1.4.2

progenetix · Feb 7, 2024 · fda7bd9 · fda7bd9
1 parent 6f46fae
commit fda7bd9
Show file tree

Hide file tree

Showing 200 changed files with 6,951 additions and 7,588 deletions.
diff --git a/bycon/__init__.py b/bycon/__init__.py
@@ -29,11 +29,12 @@
     from parse_variant_request import *
 
     byc: object = {
+        "args": {},
+        "form_data": {},
         "pkg_path": pkg_path,
         "bycon_lib_path": bycon_lib_path,
         "parsed_config_paths": [],
-        "env": "server",
-        "mongohost": environ.get("BYCON_MONGO_HOST", "localhost")
+        "env": "server"
     }
     if not environ.get('HTTP_HOST'):
         byc.update({"env": "local"})

diff --git a/bycon/beaconServer/beacon.py b/bycon/beaconServer/beacon.py
@@ -55,7 +55,6 @@ def beacon():
     byc.update({"request_path_root": "beacon"})
 
     rest_path_elements(byc)
-    get_bycon_args(byc)
     args_update_form(byc)
     prdbug(f'beacon.py - request_entity_path_id: {byc.get("request_entity_path_id")}', byc.get("debug_mode"))
 
@@ -99,19 +98,11 @@ def beacon():
 
             exit()
 
-    # TODO: replace with proper error response object
-    byc.update({
-        "service_response": {},
-        "error_response": {
-            "error": {
-                "error_code": 422,
-                "error_message": "No correct service path provided. Please refer to the documentation at http://docs.progenetix.org"
-            }
-        }
-    })
-
-    cgi_print_response(byc, 422)
-
+    e_m = "No correct service path provided. Please refer to the documentation at http://docs.progenetix.org"
+    e_r = BeaconErrorResponse(byc).error(e_m, 422)
+    print_json_response(e_r, byc["env"])
+
+
 ################################################################################
 ################################################################################
 

diff --git a/bycon/beaconServer/cohorts.py b/bycon/beaconServer/cohorts.py
@@ -24,16 +24,11 @@ def main():
 ################################################################################
 
 def cohorts():
-
     initialize_bycon_service(byc, "cohorts")
     run_beacon_init_stack(byc)
-    r = BeaconDataResponse(byc)
-    byc.update({
-        "service_response": r.collectionsResponse(),
-        "error_response": r.errorResponse()
-    })
+    r = BeaconDataResponse(byc).collectionsResponse()
+    print_json_response(r, byc["env"])
 
-    cgi_print_response( byc, 200 )
 
 ################################################################################
 ################################################################################

diff --git a/bycon/beaconServer/configuration.py b/bycon/beaconServer/configuration.py
@@ -20,14 +20,9 @@ def configuration():
     initialize_bycon_service(byc, "configuration")
     r = BeaconInfoResponse(byc)
     c_f = get_schema_file_path(byc, "beaconConfiguration")
-    c = load_yaml_empty_fallback( c_f )
+    c = load_yaml_empty_fallback(c_f)
+    print_json_response(r.populatedInfoResponse(c), byc["env"])
 
-    byc.update({
-        "service_response": r.populatedInfoResponse(c),
-        "error_response": r.errorResponse()
-    })
-
-    cgi_print_response( byc, 200 )
 
 ################################################################################
 ################################################################################

diff --git a/bycon/beaconServer/datasets.py b/bycon/beaconServer/datasets.py
@@ -25,16 +25,10 @@ def main():
 ################################################################################
 
 def datasets():
-
-    initialize_bycon_service(byc)
+    initialize_bycon_service(byc, "datasets")
     run_beacon_init_stack(byc)
     r = BeaconDataResponse(byc)
-    byc.update({
-        "service_response": r.collectionsResponse(),
-        "error_response": r.errorResponse()
-    })
-
-    cgi_print_response( byc, 200 )
+    print_json_response(r.collectionsResponse(), byc["env"])
 
 
 ################################################################################

diff --git a/bycon/beaconServer/entry_types.py b/bycon/beaconServer/entry_types.py
@@ -26,13 +26,7 @@ def entry_types():
     r = BeaconInfoResponse(byc)
     e_f = get_schema_file_path(byc, "beaconConfiguration")
     e_t_s = load_yaml_empty_fallback( e_f )
-
-    byc.update({
-        "service_response": r.populatedInfoResponse({"entry_types": e_t_s["entryTypes"] }),
-        "error_response": r.errorResponse()
-    })
-
-    cgi_print_response( byc, 200 )
+    print_json_response(r.populatedInfoResponse({"entry_types": e_t_s["entryTypes"] }), byc["env"])
 
 
 ################################################################################

diff --git a/bycon/beaconServer/filtering_terms.py b/bycon/beaconServer/filtering_terms.py
@@ -26,15 +26,8 @@ def main():
 def filtering_terms():
     initialize_bycon_service(byc, "filtering_terms")
     run_beacon_init_stack(byc)
-
     r = BeaconDataResponse(byc)
-
-    byc.update({
-        "service_response": r.filteringTermsResponse(),
-        "error_response": r.errorResponse()
-    })
-
-    cgi_print_response( byc, 200 )
+    print_json_response(r.filteringTermsResponse(), byc["env"])
 
