Unverified Commit f3ff4344 authored by John Davis's avatar John Davis Committed by GitHub
Browse files

Merge pull request #18379 from jdavcs/241_fix_usernames_in_db 

[24.1] Fix empty usernames in database + bug in username generation
parents c60f03cc 51309daf

lib/galaxy/managers/users.py

+30 −14
Original line number Diff line number Diff line
@@ -197,7 +197,7 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin): 
        private_role = self.app.security_agent.get_private_user_role(user)

        if private_role is None:

            raise exceptions.InconsistentDatabase(

                "User '%s' private role is missing while attempting to purge deleted user." % user.email

                f"User {user.email} private role is missing while attempting to purge deleted user."

            )

        # Delete History

        for active_history in user.active_histories:
@@ -664,23 +664,11 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin): 
                    self.app.security_agent.user_set_default_permissions(user)

                    self.app.security_agent.user_set_default_permissions(user, history=True, dataset=True)

        elif user is None:

            username = remote_user_email.split("@", 1)[0].lower()

            random.seed()

            user = self.app.model.User(email=remote_user_email)

            user.set_random_password(length=12)

            user.external = True

            # Replace invalid characters in the username

            for char in [x for x in username if x not in f"{string.ascii_lowercase + string.digits}-."]:

                username = username.replace(char, "-")

            # Find a unique username - user can change it later

            stmt = select(self.app.model.User).filter_by(username=username).limit(1)

            if self.session().scalars(stmt).first():

                i = 1

                stmt = select(self.app.model.User).filter_by(username=f"{username}-{str(i)}").limit(1)

                while self.session().scalars(stmt).first():

                    i += 1

                username += f"-{str(i)}"

            user.username = username

            user.username = username_from_email(self.session(), remote_user_email, self.app.model.User)

            self.session().add(user)

            with transaction(self.session()):

                self.session().commit()
@@ -896,3 +884,31 @@ def get_user_by_email(session, email: str, model_class=User, case_sensitive=True 
def get_user_by_username(session, username: str, model_class=User):

    stmt = select(model_class).filter(model_class.username == username).limit(1)

    return session.scalars(stmt).first()





def username_from_email(session, email, model_class=User):

    """Get next available username generated based on email"""

    username = email.split("@", 1)[0].lower()

    username = filter_out_invalid_username_characters(username)

    if username_exists(session, username, model_class):

        username = generate_next_available_username(session, username, model_class)

    return username





def filter_out_invalid_username_characters(username):

    """Replace invalid characters in username"""

    for char in [x for x in username if x not in f"{string.ascii_lowercase + string.digits}-."]:

        username = username.replace(char, "-")

    return username





def username_exists(session, username: str, model_class=User):

    return bool(get_user_by_username(session, username, model_class))





def generate_next_available_username(session, username, model_class=User):

    """Generate unique username; user can change it later"""

    i = 1

    while session.execute(select(model_class).where(model_class.username == f"{username}-{i}")).first():

        i += 1

    return f"{username}-{i}"

lib/galaxy/model/migrations/alembic/versions_gxy/c63848676caf_update_username_column_schema_and_data.py

0 → 100644
+89 −0
Original line number Diff line number Diff line 
"""Update username column schema and data



Revision ID: c63848676caf

Revises: c14a3c93d66b

Create Date: 2024-06-11 13:41:36.411803



"""



import string



from alembic import op

from sqlalchemy import (

    or_,

    select,

    update,

)



from galaxy.model import User

from galaxy.model.migrations.util import (

    alter_column,

    transaction,

)



# revision identifiers, used by Alembic.

revision = "c63848676caf"

down_revision = "c14a3c93d66b"

branch_labels = None

depends_on = None



table_name = "galaxy_user"

column_name = "username"





def upgrade():

    with transaction():

        _generate_missing_usernames()

        alter_column(table_name, column_name, nullable=False)





def downgrade():

    with transaction():

        # The data migration is one-way: we can change back the database schema,

        # but we can't remove the generated username values.

        alter_column(table_name, column_name, nullable=True)





def _generate_missing_usernames():

    stmt = select(User.id, User.email).where(or_(User.username.is_(None), User.username == ""))

    connection = op.get_bind()

    users = connection.execute(stmt).all()

    for id, email in users:

        new_username = username_from_email(connection, email)

        update_stmt = update(User).where(User.id == id).values(username=new_username)

        connection.execute(update_stmt)





# The code below is a near-duplicate of similar code in managers.users. The duplication is

# intentional: we want to preserve this logic in the migration script. The only differences are:

# (1) this code uses a Connection instead of a Session;

# (2) the username_exists function inlines the Select statement from managers.users::get_user_by_username.





def username_from_email(connection, email, model_class=User):

    # This function is also called from database revision scripts, which do not provide a session.

    username = email.split("@", 1)[0].lower()

    username = filter_out_invalid_username_characters(username)

    if username_exists(connection, username, model_class):

        username = generate_next_available_username(connection, username, model_class)

    return username





def filter_out_invalid_username_characters(username):

    """Replace invalid characters in username"""

    for char in [x for x in username if x not in f"{string.ascii_lowercase + string.digits}-."]:

        username = username.replace(char, "-")

    return username





def username_exists(connection, username: str, model_class=User):

    stmt = select(model_class).filter(model_class.username == username).limit(1)

    return bool(connection.execute(stmt).first())





def generate_next_available_username(connection, username, model_class=User):

    """Generate unique username; user can change it later"""

    i = 1

    while connection.execute(select(model_class).where(model_class.username == f"{username}-{i}")).first():

        i += 1

    return f"{username}-{i}"

lib/galaxy/model/migrations/alembic/versions_gxy/ddbdbc40bdc1_add_workflow_comment_table.py

+1 −0
Original line number Diff line number Diff line 
"""add workflow_comment table



Revision ID: ddbdbc40bdc1

Revises: 92fb564c7095

Create Date: 2023-08-14 13:41:59.442243

lib/galaxy/model/migrations/dbscript.py

+2 −2
Original line number Diff line number Diff line
@@ -42,8 +42,8 @@ REVISION_TAGS = { 
    "23.2": "8a19186a6ee7",

    "release_24.0": "55f02fd8ab6c",

    "24.0": "55f02fd8ab6c",

    "release_24.1": "c14a3c93d66b",

    "24.1": "c14a3c93d66b",

    "release_24.1": "c63848676caf",

    "24.1": "c63848676caf",

}