lifemonitor.yaml configuration file found on this repository.lifemonitor.yaml should be placed on the root of this repository."
labels = ['lifemonitor']
+ depends_on = [GitRepositoryWithoutMainBranch]
def check(self, repo: WorkflowRepository) -> bool:
if repo.config is None:
diff --git a/lifemonitor/api/models/issues/general/repo_layout.py b/lifemonitor/api/models/issues/general/repo_layout.py
index 98624d045..556ffbb64 100644
--- a/lifemonitor/api/models/issues/general/repo_layout.py
+++ b/lifemonitor/api/models/issues/general/repo_layout.py
@@ -24,15 +24,34 @@
from lifemonitor.api.models.issues import WorkflowRepositoryIssue
from lifemonitor.api.models.repositories import WorkflowRepository
+from lifemonitor.api.models.repositories.local import \
+ LocalGitWorkflowRepository
# set module level logger
logger = logging.getLogger(__name__)
+class GitRepositoryWithoutMainBranch(WorkflowRepositoryIssue):
+ name = "Repository without main branch"
+ description = "This repository does not have a main branch."
+ labels = ['best-practices']
+
+ def check(self, repo: WorkflowRepository) -> bool:
+ """
+ If the repository is a Git repository, check if it has a main branch.
+ """
+ if not LocalGitWorkflowRepository.is_git_repo(repo.local_path):
+ return False
+ git_repo = LocalGitWorkflowRepository(repo.local_path)
+ logger.debug("Local Git repository: %r - branches: %r", git_repo, git_repo.heads)
+ return git_repo.heads is None or len(git_repo.heads) == 0
+
+
class RepositoryNotInitialised(WorkflowRepositoryIssue):
name = "Repository not intialised"
description = "No workflow and crate metadata found on this repository."
labels = ['best-practices']
+ depends_on = [GitRepositoryWithoutMainBranch]
def check(self, repo: WorkflowRepository) -> bool:
return repo.find_workflow() is None and repo.metadata is None
diff --git a/lifemonitor/api/models/registries/registry.py b/lifemonitor/api/models/registries/registry.py
index f5f8ca12e..67f3ce665 100644
--- a/lifemonitor/api/models/registries/registry.py
+++ b/lifemonitor/api/models/registries/registry.py
@@ -227,6 +227,8 @@ def _requester(self, user, method: str, *args, **kwargs):
errors.append(str(e))
if response.status_code == 401 or response.status_code == 403:
raise lm_exceptions.NotAuthorizedException(details=response.content)
+ if response.status_code == 404:
+ raise lm_exceptions.ROCrateNotFoundException(details=response.content, resource=response.url)
raise lm_exceptions.LifeMonitorException(errors=[str(e) for e in errors])
def get_index(self, user: auth_models.User) -> List[RegistryWorkflow]:
diff --git a/lifemonitor/api/models/repositories/base.py b/lifemonitor/api/models/repositories/base.py
index 45f39105b..9d80f25a2 100644
--- a/lifemonitor/api/models/repositories/base.py
+++ b/lifemonitor/api/models/repositories/base.py
@@ -267,7 +267,7 @@ def generate_config(self, ignore_existing=False,
def write_zip(self, target_path: str):
if not self.metadata:
- raise IllegalStateException(detail="Missing RO Crate metadata")
+ raise IllegalStateException(detail="Missing RO-Crate metadata")
return self.metadata.write_zip(target_path)
def write(self, target_path: str, overwrite: bool = False) -> None:
diff --git a/lifemonitor/api/models/repositories/github.py b/lifemonitor/api/models/repositories/github.py
index 130a2de0e..0d7a15a62 100644
--- a/lifemonitor/api/models/repositories/github.py
+++ b/lifemonitor/api/models/repositories/github.py
@@ -382,9 +382,9 @@ def __del__(self):
def cleanup(self) -> None:
logger.debug("Repository cleanup")
if getattr(self, "_local_repo", None):
- local_repo_path = self.local_repo.local_path
+ local_repo_path = self._local_repo.local_path
del self._local_repo
- logger.debug("Removing temp folder %r of %r", self.local_path, self)
+ logger.debug("Removing temp folder %r of %r", self._local_path, self)
shutil.rmtree(local_repo_path, ignore_errors=True)
self._local_repo = None
diff --git a/lifemonitor/api/models/repositories/local.py b/lifemonitor/api/models/repositories/local.py
index 6a8e9d2a5..b594868ab 100644
--- a/lifemonitor/api/models/repositories/local.py
+++ b/lifemonitor/api/models/repositories/local.py
@@ -301,7 +301,8 @@ def __init__(self,