 
 ################################################################################

diff --git a/bycon/beaconServer/info.py b/bycon/beaconServer/info.py
@@ -34,10 +34,7 @@ def info():
         if k in pgx_info:
             beacon_info.update({k:pgx_info[k]})
 
-    byc.update({
-        "service_response": r.populatedInfoResponse(beacon_info),
-        "error_response": r.errorResponse()
-    })
+    response = r.populatedInfoResponse(beacon_info)
 
     # TODO: All the schemas really only here?
     beacon_schemas = []
@@ -46,9 +43,9 @@ def info():
         if e_d.get("is_entry_type", True) is True:
             beacon_schemas.append(b_s)
 
-    byc["service_response"]["meta"].update( { "returned_schemas": beacon_schemas } )
+    response.update( { "returned_schemas": beacon_schemas } )
+    print_json_response(response, byc["env"])
 
-    cgi_print_response( byc, 200 )
 
 ################################################################################
 ################################################################################

diff --git a/bycon/beaconServer/map.py b/bycon/beaconServer/map.py
@@ -25,13 +25,8 @@ def map():
     r = BeaconInfoResponse(byc)
     m_f = get_schema_file_path(byc, "beaconMap")
     beaconMap = load_yaml_empty_fallback( m_f )
+    print_json_response(r.populatedInfoResponse(beaconMap), byc["env"])
 
-    byc.update({
-        "service_response": r.populatedInfoResponse(beaconMap),
-        "error_response": r.errorResponse()
-    })
-
-    cgi_print_response( byc, 200 )
 
 ################################################################################
 ################################################################################

diff --git a/bycon/beaconServer/service_info.py b/bycon/beaconServer/service_info.py
@@ -28,12 +28,12 @@ def service_info():
     defs = byc.get("beacon_defaults", {})
     b_e_d = defs.get("entity_defaults", {})
     pgx_info = b_e_d.get("info", {})
+    c = pgx_info.get("content", {})
     info = object_instance_from_schema_name(byc, "ga4gh-service-info-1-0-0-schema", "")
-
     for k in info.keys():
-        if k in pgx_info:
-            info.update({k:pgx_info[k]})
-    print_json_response( info, byc["env"], 200 )
+        if k in c:
+            info.update({k:c[k]})
+    print_json_response(info, byc["env"])
 
 ################################################################################
 ################################################################################

