1.6.2

progenetix · Mar 7, 2024 · d15d810 · d15d810
1 parent 7b40720
commit d15d810
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Showing 14 changed files with 63 additions and 80 deletions.
diff --git a/bycon/definitions/argument_definitions.yaml b/bycon/definitions/argument_definitions.yaml
@@ -69,7 +69,9 @@ include_resultset_responses:
   type: string
   cmdFlags:
     - --includeResultsetResponses
-  description: requested schema, e.g. biosample
+  description: >-
+    * include resultset responses, e.g. HIT, MISS
+    * kind of a holdover from Beacon pre-v1
 
 # query / data selection
 
@@ -120,7 +122,7 @@ assembly_id:
   cmdFlags:
     - --assemblyId
   description: assembly id
-  default: GRCh38
+  # default: GRCh38
 
 reference_name:
   type: string

diff --git a/bycon/definitions/beacon_defaults.yaml b/bycon/definitions/beacon_defaults.yaml
@@ -71,7 +71,6 @@ entity_defaults:
     beacon_schema:
       entity_type: configuration
       schema: https://progenetix.org/services/schemas/beaconInfoResults/
-    h->o_access_key: Null
     content: {}
 
 ################################################################################
@@ -85,7 +84,6 @@ entity_defaults:
     beacon_schema:
       entity_type: map
       schema: https://progenetix.org/services/schemas/beaconMapSchema/
-    h->o_access_key: Null
 
 ################################################################################
 
@@ -98,7 +96,6 @@ entity_defaults:
     beacon_schema:
       entity_type: configuration
       schema: https://progenetix.org/services/schemas/beaconConfigurationSchema/
-    h->o_access_key: Null
 
 ################################################################################
 
@@ -111,7 +108,6 @@ entity_defaults:
     beacon_schema:
       entity_type: entryType
       schema: https://progenetix.org/services/schemas/entryTypesSchema/
-    h->o_access_key: Null
 
 ################################################################################
 
@@ -124,7 +120,6 @@ entity_defaults:
     beacon_schema:
       entity_type: filteringTerm
       schema: https://progenetix.org/services/schemas/filteringTermsSchema/
-    h->o_access_key: Null
 
 ################################################################################
 
@@ -206,7 +201,6 @@ entity_defaults:
     pagination:
       skip: 0
       limit: 10
-    include_resultset_responses: false
 
   ##############################################################################
 
@@ -222,5 +216,4 @@ entity_defaults:
     pagination:
       skip: 0
       limit: 10
-    include_resultset_responses: false
 
diff --git a/bycon/lib/beacon_response_generation.py b/bycon/lib/beacon_response_generation.py
@@ -164,14 +164,16 @@ def collectionsResponse(self):
             return
 
         colls, queries = ByconCollections(self.byc).populatedCollections()
+        colls = self.__collections_response_remap_cohorts(colls)
         self.data_response["response"].update({"collections": colls})
         self.record_queries.update({"entities": queries})
         self.__collections_response_update_summaries()
         self.__meta_add_received_request_summary_parameters()
         self.__meta_add_parameters()
         self.__meta_clean_parameters()
-        self.__response_clean_parameters()
         self.__check_switch_to_error_response()
+        # self.__response_clean_parameters()
+        self.data_response.get("meta", {}).get("received_request_summary", {}).pop("include_resultset_responses", None)
         return self.data_response
 
 
@@ -224,6 +226,31 @@ def __resultSetResponse_force_autorized_granularities(self):
             self.data_response.pop("response", None)
 
 
+    # -------------------------------------------------------------------------#
+
+    def __collections_response_remap_cohorts(self, colls=[]):
+        if not "cohort" in self.byc.get("response_entity_id", "___none___"):
+            return colls
+        pop_keys = ["_id", "child_terms", "code_matches", "count", "dataset_id", "db_key", "namespace_prefix", "ft_type", "collation_type", "hierarchy_paths", "parent_terms", "scope"]
+        for c in colls:
+            c_k = f'{c.get("scope", "")}.{c.get("db_key", "")}'
+            c.update({
+                "id": c.get("id", "___none___"),
+                "cohort_type": "beacon-defined",
+                "cohort_size": c.get("count"),
+                "name": c.get("label", ""),
+                # "inclusion_criteria": {
+                #     "description": c.get("description", "NA"),
+                #     c_k: c.get("id"),
+                #     "dataset_id": c.get("dataset_id")
+                # }
+            })
+            for k in pop_keys:
+                c.pop(k, None)
+
+        return colls
+
+
     # -------------------------------------------------------------------------#
 
     def __response_clean_parameters(self):
@@ -235,9 +262,8 @@ def __response_clean_parameters(self):
 
     def __meta_clean_parameters(self):
         r_m = self.data_response.get("meta", {})
-
-        if "beaconCollectionsResponse" in self.response_schema:
-            r_m.get("received_request_summary", {}).pop("include_resultset_responses", None)
+        # TBD?!
+
 
