DEV-1396: add gdcdatamodel2 dependency and bump dictionary

dev-requirements.txt

@@ -1,5 +1,5 @@
 #
-# This file is autogenerated by pip-compile with python 3.6
+# This file is autogenerated by pip-compile
 # To update, run:
 #
 #    pip-compile dev-requirements.in
@@ -14,20 +14,20 @@
     #   indexd
 -e git+ssh://git@github.com/NCI-GDC/indexd.git@2.9.0-rc.1#egg=indexd
     # via -r dev-requirements.in
-attrs==20.3.0
+attrs==22.2.0
     # via
     #   -c requirements.txt
     #   jsonschema
     #   pytest
-cdislogging==1.0.0
+cdislogging==1.1.1
     # via
     #   -c requirements.txt
     #   indexd
-certifi==2020.12.5
+certifi==2022.12.7
     # via
     #   -c requirements.txt
     #   requests
-chardet==4.0.0
+charset-normalizer==2.0.12
     # via
     #   -c requirements.txt
     #   requests
@@ -41,15 +41,15 @@ decorator==4.4.2
     #   jsonpath-rw
 flask==1.1.2
     # via indexd
-future==0.18.2
+future==0.18.3
     # via
     #   -c requirements.txt
     #   indexd
-idna==2.10
+idna==3.4
     # via
     #   -c requirements.txt
     #   requests
-importlib-metadata==2.1.1
+importlib-metadata==4.8.3
     # via
     #   -c requirements.txt
     #   jsonschema
@@ -87,49 +87,54 @@ py==1.10.0
     # via pytest
 pyparsing==2.4.7
     # via packaging
-pyrsistent==0.17.3
+pyrsistent==0.16.1
     # via
     #   -c requirements.txt
     #   jsonschema
+pytest-cov==2.10.1
+    # via -r dev-requirements.in
 pytest==7.0.1
     # via
     #   -r dev-requirements.in
     #   pytest-cov
-pytest-cov==2.10.1
-    # via -r dev-requirements.in
 python-dateutil==2.8.0
     # via -r dev-requirements.in
-requests==2.25.1
+requests==2.27.1
     # via
     #   -c requirements.txt
     #   doiclient
     #   dosclient
-six==1.15.0
+six==1.16.0
     # via
     #   -c requirements.txt
     #   jsonpath-rw
     #   jsonschema
     #   mock
+    #   pyrsistent
     #   python-dateutil
     #   sqlalchemy-utils
+sqlalchemy-utils==0.36.3
+    # via indexd
 sqlalchemy==1.3.3
     # via
     #   -c requirements.txt
     #   indexd
     #   sqlalchemy-utils
-sqlalchemy-utils==0.36.3
-    # via indexd
 tomli==1.2.3
     # via pytest
-urllib3==1.26.2
+typing-extensions==4.1.1
+    # via
+    #   -c requirements.txt
+    #   importlib-metadata
+urllib3==1.26.14
     # via
     #   -c requirements.txt
     #   requests
 werkzeug==0.16.1
     # via
     #   flask
     #   indexd
-zipp==1.2.0
+zipp==3.6.0
     # via
     #   -c requirements.txt
     #   importlib-metadata

esbuild/__init__.py

@@ -0,0 +1,3 @@
+import os
+
+os.environ["GDCDICTIONARY_NAMESPACE"] = "gdc2"

esbuild/graph/common/mappings.py

@@ -3,7 +3,7 @@
 Common definitions for building GDC Elasticsearch mappings
 
 """
-
+import typing as t
 from copy import deepcopy
 
 from addict import Dict
@@ -313,17 +313,17 @@ def _get_header(cls, source):
         return header
 
     @classmethod
-    def get_base_properties(cls, source, include_id=True):
+    def get_base_properties(cls, node_label: str, include_id=True):
         # Get properties from schema
-        node_type = Node.get_subclass(source)
-        assert node_type, f"No model for {source}"
+        node_type = Node.get_subclass(node_label)
+        assert node_type, f"No model for {node_label}"
 
-        properties = dict(node_type.get_pg_properties())
+        properties: t.Dict[str, t.Tuple[t.Type]] = dict(node_type.get_pg_properties())
         doc = Dict()
 
         if include_id:
             # Add id to document
-            id_name = f"{source}_id"
+            id_name = f"{node_label}_id"
             doc[id_name] = STRING
 
         if properties.pop("submitter_id", None):
@@ -335,12 +335,12 @@ def get_base_properties(cls, source, include_id=True):
             # assign the type
             doc[field] = {"type": _type}
 