diff --git a/bycon/beaconServer/tests/PUT-biosamples-from-NCIT-filters-no-descendants.json b/bycon/beaconServer/tests/PUT-biosamples-from-NCIT-filters-no-descendants.json
@@ -15,16 +15,16 @@
                 "datasetIds": ["progenetix"]
             }
         },
+        "filters": [
+            { "id": "NCIT:C102872", "scope": "analyses", "includeDescendantTerms": false }
+        ],
         "filterLogic": "OR"
     },
     "pagination": {
         "skip": 0,
         "limit": 10
     },   
-    "filters": [
-        { "id": "NCIT:C102872", "scope": "analyses", "includeDescendantTerms": false }
-    ],
     "includeResultsetResponses": "HIT",
     "requestedGranularity": "count",
-    "debug": 0
+    "debugMode": 0
 }
diff --git a/bycon/beaconServer/tests/PUT-biosamples-from-NCIT-filters.json b/bycon/beaconServer/tests/PUT-biosamples-from-NCIT-filters.json
@@ -15,18 +15,18 @@
                 "datasetIds": ["progenetix"]
             }
         },
+        "filters": [
+            { "id": "NCIT:C4536", "scope": "biosamples", "includeDescendantTerms": false },
+            { "id": "NCIT:C95597", "scope": "biosamples", "includeDescendantTerms": false },
+            { "id": "NCIT:C7712", "scope": "biosamples", "includeDescendantTerms": false }
+        ],
         "filterLogic": "OR"
     },
     "pagination": {
         "skip": 0,
         "limit": 10
     },   
-    "filters": [
-        { "id": "NCIT:C4536", "scope": "biosamples", "includeDescendantTerms": false },
-        { "id": "NCIT:C95597", "scope": "biosamples", "includeDescendantTerms": false },
-        { "id": "NCIT:C7712", "scope": "biosamples", "includeDescendantTerms": false }
-    ],
     "includeResultsetResponses": "HIT",
     "requestedGranularity": "record",
-    "debug": 0
+    "debugMode": 0
 }
diff --git a/bycon/beaconServer/tests/PUT-core-from-NCIT-filters.json b/bycon/beaconServer/tests/PUT-core-from-NCIT-filters.json
@@ -12,12 +12,12 @@
                 "datasetIds": ["progenetix"]
             }
         },
+        "filters": [
+            { "id": "NCIT:C4536" },
+            { "id": "NCIT:C95597" },
+            { "id": "NCIT:C7712" }
+        ],
         "filterLogic": "OR"
     },
-    "filters": [
-        { "id": "NCIT:C4536" },
-        { "id": "NCIT:C95597" },
-        { "id": "NCIT:C7712" }
-    ],
-    "debug": 1
+    "debugMode": 1
 }
diff --git a/bycon/beaconServer/tests/PUT-individuals-from-NCIT-filters.json b/bycon/beaconServer/tests/PUT-individuals-from-NCIT-filters.json
@@ -12,12 +12,7 @@
                 "datasetIds": ["progenetix"]
             }
         },
-        "filterLogic": "OR"
+        "filters": [{ "id": "NCIT:C4536" }]
     },
-    "filters": [
-        { "id": "NCIT:C4536" },
-        { "id": "NCIT:C95597" },
-        { "id": "NCIT:C7712" }
-    ],
-    "debug": 0
+    "debugMode": 0
 }
diff --git a/bycon/beaconServer/tests/PUT-phenopackets-from-NCIT-filters.json b/bycon/beaconServer/tests/PUT-phenopackets-from-NCIT-filters.json
@@ -15,16 +15,13 @@
                 "datasetIds": ["progenetix"]
             }
         },
-        "filterLogic": "OR"
+        "filters": [
+            { "id": "NCIT:C4536" },
+        ]
     },
     "pagination": {
         "skip": 0,
         "limit": 10
     },   
-    "filters": [
-        { "id": "NCIT:C4536" },
-        { "id": "NCIT:C95597" },
-        { "id": "NCIT:C7712" }
-    ],
-    "debug": 1
+    "debugMode": 1
 }
diff --git a/bycon/beaconServer/tests/PUT-variants-for-CDKN2A-DEL-gliomas.json b/bycon/beaconServer/tests/PUT-variants-for-CDKN2A-DEL-gliomas.json
@@ -21,14 +21,14 @@
                 "end": [21967753, 22500000], 
                 "variantType": "DEL"
             }
-        }
+        },
+        "filters": [
+            { "id": "NCIT:C3058" }
+        ],
     },
     "pagination": {
         "skip": 0,
         "limit": 5
     },   
-    "filters": [
-        { "id": "NCIT:C3058" }
-    ],
-    "debug": 0
+    "debugMode": 0
 }
diff --git a/bycon/beaconServer/tests/PUT-variants-for-biosampleIds.json b/bycon/beaconServer/tests/PUT-variants-for-biosampleIds.json
@@ -19,8 +19,8 @@
                 "pgxbs-kftvhaqa",
                 "pgxbs-kftvj1nt"
             ]
-        }
+        },
+        "filters": [ ]
     },
-    "filters": [ ],
-    "debug": 0
+    "debugMode": 0
 }
diff --git a/bycon/beaconServer/tests/PUT-variants-for-specific-alt-bases.json b/bycon/beaconServer/tests/PUT-variants-for-specific-alt-bases.json
@@ -14,16 +14,19 @@
             "datasets": {
                 "datasetIds": ["progenetix"]
             },
-            "referenceName": "NC_000017.11",
-            "start": [7577120],
-            "referenceBases": "G",
-            "alternateBases": "A"
-        }
+            "g_variant": {
+                "referenceName": "refseq:NC_000017.11",
+                "start": [7577120],
+                "referenceBases": "G",
+                "alternateBases": "A"
+            }
+        },
+        "filters": []
     },
     "requestedGranularity": "record",
     "pagination": {
         "skip": 0,
         "limit": 5
     },
-    "filters": []
+    "debugMode": true
 }
diff --git a/bycon/beaconServer/tests/terminal-examples.md b/bycon/beaconServer/tests/terminal-examples.md
@@ -1,32 +1,5 @@
 # Command line tests
 
 ```
-./beaconServer/beacon.py --filters "pgx:icdom-81703" --requestedSchema biosample --referenceName 9 --start 10000000,12000000 --end 12500000,15000000 --variantType DEL
-```
-
-```
-./beaconServer/beacon.py --requestedSchema genomicVariant --referenceName 9 --start 10000000,12000000 --end 12500000,15000000 --variantType DEL --output pgxseg > ~/Desktop/test.pgxseg
-```
-
-```
-./beaconServer/beacon.py --filters "pgx:icdom-81703" --requestedSchema analysis --referenceName 9 --start 10000000,12000000 --end 12500000,15000000 --variantType DEL --output pgxmatrix > ~/Desktop/test.pgxmatrix
-```
-
-```
-./beaconServer/beacon.py --filters "NCIT:C3058" --output pgxmatrix > ~/Desktop/NCIT_C3058.pgxmatrix
-```
-
-```
-./services/cytomapper.py --cytoBands 8q24
-./services/cytomapper.py --chroBases "9:0-50000000"
-```
-
-```
-./services/genespans.py --geneId TP53
-./services/genespans.py --geneId TP53 --filterPrecision start
-```
-
-```
-./services/geolocations.py --city Heidel
-./services/geolocations.py --geoDistance 20000 --geoLatitude 47.3 --geoLongitude 8.55
+curl --json @PUT-individuals-from-NCIT-filters.json  "http://progenetix.org/beacon/individuals/"
 ```