 
     # -------------------------------------------------------------------------#

diff --git a/bycon/lib/bycon_helpers.py b/bycon/lib/bycon_helpers.py
@@ -40,7 +40,9 @@ def set_debug_state(debug=False) -> bool:
 def refactor_value_from_defined_type(parameter, values, definition):
     p_d_t = definition.get("type", "string")
     values = list(x for x in values if x is not None)
-    values = list(x for x in values if x != "None")
+    values = list(x for x in values if x.lower() not in ["none", "null"])
+    if len(values) == 0:
+        return None
     if "array" in p_d_t:
         p_i_t = definition.get("items", "string")
         if "int" in p_i_t:

diff --git a/bycon/lib/cgi_parsing.py b/bycon/lib/cgi_parsing.py
@@ -86,7 +86,8 @@ def parse_GET(byc):
         # CAVE: Only predefined parameters are accepted!
         if p_d in a_defs:
             values = form_return_listvalue(form_data, p)
-            BYC_PARS.update({p_d: refactor_value_from_defined_type(p, values, a_defs[p_d])})
+            if (v := refactor_value_from_defined_type(p, values, a_defs[p_d])):
+                BYC_PARS.update({p_d: v})
         else:
             w_m = '!!! Unmatched parameter {p_d}: {form_data.getvalue(p)}'
             BYC["WARNINGS"].append(w_m)

diff --git a/bycon/lib/variant_mapping.py b/bycon/lib/variant_mapping.py
@@ -149,7 +149,8 @@ def vrsVariant(self, variant):
         # TODO: since the vrs_variant has been created as a new object we now
         #       add the annotation fields back (should empties be omitted?)
         for v_s in ("biosample_id", "callset_id", "id", "variant_internal_id"):
-            vrs_v.update({v_s: self.byc_variant.get(v_s)})
+            if (v_v := self.byc_variant.get(v_s)):
+                vrs_v.update({v_s: v_v})
         vrs_v.update({"variant_alternative_ids": self.byc_variant.get("variant_alternative_ids", [])})
         for v_o in ("identifiers", "info", "molecular_attributes", "variant_level_data"):
             vrs_v.update({v_o: self.byc_variant.get(v_o, {})})
@@ -222,7 +223,6 @@ def __vrs_cnv(self):
     def __create_canonical_variant(self):
         v = self.byc_variant
         v.update({"errors": []})
-
         self.__byc_variant_normalize_type()
         self.__byc_variant_normalize_chromosome()
         self.__byc_variant_normalize_positions()

diff --git a/bycon/schemas/models/json/progenetix-model/cohorts/endpoints.json b/bycon/schemas/models/json/progenetix-model/cohorts/endpoints.json
@@ -274,17 +274,7 @@
                 "content": {
                     "application/json": {
                         "schema": {
-                            "oneOf": [
-                                {
-                                    "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconBooleanResponse.json"
-                                },
-                                {
-                                    "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCountResponse.json"
-                                },
-                                {
-                                    "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json"
-                                }
-                            ]
+                            "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCollectionsResponse.json"
                         }
                     }
                 }
@@ -294,17 +284,7 @@
                 "content": {
                     "application/json": {
                         "schema": {
-                            "oneOf": [
-                                {
-                                    "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconBooleanResponse.json"
-                                },
-                                {
-                                    "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCountResponse.json"
-                                },
-                                {
-                                    "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCollectionsResponse.json"
-                                }
-                            ]
+                            "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCollectionsResponse.json"
                         }
                     }
                 }

