2.0.10

progenetix · Nov 13, 2024 · 8a68001 · 8a68001
1 parent ed3f7c8
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Showing 6 changed files with 61 additions and 26 deletions.
diff --git a/bycon/config/datatable_mappings.yaml b/bycon/config/datatable_mappings.yaml
@@ -100,7 +100,6 @@ ordered_metadata_core:
   - analysis_operation_label
   - geoprov_id
 
-
 ordered_variants_core:
   - analysis_id
   - biosample_id
@@ -285,6 +284,7 @@ $defs:
         beacon_model_path: biosamples.sampleOriginDetail.label
       tnm:
         type: array
+        split_by: '&&'
         items:
           type: object
           parameters:
@@ -296,7 +296,7 @@ $defs:
         db_key: pathological_tnm_findings
         beacon_model_path: biosamples.pathologicalTnmFindings.id
         examples:
-          - "NCIT:C48721::T1a Stage Finding,NCIT:C48699::M0 Stage Finding"
+          - "NCIT:C48721::T1a Stage Finding&&NCIT:C48699::M0 Stage Finding"
       tumor_grade_id:
         type: string
         db_key: tumor_grade.id
@@ -373,17 +373,22 @@ $defs:
         type: string
         db_key: references.tcgaproject.label
         beacon_model_path: False
-      cohort_ids:
+      cohorts:
         type: array
+        split_by: '&&'
+        items:
+          type: object
+          parameters:
+            - id
+            - label
+          indexed:
+            - id
+          split_by: '::'
         beacon_model_path: False
-        db_key: cohort_ids
+        db_key: cohorts
         indexed: True
         examples:
-          - pgx:cohort-2021progenetix
-          - pgx:cohort-DIPG
-          - pgx:cohort-TCGA
-          - pgx:cohort-TCGAcancers
-          - pgx:cohort-arraymap
+          - pgx:cohort-TCGAcancers::TCGA Cancer samples&&pgx:cohort-TCGA::TCGA Samples
       geoprov_id:
         type: string
         db_key: geo_location.properties.id
@@ -405,6 +410,7 @@ $defs:
         computed: True
       geoprov_long_lat:
         type: array
+        split_by: ','
         items:
         type: number
         db_key: geo_location.geometry.coordinates
@@ -434,6 +440,17 @@ $defs:
         type: string
         db_key: id
         indexed: True
+      individual_name:
+        description: >-
+          The legacy name for the individual, which is an identifier
+          used during import, e.g. the id used in the donor publication or study.
+          It is *not* considered unique in the database but just used during
+          import the stage when generating the unique `id` values. Also, it does
+          not have to/should correspond to a real (human) name.
+        type: string
+        db_key: name
+        beacon_model_path: False
+        indexed: True
       sex_id:
         type: string
         db_key: sex.id
@@ -452,6 +469,7 @@ $defs:
         computed: True
       external_references:
         type: array
+        split_by: '&&'
         items:
           type: object
           parameters:
@@ -482,7 +500,7 @@ $defs:
       notes:
         description: >-
           Any relevant info about the biosample that does not fit into any
-          other field in the schema. In teh context of biosample it goes into
+          other field in the schema. In the context of biosample it goes into
           `notes`.
         db_key: index_disease.notes
       index_disease_followup_time:
@@ -572,6 +590,7 @@ $defs:
         indexed: True
       adjoined_sequences:
         type: array
+        split_by: '&&'
         items:
           type: object
           parameters:
@@ -591,6 +610,8 @@ $defs:
           split_by: '::'
         db_key: adjoined_sequences
         indexed: True
+        examples:
+          - refseq:NC_000014.9::14::89300000::107043718&&refseq:NC_000018.10::18::45900000::63900000
       variant_state_id:
         type: string
         db_key: variant_state.id

diff --git a/bycon/config/services_entity_defaults.yaml b/bycon/config/services_entity_defaults.yaml
@@ -1,7 +1,6 @@
 ################################################################################
-# Beacon entry type defaults - please adjust esp. info and schema paths...
-# TODO: Some of the entry type configuration duplicates data from the Beacon
-# framework and might be disentangled further on ...
+# byconServices modules & their path values
+# the keys correspond to the names of byconServices modules
 ################################################################################
 
 byconschemas:
@@ -32,9 +31,13 @@ collationplots:
     schema: NA
   path_id_value_bycon_parameter: filters
 