self._remote_repo_info = None
try:
self._remote_repo_info = RemoteGitRepoInfo.parse(self._git_repo.remotes.origin.url)
- except git.exc.GitCommandError as e:
+ except (git.exc.GitCommandError, AttributeError) as e:
+ logger.warning("Unable to parse remote repository info: %s", e)
if logger.isEnabledFor(logging.DEBUG):
logger.exception(e)
@@ -309,6 +310,14 @@ def __init__(self,
def main_branch(self) -> str:
return self._git_repo.active_branch.name
+ @property
+ def remotes(self) -> List[str]:
+ return [r.name for r in self._git_repo.remotes]
+
+ @property
+ def heads(self) -> List[str]:
+ return [h.name for h in self._git_repo.heads]
+
@property
def owner(self) -> str:
return super().owner or \
diff --git a/lifemonitor/api/models/workflows.py b/lifemonitor/api/models/workflows.py
index a27b189ac..7dc723088 100644
--- a/lifemonitor/api/models/workflows.py
+++ b/lifemonitor/api/models/workflows.py
@@ -22,12 +22,11 @@
import logging
from typing import List, Optional, Set, Union
+from uuid import UUID
from sqlalchemy.ext.hybrid import hybrid_property
from sqlalchemy.orm import aliased
-from sqlalchemy.orm.collections import (MappedCollection,
- attribute_mapped_collection,
- collection)
+from sqlalchemy.orm.collections import attribute_mapped_collection
from sqlalchemy.orm.exc import NoResultFound
from sqlalchemy.sql.expression import true
@@ -183,22 +182,6 @@ def get_hosted_workflows_by_uri(cls, hosting_service: HostingService, uri: str,
return query.all()
-class WorkflowVersionCollection(MappedCollection):
-
- def __init__(self) -> None:
- super().__init__(lambda wv: wv.workflow.uuid)
-
- @collection.internally_instrumented
- def __setitem__(self, key, value, _sa_initiator=None):
- current_value = self.get(key, set())
- current_value.add(value)
- super(WorkflowVersionCollection, self).__setitem__(key, current_value, _sa_initiator)
-
- @collection.internally_instrumented
- def __delitem__(self, key, _sa_initiator=None):
- super(WorkflowVersionCollection, self).__delitem__(key, _sa_initiator)
-
-
class WorkflowVersion(ROCrate):
id = db.Column(db.Integer, db.ForeignKey(ROCrate.id), primary_key=True)
submitter_id = db.Column(db.Integer, db.ForeignKey(User.id), nullable=True)
@@ -211,8 +194,7 @@ class WorkflowVersion(ROCrate):
test_suites = db.relationship("TestSuite", back_populates="workflow_version",
cascade="all, delete")
submitter = db.relationship("User", uselist=False,
- backref=db.backref("workflows", cascade="all, delete-orphan",
- collection_class=WorkflowVersionCollection))
+ backref=db.backref("workflow_versions", cascade="all, delete-orphan"))
__mapper_args__ = {
'polymorphic_identity': 'workflow_version'
@@ -439,3 +421,23 @@ def get_hosted_workflow_versions_by_uri(cls, hosting_service: HostingService, ur
.join(WorkflowVersion, WorkflowVersion.hosting_service_id == hosting_service.id)\
.filter(HostingService.uuid == lm_utils.uuid_param(hosting_service.uuid))\
.filter(WorkflowVersion.uri == uri).all()
+
+
+def __get_user_workflows_map__(user: User) -> dict[UUID, Set[WorkflowVersion]]:
+ '''
+ utility function to get the workflows of a user from the list of workflow versions
+ submitted by the user
+ '''
+ workflows = {}
+ for v in user.workflow_versions:
+ w_set = workflows.get(v.workflow.uuid, None)
+ if w_set is None:
+ workflows[v.workflow.uuid] = {v}
+ else:
+ w_set.add(v)
+
+ return workflows
+
+
+# augmentg the User class with the "workflow" property
+User.workflows = property(lambda self: __get_user_workflows_map__(self))
diff --git a/lifemonitor/auth/controllers.py b/lifemonitor/auth/controllers.py
index 45de399af..73862da6d 100644
--- a/lifemonitor/auth/controllers.py
+++ b/lifemonitor/auth/controllers.py
@@ -40,7 +40,7 @@
from .forms import (EmailForm, LoginForm, NotificationsForm, Oauth2ClientForm,
RegisterForm, SetPasswordForm)
from .models import db
-from .oauth2.client.services import (get_current_user_identity, get_providers,
+from .oauth2.client.services import (get_current_user_identity, get_providers, merge_users,
save_current_user_identity)
from .oauth2.server.services import server
from .services import (authorized, current_registry, current_user,
@@ -515,29 +515,46 @@ def disable_registry_sync():
