Merge pull request #30 from gyorilab/fix-cors

Fix cors, docker build and requirements

docker/Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:latest
+FROM ubuntu:20.04
 
 ENV DIRPATH /sw
 WORKDIR $DIRPATH
@@ -20,7 +20,6 @@ RUN git clone https://github.com/indralab/indra_network_search.git && \
     python -m indra.ontology.bio build
 
 ADD indranet_dir_graph.pkl $NETWORK_CACHE
-ADD indranet_sign_edge_graph.pkl $NETWORK_CACHE
 ADD indranet_sign_node_graph.pkl $NETWORK_CACHE
 
 ENV PYTHONPATH /sw/depmap_analysis:/sw/indra_network_search

indra_network_search/data_models/rest_models.py

@@ -13,7 +13,6 @@
 
 __all__ = ["Health", "ServerStatus"]
 
-
 STR_STATUS = Literal["booting", "available"]
 
 
@@ -26,9 +25,9 @@ class Health(BaseModel):
 class ServerStatus(BaseModel):
     """Status with more detail than health"""
 
-    unsigned_nodes: Optional[int] = Field(None, description="Number of " "unsigned nodes " "in the graph")
-    signed_nodes: Optional[int] = Field(None, description="Number of signed " "nodes in the graph")
-    unsigned_edges: Optional[int] = Field(None, description="Number of " "unsigned edges " "in the graph")
-    signed_edges: Optional[int] = Field(None, description="Number of signed " "edges in the graph")
-    graph_date: Optional[date] = Field(None, description="Date of the " "graph creation from the database")
+    unsigned_nodes: Optional[int] = Field(None, description="Number of unsigned nodes in the graph")
+    signed_nodes: Optional[int] = Field(None, description="Number of signed nodes in the graph")
+    unsigned_edges: Optional[int] = Field(None, description="Number of unsigned edges in the graph")
+    signed_edges: Optional[int] = Field(None, description="Number of signed edges in the graph")
+    graph_date: Optional[date] = Field(None, description="Date of the graph creation from the database")
     status: STR_STATUS = Field(..., description="Status of the server")

indra_network_search/rest_api.py

@@ -12,6 +12,7 @@
 from fastapi import Query as RestQuery
 from indra.databases import get_identifiers_url
 from pydantic import ValidationError
+from fastapi.middleware.cors import CORSMiddleware
 from tqdm import tqdm
 
 from indra_network_search.autocomplete import NodesTrie, Prefixes
@@ -44,6 +45,15 @@
     version=VERSION,
 )
 
+# Add cors middleware for https://discovery.indra.bio
+app.add_middleware(
+    CORSMiddleware,
+    allow_origins=["https://discovery.indra.bio"],
+    allow_credentials=True,
+    allow_methods=["*"],
+    allow_headers=["*"],
+)
+
 DEBUG = environ.get("API_DEBUG") == "1"
 USE_CACHE = environ.get("USE_CACHE") == "1"
 HEALTH = Health(status="booting")

setup.cfg

@@ -5,7 +5,7 @@ description = INDRA Network Search
 long_description = file: README.md
 long_description_content_type = text/markdown
 author = Klas Karis
-author_email = [email protected].edu
+author_email = k.karis@northeastern.edu
 url = https://github.com/indralab/indra_network_search
 download_url = https://github.com/indralab/indra_network_search/releases
 license_file = LICENSE
@@ -25,8 +25,8 @@ classifiers =
 install_requires =
     indra @ git+https://github.com/sorgerlab/indra.git
     indra_db @ git+https://github.com/indralab/indra_db.git
-    pydantic
-    fastapi
+    fastapi<0.100.0
+    pydantic!=1.8,!=1.8.1,<2.0.0,>=1.7.4
     networkx
     boto3
     requests