Merge pull request #249 from sennetconsortium/tjmadonna/add-vitessce-…

…config

Tjmadonna/add vitessce config

src/app.py

@@ -20,6 +20,7 @@
 from routes.validation import validation_blueprint
 from routes.file import file_blueprint
 from routes.assayclassifier import assayclassifier_blueprint
+from routes.vitessce import vitessce_blueprint
 
 # Local Modules
 from lib.file_upload_helper import UploadFileHelper
@@ -43,6 +44,7 @@
 app.register_blueprint(validation_blueprint)
 app.register_blueprint(file_blueprint)
 app.register_blueprint(assayclassifier_blueprint)
+app.register_blueprint(vitessce_blueprint)
 
 # Suppress InsecureRequestWarning warning when requesting status on https with ssl cert verify disabled
 requests.packages.urllib3.disable_warnings(category=InsecureRequestWarning)

src/routes/assayclassifier/rule_chain.py → src/lib/rule_chain.py

@@ -1,7 +1,10 @@
 import json
 import logging
 from pathlib import Path
+from sys import stdout
+import urllib.request
 
+from flask import current_app
 from hubmap_commons.schema_tools import check_json_matches_schema
 from rule_engine import Rule, EngineError, Context
 import yaml
@@ -12,6 +15,34 @@
 SCHEMA_BASE_URI = "http://schemata.hubmapconsortium.org/"
 
 
+rule_chain = None
+
+
+def initialize_rule_chain():
+    global rule_chain
+    rule_src_uri = current_app.config["RULE_CHAIN_URI"]
+    try:
+        json_rules = urllib.request.urlopen(rule_src_uri)
+    except json.decoder.JSONDecodeError as excp:
+        raise RuleSyntaxException(excp) from excp
+    rule_chain = RuleLoader(json_rules).load()
+    print("RULE CHAIN FOLLOWS")
+    rule_chain.dump(stdout)
+    print("RULE CHAIN ABOVE")
+
+
+def calculate_assay_info(metadata: dict) -> dict:
+    if not rule_chain:
+        initialize_rule_chain()
+    for key, value in metadata.items():
+        if type(value) is str:
+            if value.isdigit():
+                metadata[key] = int(value)
+    rslt = rule_chain.apply(metadata)
+    # TODO: check that rslt has the expected parts
+    return rslt
+
+
 class NoMatchException(Exception):
     pass
 

src/requirements.txt

@@ -4,7 +4,7 @@ hubmap-sdk==1.0.4
 Werkzeug==2.3.7
 
 # The commons package requires requests>=2.22.0
-requests==2.25.1
+requests==2.27.1
 
 # Use the published package from PyPI as default
 # Use the branch name of commons from github for testing new changes made in commons from different branch
@@ -16,5 +16,8 @@ atlas-consortia-commons==1.0.5
 # For assay type rules
 rule_engine==4.1.0
 
+# For vitessce config generation
+https://github.com/hubmapconsortium/portal-visualization/archive/refs/tags/0.1.0.zip
+
 # Testing
 pytest==7.3.1

src/routes/assayclassifier/__init__.py

@@ -1,7 +1,4 @@
-import json
 import logging
-from sys import stdout
-import urllib.request
 
 from flask import Blueprint, request, Response, current_app, jsonify
 from hubmap_commons.exceptions import HTTPException
@@ -12,46 +9,19 @@
 
 from lib.decorators import require_json
 from lib.exceptions import ResponseException
-from .rule_chain import (
+from lib.rule_chain import (
     NoMatchException,
-    RuleLoader,
     RuleLogicException,
     RuleSyntaxException,
+    initialize_rule_chain,
+    calculate_assay_info,
 )
 
 assayclassifier_blueprint = Blueprint("assayclassifier", __name__)
 
 logger: logging.Logger = logging.getLogger(__name__)
 
 
-rule_chain = None
-
-
-def initialize_rule_chain():
-    global rule_chain
-    rule_src_uri = current_app.config["RULE_CHAIN_URI"]
-    try:
-        json_rules = urllib.request.urlopen(rule_src_uri)
-    except json.decoder.JSONDecodeError as excp:
-        raise RuleSyntaxException(excp) from excp
-    rule_chain = RuleLoader(json_rules).load()
-    print("RULE CHAIN FOLLOWS")
-    rule_chain.dump(stdout)
-    print("RULE CHAIN ABOVE")
-
-
-def calculate_assay_info(metadata: dict) -> dict:
-    if not rule_chain:
-        initialize_rule_chain()
-    for key, value in metadata.items():
-        if type(value) is str:
-            if value.isdigit():
-                metadata[key] = int(value)
-    rslt = rule_chain.apply(metadata)
-    # TODO: check that rslt has the expected parts
-    return rslt
-
-
 @assayclassifier_blueprint.route("/assaytype/<ds_uuid>", methods=["GET"])
 def get_ds_assaytype(ds_uuid: str):
     try:

src/routes/vitessce/__init__.py

@@ -0,0 +1,44 @@
+import logging
+
+from flask import Blueprint, Response, current_app, jsonify, request
+from hubmap_commons.hm_auth import AuthHelper
+from portal_visualization.builder_factory import get_view_config_builder
+
+from lib.decorators import require_json
+from lib.rule_chain import calculate_assay_info
+
+vitessce_blueprint = Blueprint("vitessce", __name__)
+logger = logging.getLogger(__name__)
+
+
+@vitessce_blueprint.route("/vitessce/config", methods=["POST"])
+@require_json(param="entity")
+def vitessce_config(entity: dict):
+    def get_assaytype(entity):
+        if "metadata" in entity.get("metadata", {}):
+            metadata = entity["metadata"]["metadata"]
+        else:
+            if "data_types" in entity and entity.get("data_types"):
+                metadata = {
+                    "entity_type": entity.get("entity_type"),
+                    "data_types": entity.get("data_types"),
+                }
+            else:
+                metadata = {
+                    "entity_type": entity.get("entity_type"),
+                    "data_types": [entity.get("dataset_type")],
+                }
+        return calculate_assay_info(metadata)
+
+    try:
+        auth_helper_instance = AuthHelper.instance()
+        groups_token = auth_helper_instance.getAuthorizationTokens(request.headers)
+        BuilderCls = get_view_config_builder(entity, get_assaytype)
+        builder = BuilderCls(
+            entity, groups_token, current_app.config["ASSETS_WEBSERVICE_URL"]
+        )
+        vitessce_conf = builder.get_conf_cells(marker=None)
+        return jsonify(vitessce_conf[0] or {}), 200
+    except Exception as e:
+        logger.error(e)
+        return Response("Unexpected error while retrieving Vitessce config", 500)