@blueprint.route("/merge", methods=("GET", "POST"))
@login_required
def merge():
+ # get the username and provider from the request
username = request.args.get("username")
provider = request.args.get("provider")
- flash(f"Your {provider} identity is already linked to the username "
- f"{username} and cannot be merged to {current_user.username}",
- category="warning")
- return redirect(url_for('auth.profile'))
- # form = LoginForm(data={
- # "username": username,
- # "provider": provider})
- # if form.validate_on_submit():
- # user = form.get_user()
- # if user:
- # if user != current_user:
- # merge_users(current_user, user, request.args.get("provider"))
- # flash(
- # "User {username} has been merged into your account".format(
- # username=user.username
- # )
- # )
- # return redirect(url_for("auth.index"))
- # else:
- # form.username.errors.append("Cannot merge with yourself")
- # return render_template("auth/merge.j2", form=form)
+
+ # Uncomment to disable the merge feature
+ # flash(f"Your {p>rovider} identity is already linked to the username "
+ # f"{username} and cannot be merged to {current_user.username}",
+ # category="warning")
+ # return redirect(url_for('auth.profile'))
+
+ # Check the authenticity of the identity before merging
+ form = LoginForm(data={
+ "username": username,
+ "provider": provider})
+ if form.validate_on_submit():
+ user = form.get_user()
+ if user:
+ # check if the user is the same as the current user
+ if user == current_user:
+ flash("Cannot merge with yourself", category="warning")
+ form.username.errors.append("Cannot merge with yourself")
+ else:
+ # merge the users
+ resulting_user = merge_users(current_user, user, request.args.get("provider"))
+ logger.debug("User obtained by the merging process: %r", resulting_user)
+ logout_user()
+ # login the resulting user
+ login_user(resulting_user)
+ # redirect to the profile page with a flash message
+ flash(
+ "User {username} has been merged into your account".format(
+ username=resulting_user.username
+ ), category="success"
+ )
+ return profile()
+ # render the merge page
+ return render_template("auth/merge.j2", form=form, identity={
+ "username": username,
+ "provider": provider
+ })
@blueprint.route("/create_apikey", methods=("POST",))
diff --git a/lifemonitor/auth/forms.py b/lifemonitor/auth/forms.py
index 9a819526f..a59d8053d 100644
--- a/lifemonitor/auth/forms.py
+++ b/lifemonitor/auth/forms.py
@@ -59,7 +59,10 @@ def get_user(self):
if not user:
self.username.errors.append("Username not found")
return None
- if not user.verify_password(self.password.data):
+ if not user.has_password:
+ self.password.errors.append("The user has no password set")
+ return None
+ if not self.password.data or not user.verify_password(self.password.data):
self.password.errors.append("Invalid password")
return None
return user
diff --git a/lifemonitor/auth/models.py b/lifemonitor/auth/models.py
index ec4283812..a3a2d28c7 100644
--- a/lifemonitor/auth/models.py
+++ b/lifemonitor/auth/models.py
@@ -105,7 +105,7 @@ def get_authorization(self, resource: Resource):
@property
def current_identity(self):
from .services import current_registry, current_user
- if not current_user.is_anonymous:
+ if not current_user.is_anonymous and current_user.id == self.id:
return self.oauth_identity
if current_registry:
for p, i in self.oauth_identity.items():
@@ -130,6 +130,8 @@ def has_password(self):
return bool(self.password_hash)
def verify_password(self, password):
+ if not self.password_hash:
+ return False
return check_password_hash(self.password_hash, password)
def _generate_random_code(self, chars=string.ascii_uppercase + string.digits):
diff --git a/lifemonitor/auth/oauth2/client/services.py b/lifemonitor/auth/oauth2/client/services.py
index 7eaa66aeb..bc0869c90 100644
--- a/lifemonitor/auth/oauth2/client/services.py
+++ b/lifemonitor/auth/oauth2/client/services.py
@@ -23,6 +23,7 @@
import logging
from flask import current_app, session
+
from lifemonitor import exceptions
from lifemonitor.db import db, db_initialized
@@ -78,21 +79,86 @@ def config_oauth2_registry(app, providers=None):
logger.debug("OAuth2 registry configured!")
