Skip to content

Commit

Permalink
Added some fixes for peregrine
Browse files Browse the repository at this point in the history
  • Loading branch information
emalinowski committed Sep 6, 2024
1 parent ffed8dd commit 5fe3a8c
Show file tree
Hide file tree
Showing 9 changed files with 13 additions and 13 deletions.
2 changes: 1 addition & 1 deletion bin/setup_notifications.py
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
"""

from sqlalchemy import create_engine
from gdcdatamodel.models.notifications import Base
from gen3datamodel.models.notifications import Base


def setup(host, user, password, database):
Expand Down
2 changes: 1 addition & 1 deletion bin/setup_psqlgraph.py
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
from sqlalchemy import create_engine
import logging

from gdcdatamodel.models import *
from gen3datamodel.models import *
from psqlgraph import create_all, Node, Edge


Expand Down
2 changes: 1 addition & 1 deletion bin/setup_transactionlogs.py
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@

import argparse
from sqlalchemy import create_engine
from gdcdatamodel.models.submission import Base
from gen3datamodel.models.submission import Base


def setup(host, user, password, database):
Expand Down
2 changes: 1 addition & 1 deletion deployment/wsgi/wsgi.py
Original file line number Diff line number Diff line change
Expand Up @@ -2,4 +2,4 @@

sys.path.append("/var/www/peregrine/")
sys.path.append("/peregrine/")
from peregrine.api import app as application
from wsgi import app as application
4 changes: 2 additions & 2 deletions peregrine/api.py
Original file line number Diff line number Diff line change
Expand Up @@ -103,8 +103,8 @@ def dictionary_init(app):

d = gdcdictionary.gdcdictionary
dictionary.init(d)
from gdcdatamodel import models as md
from gdcdatamodel import validators as vd
from gen3datamodel import models as md
from gen3datamodel import validators as vd

datamodelutils.validators.init(vd)
datamodelutils.models.init(md)
Expand Down
6 changes: 3 additions & 3 deletions peregrine/models.py
Original file line number Diff line number Diff line change
@@ -1,19 +1,19 @@
"""
This module generalizes the data model used by the peregrine blueprint, and
must be initialized using another ``models`` module to set the attributes of
this module. For example, using ``gdcdatamodel.models`` as the models:
this module. For example, using ``gen3datamodel.models`` as the models:
.. code-block:: python
peregrine.models.init(gdcdatamodel.models)
peregrine.models.init(gen3datamodel.models)
Then this module can be imported elsewhere in ``peregrine``:
.. code-block:: python
from peregrine import models
# This is effectively an alias of ``gdcdatamodel.models.Project``.
# This is effectively an alias of ``gen3datamodel.models.Project``.
models.Project
"""

Expand Down
4 changes: 2 additions & 2 deletions peregrine/resources/submission/graphql/node.py
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
peregrine.resources.submission.graphql.node
----------------------------------
Implements GraphQL queries for each gdcdatamodel.model node type
Implements GraphQL queries for each gen3datamodel.model node type
using the Graphene GraphQL library
"""

Expand Down Expand Up @@ -424,7 +424,7 @@ def resolve_node(self, info, **args):
:returns:
A list of graphene object classes (e.g. a Case query object
(not a gdcdatamodel Case)).
(not a gen3datamodel Case)).
"""

Expand Down
2 changes: 1 addition & 1 deletion poetry.lock

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

2 changes: 1 addition & 1 deletion pyproject.toml
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ include = [
[tool.poetry.dependencies]
python = ">=3.9,<3.10"
authutils = {git = "https://git@github.com/uc-cdis/authutils.git", branch = "feat/jq-testing"}
gen3datamodel = {git = "https://git@github.com/uc-cdis/gdcdatamodel.git", branch = "fix/fips-hashing"}
gen3datamodel = {git = "https://git@github.com/uc-cdis/gen3datamodel.git", branch = "fix/fips-hashing"}
datamodelutils = ">=1.0"
defusedxml = ">=0.5"
dictionaryutils = ">=3.4.10"
Expand Down

0 comments on commit 5fe3a8c

Please sign in to comment.