-collation:
+collations:
   request_entity_path_id: collations
+  request_entity_id: collation
+  response_entity_id: collation
   collection: collations
+  request_entity_path_aliases:
+    - collations
   response_schema: byconautServiceResponse
   beacon_schema:
     entity_type: Collation
@@ -48,17 +51,17 @@ cytomapper:
     schema: https://progenetix.org/services/schemas/CytobandMapping/
   path_id_value_bycon_parameter: cyto_bands
 
-endpoints:
-  request_entity_path_id: endpoints
-
 dbstats:
   request_entity_path_id: dbstats
   beacon_schema:
     entity_type: dbstats
     schema: https://progenetix.org/services/schemas/DBstats/
   path_id_value_bycon_parameter: dataset_ids
 
-gene:
+endpoints:
+  request_entity_path_id: endpoints
+
+genespans:
   request_entity_path_id: genespans
   request_entity_path_aliases:
     - genes
@@ -70,10 +73,11 @@ gene:
     schema: https://progenetix.org/services/schemas/ProgenetixGene/
   path_id_value_bycon_parameter: gene_ids
 
-geoLocation:
+geolocations:
   request_entity_path_id: geolocations
   request_entity_path_aliases:
     - geolocs
+    - geoLocations
   response_entity_id: geoLocation
   collection: geolocs
   response_schema: beaconCollectionsResponse
@@ -118,7 +122,7 @@ pgxsegvariants:
   # TODO: change? a bit non-standard... 
   path_id_value_bycon_parameter: biosample_ids
 
-publication:
+publications:
   request_entity_path_id: publications
   response_entity_id: publication
   collection: publications

diff --git a/docs/changes.md b/docs/changes.md
@@ -6,6 +6,13 @@ While changes are documented for individual point versions we actually do not
 push releases out for all of them; they serve more as internal development
 milestones.
 
+### 2024-11-13 (v2.0.10)
+
+* fixed some intermediary issue with a few service calls
+* more explicit definition of `array` columns in import tables
+* documentation now with generated and inlined information from
+  some schemas into <https://bycon.progenetix.org/API/#api-beacon-responses>
+
 ### 2024-11-10 (v2.0.9)
 
 Mostly work on schemas and generated documentation:

diff --git a/requirements.txt b/requirements.txt
@@ -2,9 +2,11 @@ base36==0.1.1
 deepmerge==1.1.1
 isodate==0.6.1
 json_ref_dict==0.7.2
-liftover==1.1.18
+numpy==2.1.3
+Pillow==11.0.0
+progress==1.6
 pyhumps==3.7.3
-pymongo==4.6.1
-PyYAML==6.0.1
-PyYAML==6.0.1
+pymongo==4.7.2
+PyYAML==6.0.2
+scipy==1.14.1
 setuptools==67.7.2
diff --git a/setup.py b/setup.py
@@ -11,7 +11,7 @@
 
 setup(
     name="bycon",
-    version="2.0.9",
+    version="2.0.10",
     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
@@ -5,10 +5,11 @@ pip3 uninstall bycon --break-system-packages
 python3 -m build --sdist .
 BY=(./dist/*tar.gz)
 pip3 install $BY --break-system-packages
+./bycon/schemas/bin/yamlerRunner.sh
 ./markdowner.py
 # pipreqs --force .
 # python3 -m build --wheel && twine upload dist/*
-# git tag v2.0.5  & git push --tags
+# git tag v2.0.9  & git push --tags
 ./install.py
 rm -rf ./build
 rm -rf ./dist