Merge pull request #7 from ecell/fix

[v1.2.0] Return API list

Author: LittleCoinCoin

README.md

@@ -37,8 +37,8 @@ Call those commands from the root of this repository
 ```
 wget http://bigg.ucsd.edu/static/namespace/bigg_models_reactions.txt -OutFile ./models/bigg_models_reactions.txt
 wget http://bigg.ucsd.edu/static/namespace/bigg_models_metabolites.txt -OutFile ./models/bigg_models_metabolites.txt
-wget https://www.metanetx.org/cgi-bin/mnxget/mnxref/reac_prop.tsv -OutFile ./models/reac_prop.txt
-wget https://github.com/ecell/id2id/releases/download/test2/id2id.tsv -OutFile ./models/id2id.txt
+wget https://www.metanetx.org/cgi-bin/mnxget/mnxref/reac_prop.tsv -OutFile ./models/reac_prop.tsv
+wget https://github.com/ecell/id2id/releases/download/test2/id2id.tsv -OutFile ./models/id2id.tsv
 ```
 
 *Note: Currently, we are indeed downloading the content of the database and store them locally. This is to avoid the hassle of handling the query API of each databases and to focus on handling the requests between other systems and Kosmogora (as it is the case with [ECellDive](https://github.com/ecell/ECell_Dive))*

api_definition.py

@@ -0,0 +1,109 @@
+
+schema = {
+    "list_models": {
+        "httpMethod": "GET",
+        "request": {
+            "pathParameters" : [],
+            "queryParameters": [],
+        },
+        "responce" : {
+            "key": "models", "value_type": "str",
+        },
+    },
+    "list_views" : {
+        "httpMethod": "GET",
+        "request": {
+            "pathParameters" : [],
+            "queryParameters": [
+                {"id": "model_name", "type": "str" }
+            ]
+        },
+        "responce" : {
+            "key": "views", 
+            "value_type": "str",
+        },
+    },
+    "list_user_model" : {
+        "httpMethod": "GET",
+        "request": {
+            "pathParameters" : [],
+            "queryParameters": [
+                {"id": "base_model_name", "value_type": "str" }
+            ]
+        },
+        "response": {
+            "key": "user_models",
+            "value_type" : "str"
+        }
+    },
+    "list_reaction_id" : {
+        "httpMethod": "GET",
+        "request": {
+            "pathParameters" : [],
+            "queryParameters": [
+                {"id": "model_name", "type": "str" }
+            ]
+        },
+        "response": "list[str]",
+    },
+
+    "solve": {
+        "httpMethod": "GET",
+        "request" : {
+            "pathParameters" : [
+                {"id": "modelName", "type" : "str"}
+            ],
+            "queryParameters": [
+                {"id": "command", "type" : "list[str]"},
+                {"id": "view_name", "type" : "str"},
+            ]
+        }, 
+        "responce": {
+            "key" : "fluxes",
+            "value_type": "list[list[str, float]]",
+        }
+    },
+
+    "save": {
+        "httpMethod": "GET",
+        "request" : {
+            "pathParameters" : [
+                {"id": "model_name", "type" : "str"},
+                {"id": "author", "type" : "str"},
+                {"id": "new_model_name", "type" : "str"},
+            ],
+            "queryParameters": [
+                {"id": "command", "type" : "list[str]"},
+                {"id": "view_name", "type" : "str"},
+            ]
+        }, 
+        "responce": {
+            "key" : "new_model_name",
+            "value_type": "str",
+        }
+    },
+
+    "reaction_information" : {
+        "httpMethod": "GET",
+        "request" : {
+            "pathParameters" : [
+                {"id" : "model_name", "type" : "str"},
+                {"id" : "reaction_id", "type" : "str"}
+            ],
+            "queryParameters" : [
+                {"id" : "db_src", "type" : "str"},
+                {"id" : "view_name", "type" : "str"},
+            ]
+        },
+        "response": {
+            "key" : "reaction_information",
+            "value" : {
+                "ID" : "reaction_id" ,
+                "NAME" : "reaction_name" ,
+                "REACTION" : "reaction_expression" ,
+                "MODEL_LIST" : "model_list" ,
+            }
+        }
+    }
+}
+

app.py

@@ -3,6 +3,8 @@
 from model_handler import ModelHandler
 from typing import Tuple, List, Union
 import os
+from fastapi.encoders import jsonable_encoder
+from fastapi.responses import JSONResponse
 
 class XMLResponse(Response):
     media_type = "application/xml"
@@ -365,6 +367,37 @@ def get_reaction_info(model_name: str, reaction_id: str,
         raise HTTPException(status_code=404, detail="Reaction {} not found at {}".format(reaction_id, db_src))
 
 
+@app.get("/modules")
+def get_module_information():
+    return {"modules": ["FBA"]}
 
-
-
+@app.get("/apis/")
+def get_api_information(api_id: str = Query(None)):
+    import api_definition
+    import json
+    if api_id == None:
+        api_list = [
+            "list_models", 
+            "user_model_tree", 
+            "list_views", 
+            "open_sbml", 
+            "open_sbml", 
+            "get_model_property", 
+            "open_view",
+            "get_view_property",
+            "list_user_model",
+            "open_user_model",
+            "list_reaction_id",
+            "solve",
+            "save",
+            "metabolite_information",
+            "reaction_information",
+        ]
+        s = {"apis" : api_list} 
+        return JSONResponse(content = s)
+    else:
+        if api_id in api_definition.schema:
+            s = json.dumps( api_definition.schema[api_id] )
+            return JSONResponse(content = s)
+        else:
+            return None