManager(
-                project=project,
-                no_prompt=click_ctx.get("NO_PROMPT", False),
-                token_path=click_ctx.get("TOKEN_PATH"),
-            ) as updater:
-                updater.update_status(new_status="Archived", is_aborted=abort)
-        except (
-            dds_cli.exceptions.APIError,
-            dds_cli.exceptions.AuthenticationError,
-            dds_cli.exceptions.DDSCLIException,
-            dds_cli.exceptions.ApiResponseError,
-            dds_cli.exceptions.ApiRequestError,
-        ) as err:
-            LOG.error(err)
-            sys.exit(1)
+    try:
+        with dds_cli.project_status.ProjectStatusManager(
+            project=project,
+            no_prompt=click_ctx.get("NO_PROMPT", False),
+            token_path=click_ctx.get("TOKEN_PATH"),
+        ) as updater:
+            updater.update_status(new_status="Archived", is_aborted=abort)
+    except (
+        dds_cli.exceptions.APIError,
+        dds_cli.exceptions.AuthenticationError,
+        dds_cli.exceptions.DDSCLIException,
+        dds_cli.exceptions.ApiResponseError,
+        dds_cli.exceptions.ApiRequestError,
+    ) as err:
+        LOG.error(err)
+        sys.exit(1)
 
 
 # -- dds project status delete -- #
@@ -1231,28 +1225,56 @@ def delete_project(click_ctx, project: str):
     Certain meta data is kept (nothing sensitive) and it will still be listed in your projects. All
     data within the project is deleted. You cannot revert this change.
     """
-    proceed_deletion = (
-        True
-        if click_ctx.get("NO_PROMPT", False)
-        else dds_cli.utils.get_deletion_confirmation(action="delete", project=project)
-    )
-    if proceed_deletion:
-        try:
-            with dds_cli.project_status.ProjectStatusManager(
-                project=project,
-                no_prompt=click_ctx.get("NO_PROMPT", False),
-                token_path=click_ctx.get("TOKEN_PATH"),
-            ) as updater:
-                updater.update_status(new_status="Deleted")
-        except (
-            dds_cli.exceptions.APIError,
-            dds_cli.exceptions.AuthenticationError,
-            dds_cli.exceptions.DDSCLIException,
-            dds_cli.exceptions.ApiResponseError,
-            dds_cli.exceptions.ApiRequestError,
-        ) as err:
-            LOG.error(err)
-            sys.exit(1)
+    try:
+        with dds_cli.project_status.ProjectStatusManager(
+            project=project,
+            no_prompt=click_ctx.get("NO_PROMPT", False),
+            token_path=click_ctx.get("TOKEN_PATH"),
+        ) as updater:
+            updater.update_status(new_status="Deleted")
+    except (
+        dds_cli.exceptions.APIError,
+        dds_cli.exceptions.AuthenticationError,
+        dds_cli.exceptions.DDSCLIException,
+        dds_cli.exceptions.ApiResponseError,
+        dds_cli.exceptions.ApiRequestError,
+    ) as err:
+        LOG.error(err)
+        sys.exit(1)
+
+
+# -- dds project status extend -- #
+@project_status.command(name="extend", no_args_is_help=True)
+# Options
+@project_option(required=True)
+@click.option(
+    "--new-deadline",
+    required=False,
+    type=int,
+    help="Number of days to extend the deadline.",
+)
+@click.pass_obj
+def extend_deadline(click_ctx, project: str, new_deadline: int):
+    """Extend a project deadline by an specified number of days.
+
+    It consumes one of allowed times to renew data access.
+    """
+    try:
+        with dds_cli.project_status.ProjectStatusManager(
+            project=project,
+            no_prompt=click_ctx.get("NO_PROMPT", False),
+            token_path=click_ctx.get("TOKEN_PATH"),
+        ) as updater:
+            updater.extend_deadline(new_deadline=new_deadline)
+    except (
+        dds_cli.exceptions.APIError,
+        dds_cli.exceptions.AuthenticationError,
+        dds_cli.exceptions.DDSCLIException,
+        dds_cli.exceptions.ApiResponseError,
+        dds_cli.exceptions.ApiRequestError,
+    ) as err:
+        LOG.error(err)
+        sys.exit(1)
 
 
 # -- dds project status busy -- #

dds_cli/base.py

@@ -133,6 +133,43 @@ def __exit__(self, exception_type, exception_value, traceback, max_fileerrs: int
 
         return True
 
+    # Public methods ############################### Public methods #
+
+    def get_project_info(self):
+        """Collect project information from API."""
+
+        # Get info about a project from API
+        response, _ = dds_cli.utils.perform_request(
+            DDSEndpoint.PROJ_INFO,
+            method="get",
+            headers=self.token,
+            params={"project": self.project},
+            error_message="Failed to get project information",
+        )
+
+        project_info = response.get("project_info")
+
+        # If not project info was retrieved from the request, throw an exception
+        if not project_info:
+            raise dds_cli.exceptions.ApiResponseError(message="No project information to display.")
+
+        return project_info
+
+    def generate_project_table(self, project_info):
+        """Generate a table from some project info provided"""
+
+        # Print project info table
+        table = dds_cli.utils.create_table(
+            title="Project information.",
+            columns=["Project ID", "Created by", "Status", "Last updated", "Size"],
+            rows=[
+                project_info,
+            ],
+            caption=f"Information about project {project_info['Project ID']}",
+        )
+
+        return table
+
     # Private methods ############################### Private methods #
     def __get_safespring_keys(self):
         """Get safespring keys."""

dds_cli/file_encryptor.py

@@ -132,7 +132,7 @@ def verify_checksum(file: pathlib.Path, correct_checksum):
         else:
             if checksum.hexdigest() == correct_checksum:
                 verified, error = (True, "File integrity verified.")
-                LOG.info("Checksum verification successful. File integrity verified.")
+                LOG.debug("Checksum verification successful. File integrity verified.")
             else:
                 error = "Checksum verification failed. File compromised."
                 LOG.warning(error)