-def merge_users(merge_from: User, merge_into: User, provider: str):
+def merge_users(merge_from: User, merge_into: User, provider: str = None):
assert merge_into != merge_from
- logger.debug("Trying to merge %r, %r, %r", merge_into, merge_from, provider)
- for identity in list(merge_from.oauth_identity.values()):
- identity.user = merge_into
- db.session.add(identity)
- # TODO: Move all oauth clients to the new user
- for client in list(merge_from.clients):
- client.user = merge_into
- db.session.add(client)
- # TODO: Check for other links to move to the new user
- # e.g., tokens, workflows, tests, ....
- db.session.delete(merge_from)
- db.session.commit()
- return merge_into
+ try:
+ # start a new transaction
+ with db.session.no_autoflush:
+ logger.debug("Trying to merge user %r into %r (provider: %r)", merge_from, merge_into, provider)
+ # make a copy of the workflow versions submitted by the "merge_from" user
+ workflow_versions = list(merge_from.workflow_versions)
+ # update the submitter of the workflow versions
+ for v in workflow_versions:
+ v.submitter = merge_into
+ db.session.add(v)
+ # update suites submitted by the "merge_from" user
+ for s in v.test_suites:
+ if s.submitter == merge_from:
+ s.submitter = merge_into
+ db.session.add(s)
+ # update test instances submitted by the "merge_from" user
+ for i in s.test_instances:
+ if i.submitter == merge_from:
+ i.submitter = merge_into
+ db.session.add(i)
+
+ # update all the remaining permissions
+ for permission in list(merge_from.permissions):
+ permission.user = merge_into
+ db.session.add(permission)
+
+ # move all the authorizations granted to the "merge_from" user to the "merge_into" user
+ for auth in list(merge_from.authorizations):
+ auth.user = merge_into
+ db.session.add(auth)
+
+ # move all the notification of the user "merge_from" to the user "merge_into"
+ merge_into_notification_ids = [un.notification.id for un in merge_into.notifications]
+ for user_notification in list(merge_from.notifications):
+ if user_notification.notification.id not in merge_into_notification_ids:
+ user_notification.user = merge_into
+ db.session.add(user_notification)
+
+ # move all the subscriptions of the user "merge_from" to the user "merge_into"
+ for subscription in list(merge_from.subscriptions):
+ subscription.user = merge_into
+ db.session.add(subscription)
+
+ # move all the api keys of the user "merge_from" to the user "merge_into"
+ for api_key in list(merge_from.api_keys):
+ api_key.user = merge_into
+ db.session.add(api_key)
+
+ # move all the oauth identities of the user "merge_from" to the user "merge_into"
+ for identity in list(merge_from.oauth_identity):
+ identity.user = merge_into
+ db.session.add(identity)
+
+ # move all the clients of the user "merge_from" to the user "merge_into"
+ for client in list(merge_from.clients):
+ client.user = merge_into
+ db.session.add(client)
+
+ # remove the "merge_from" user
+ db.session.delete(merge_from)
+
+ # commit the changes
+ db.session.add(merge_into)
+ db.session.commit()
+
+ # remove the "merge_from" user
+ db.session.delete(merge_from)
+
+ # flush the changes
+ db.session.flush()
+ # remove the "merge_from" user
+ return merge_into
+ except Exception as e:
+ logger.error("Unable to merge users: %r", e)
+ if logger.isEnabledFor(logging.DEBUG):
+ logger.exception(e)
+ db.session.rollback()
+ raise exceptions.LifeMonitorException(title="Unable to merge users") from e
def save_current_user_identity(identity: OAuthIdentity):
diff --git a/lifemonitor/auth/templates/auth/merge.j2 b/lifemonitor/auth/templates/auth/merge.j2
index 5406e5e55..43708be94 100644
--- a/lifemonitor/auth/templates/auth/merge.j2
+++ b/lifemonitor/auth/templates/auth/merge.j2
@@ -1,15 +1,60 @@
{% extends 'base.j2' %}
{% import 'macros.j2' as macros %}
+
+{% block body_class %} login-page {% endblock %}
+{% block body_style %} height: auto; {% endblock %}
+
{% block body %}
- If you want to merge another account into this one, log in to that account here. That account must have a password set.
-