-        if source == "project":
+        if node_label == "project":
             # Remove some fields from project document
             for key in cls.project_keys_to_hide:
                 doc.pop(key)
 
-        if source != "project":
+        if node_label != "project":
             doc.pop("project_id", None)
             doc.pop("batch_id", None)
             doc.pop("file_state", None)

requirements.txt

@@ -1,105 +1,110 @@
 #
-# This file is autogenerated by pip-compile with python 3.6
+# This file is autogenerated by pip-compile
 # To update, run:
 #
 #    pip-compile
 #
 addict==2.1.3
     # via esbuild (setup.py)
-attrs==20.3.0
+attrs==22.2.0
     # via jsonschema
 backports.tempfile==1.0
     # via normalizer
 backports.weakref==1.0.post1
     # via backports.tempfile
-cdislogging==1.0.0
+cdislogging==1.1.1
     # via esbuild (setup.py)
-certifi==2020.12.5
+certifi==2022.12.7
     # via
     #   elasticsearch
     #   requests
-chardet==4.0.0
+charset-normalizer==2.0.12
     # via requests
-datadog==0.39.0
+datadog==0.43.0
     # via esbuild (setup.py)
 decorator==4.4.2
     # via
-    #   datadog
+    #   gdcdatamodel
     #   networkx
 deepdiff==4.3.2
     # via esbuild (setup.py)
 dictdiffer==0.8.1
     # via esbuild (setup.py)
-elasticsearch==7.10.1
+elasticsearch==7.17.8
     # via
     #   esbuild (setup.py)
     #   gdcmodels
-future==0.18.2
+future==0.18.3
     # via esbuild (setup.py)
-gdc-ng-models @ git+ssh://git@github.com/NCI-GDC/gdc-ng-models.git@1.5.2
+git+ssh://git@github.com/NCI-GDC/gdc-ng-models.git@1.5.2#egg=gdc_ng_models
     # via
     #   esbuild (setup.py)
     #   gdcdatamodel
-gdcdatamodel @ git+ssh://git@github.com/NCI-GDC/gdcdatamodel.git@3.4.0
+git+ssh://git@github.com/NCI-GDC/gdcdatamodel2.git@2.4.2#egg=gdcdatamodel2
+    # via esbuild (setup.py)
+git+ssh://git@github.com/NCI-GDC/gdcdatamodel.git@3.6.5#egg=gdcdatamodel
     # via esbuild (setup.py)
-gdcdictionary @ git+ssh://git@github.com/NCI-GDC/gdcdictionary.git@2.4.0
+git+ssh://git@github.com/NCI-GDC/gdcdictionary.git@2.4.2#egg=gdcdictionary
     # via
     #   esbuild (setup.py)
     #   gdcdatamodel
-gdcmodels @ git+ssh://git@github.com/NCI-GDC/gdc-models.git@2.8.1-rc.2
+git+ssh://git@github.com/NCI-GDC/gdc-models.git@2.8.1-rc.2#egg=gdcmodels
     # via
     #   esbuild (setup.py)
     #   normalizer
-gitdb==4.0.5
-    # via gitdb2
 gitdb2==4.0.2
     # via gitpython
+gitdb==4.0.9
+    # via gitdb2
 gitpython==2.1.11
     # via normalizer
-graphviz==0.4.10
+graphviz==0.16
     # via gdcdatamodel
-idna==2.10
+idna==3.4
     # via requests
-importlib-metadata==2.1.1
+importlib-metadata==4.8.3
     # via jsonschema
-indexclient @ git+ssh://git@github.com/NCI-GDC/indexclient.git@2.1.0-rc.4
+git+ssh://git@github.com/NCI-GDC/indexclient.git@2.1.0-rc.4#egg=indexclient
     # via esbuild (setup.py)
 jsonschema==3.2.0
     # via
     #   gdcdatamodel
     #   gdcdictionary
 networkx==2.4
     # via esbuild (setup.py)
-normalizer @ git+ssh://git@github.com/NCI-GDC/normalizer.git@2.0.4
+git+ssh://git@github.com/NCI-GDC/normalizer.git@2.0.4#egg=normalizer
     # via esbuild (setup.py)
 ordered-set==4.0.2
     # via deepdiff
 pika==1.1.0
     # via queueclient
-progressbar2==3.53.1
+progressbar2==3.55.0
     # via esbuild (setup.py)
-psqlgraph @ git+ssh://git@github.com/NCI-GDC/psqlgraph.git@3.3.0
+git+ssh://git@github.com/NCI-GDC/psqlgraph.git@3.4.2#egg=psqlgraph
     # via
     #   esbuild (setup.py)
     #   gdcdatamodel
+    #   gdcdatamodel2
 psycopg2==2.8.6
     # via psqlgraph
-pyrsistent==0.17.3
-    # via jsonschema
+pyrsistent==0.16.1
+    # via
+    #   gdcdatamodel
+    #   jsonschema
 python-dotenv==0.10.5
     # via esbuild (setup.py)
-python-utils==2.4.0
+python-utils==3.4.5
     # via progressbar2
-pytz==2020.4
+pytz==2020.5
     # via gdcdatamodel
-pyyaml==5.3.1
+pyyaml==5.4.1
     # via
     #   gdcdictionary
     #   gdcmodels
     #   normalizer
-queueclient @ git+ssh://git@github.com/NCI-GDC/queueclient.git@1.2.0
+git+ssh://git@github.com/NCI-GDC/queueclient.git@1.2.0#egg=queueclient
     # via esbuild (setup.py)
-requests==2.25.1
+requests==2.27.1
     # via
     #   datadog
     #   esbuild (setup.py)
@@ -109,26 +114,27 @@ rstr==2.2.6
     # via psqlgraph
 simplejson==3.16.0
     # via queueclient
-six==1.15.0
+six==1.16.0
     # via
     #   gdcmodels
     #   jsonschema
     #   progressbar2
-    #   psqlgraph
-    #   python-utils
-smmap==3.0.4
+    #   pyrsistent
+smmap==5.0.0
     # via gitdb
 sqlalchemy==1.3.3
     # via
     #   esbuild (setup.py)
     #   psqlgraph
-urllib3==1.26.2
+typing-extensions==4.1.1
+    # via importlib-metadata
+urllib3==1.26.14
     # via
     #   elasticsearch
     #   requests
 xlocal==0.5
     # via psqlgraph
-zipp==1.2.0
+zipp==3.6.0
     # via importlib-metadata
 