diff --git a/bycon/schemas/models/json/progenetix-model/datasets/endpoints.json b/bycon/schemas/models/json/progenetix-model/datasets/endpoints.json
@@ -397,17 +397,7 @@
                 "content": {
                     "application/json": {
                         "schema": {
-                            "oneOf": [
-                                {
-                                    "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconBooleanResponse.json"
-                                },
-                                {
-                                    "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCountResponse.json"
-                                },
-                                {
-                                    "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json"
-                                }
-                            ]
+                            "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCollectionsResponse.json"
                         }
                     }
                 }
@@ -417,17 +407,7 @@
                 "content": {
                     "application/json": {
                         "schema": {
-                            "oneOf": [
-                                {
-                                    "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconBooleanResponse.json"
-                                },
-                                {
-                                    "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCountResponse.json"
-                                },
-                                {
-                                    "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCollectionsResponse.json"
-                                }
-                            ]
+                            "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCollectionsResponse.json"
                         }
                     }
                 }

diff --git a/bycon/schemas/models/src/progenetix-model/cohorts/endpoints.yaml b/bycon/schemas/models/src/progenetix-model/cohorts/endpoints.yaml
@@ -169,19 +169,13 @@ components:
       content:
         application/json:
           schema:
-            oneOf:
-              - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconBooleanResponse.json
-              - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCountResponse.json
-              - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json
+            $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCollectionsResponse.json
     CollectionsResponse:
       description: Successful collection list operation.
       content:
         application/json:
           schema:
-            oneOf:
-              - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconBooleanResponse.json
-              - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCountResponse.json
-              - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCollectionsResponse.json
+            $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCollectionsResponse.json
   parameters:
     requestedSchema:
       name: requestedSchema

diff --git a/bycon/schemas/models/src/progenetix-model/datasets/endpoints.yaml b/bycon/schemas/models/src/progenetix-model/datasets/endpoints.yaml
@@ -244,19 +244,13 @@ components:
       content:
         application/json:
           schema:
-            oneOf:
-              - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconBooleanResponse.json
-              - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCountResponse.json
-              - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json
+            $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCollectionsResponse.json
     CollectionsResponse:
       description: Successful collection list operation.
       content:
         application/json:
           schema:
-            oneOf:
-              - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconBooleanResponse.json
-              - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCountResponse.json
-              - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCollectionsResponse.json
+            $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCollectionsResponse.json
   parameters:
     requestedSchema:
       name: requestedSchema

diff --git a/docs/changes.md b/docs/changes.md
@@ -13,6 +13,18 @@ through the Perl based [**PGX** project](http://github.com/progenetix/PGX/).
 
 ## Changes Tracker
 
+### 2024-03-07 (v1.6.2)
+
+* adding a `__collections_response_remap_cohorts(self, colls=[])` function
+  to reformat the collections response for cohorts from the collations format
+    - TODO: define cohorts as separate entities which are read in during collations
+      generation, with their additional parameters etc.
+* fixed the openAPI endpoints for collation responses (datasets & cohorts); are
+  [incorrect in current Beacon spec.](https://github.com/ga4gh-beacon/beacon-v2/issues/116)
+* bug fix `byconaut`: matrix export was broken since 1.6.1
+* exception capture for wrong form values: string values of "None", "none", "Null",
+  "null" from GET requests are now converted to logical `None` (i.e. removed)
+
 ### 2024-03-06 (v1.6.1)
 
 * bug fix: individuals & phenopackets endpoints were broken in 1.6.0 due to missed

diff --git a/local/beacon_defaults.yaml b/local/beacon_defaults.yaml
@@ -51,7 +51,6 @@ entity_defaults:
     beacon_schema:
       entity_type: configuration
       schema: https://progenetix.org/services/schemas/beaconInfoResults/
-    h->o_access_key: Null
     # TODO: move `content` to `local` file.
     content:
       beacon_id: org.progenetix

diff --git a/setup.py b/setup.py
@@ -12,7 +12,7 @@
 
 setup(
     name="bycon",
-    version="1.6.0",
+    version="1.6.2",
     description="A Python-based environment for the Beacon v2 genomics API",
     long_description=long_description,
     long_description_content_type="text/markdown",

diff --git a/updev.sh b/updev.sh
@@ -9,6 +9,6 @@ BY=(./dist/*tar.gz)
 pip3 install $BY
 # pipreqs --force .
 # python3 -m build --wheel && twine upload dist/*
-# git tag v1.6.0  & git push --tags
+# git tag v1.6.2  & git push --tags
 ./install.py
 ../byconaut/install.py