Added some fixes for peregrine

Author: emalinowski

bin/setup_notifications.py

@@ -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):

bin/setup_psqlgraph.py

@@ -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
 
 

bin/setup_transactionlogs.py

@@ -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):

deployment/wsgi/wsgi.py

@@ -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

peregrine/api.py

@@ -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)

peregrine/models.py

@@ -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
 """
 

peregrine/resources/submission/graphql/node.py

@@ -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
 """
 
@@ -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)).
 
     """
 

poetry.lock

@@ -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"