 # The following packages are considered to be unsafe in a requirements file:

setup.py

@@ -23,9 +23,10 @@
         "python-dotenv~=0.10.3",
         "requests~=2.7",
         "SQLAlchemy==1.3.3",
-        "psqlgraph @ git+ssh://git@github.com/NCI-GDC/psqlgraph.git@3.3.0#egg=psqlgraph",
-        "gdcdictionary @ git+ssh://git@github.com/NCI-GDC/gdcdictionary.git@2.4.0#egg=gdcdictionary",
-        "gdcdatamodel @ git+ssh://git@github.com/NCI-GDC/gdcdatamodel.git@3.4.0#egg=gdcdatamodel",
+        "psqlgraph @ git+ssh://git@github.com/NCI-GDC/psqlgraph.git@3.4.2#egg=psqlgraph",
+        "gdcdictionary @ git+ssh://git@github.com/NCI-GDC/gdcdictionary.git@2.4.2#egg=gdcdictionary",
+        "gdcdatamodel @ git+ssh://git@github.com/NCI-GDC/gdcdatamodel.git@3.6.5#egg=gdcdatamodel",
+        "gdcdatamodel2 @ git+ssh://git@github.com/NCI-GDC/gdcdatamodel2.git@2.4.2#egg=gdcdatamodel2",
         "gdc_ng_models @ git+ssh://git@github.com/NCI-GDC/gdc-ng-models.git@1.5.2#egg=gdc_ng_models",
         "indexclient @ git+ssh://git@github.com/NCI-GDC/indexclient.git@2.1.0-rc.4#egg=indexclient",
         "queueclient @ git+ssh://git@github.com/NCI-GDC/queueclient.git@1.2.0#egg=queueclient",

tests/__init__.py

@@ -0,0 +1,3 @@
+import os
+
+os.environ["GDCDICTIONARY_NAMESPACE"] = "gdc2"