more doc

bycon/byconServiceLibs/datatable_utils.py

@@ -9,10 +9,10 @@
 def export_datatable_download(flattened_data):
     dt_m = BYC["datatable_mappings"]
     r_t = BYC.get("response_entity_id", "___none___")
-    if not r_t in dt_m["definitions"]:
+    if not r_t in dt_m["$defs"]:
         return
     sel_pars = BYC_PARS.get("delivery_keys", [])
-    io_params = dt_m["definitions"][ r_t ]["parameters"]
+    io_params = dt_m["$defs"][ r_t ]["parameters"]
     if len(sel_pars) > 0:
         io_params = { k: v for k, v in io_params.items() if k in sel_pars }
     prdlhead(f'{r_t}.tsv')
@@ -39,9 +39,9 @@ def export_datatable_download(flattened_data):
 
 def import_datatable_dict_line(parent, fieldnames, lineobj, primary_scope="biosample"):
     dt_m = BYC["datatable_mappings"]
-    if not primary_scope in dt_m["definitions"]:
+    if not primary_scope in dt_m["$defs"]:
         return
-    io_params = dt_m["definitions"][ primary_scope ]["parameters"]
+    io_params = dt_m["$defs"][ primary_scope ]["parameters"]
     def_params = create_table_header(io_params)
     for f_n in fieldnames:
         if "#"in f_n:

bycon/byconServiceLibs/export_file_generation.py

@@ -55,7 +55,7 @@ def stream_pgx_meta_header(ds_id, ds_results):
 
 def pgxseg_biosample_meta_line(biosample, group_id_key="histological_diagnosis_id"):
     dt_m = BYC["datatable_mappings"]
-    io_params = dt_m["definitions"][ "biosample" ]["parameters"]
+    io_params = dt_m["$defs"][ "biosample" ]["parameters"]
 
     g_id_k = group_id_key
     g_lab_k = re.sub("_id", "_label", g_id_k)

docs/API.md

@@ -12,7 +12,7 @@ are indicated by the `@` symbol.\n\n
 
 #### Schemas **{S}**, Tests **{T}** and Examples **{E}**
 Tests, examples and schemas are run from the server defined in this site's build instructions
-(see the `reference_server_url` entry in `mkdocs.yaml` file in the repository's root).
+(see the current _{{config.reference_server_url}}_ entry for `reference_server_url` entry in `mkdocs.yaml` file in the [{{config.repo_url}}](repository's root).
 
 {%
     include-markdown "generated/beacon-responses.md"

housekeepers/mongodbIndexer.py

@@ -33,7 +33,7 @@ def mongodb_indexer():
             print(f"¡¡¡ Collection {collname} does not exist in {ds_id} !!!")
             continue
         i_coll = data_db[ collname ]
-        io_params = dt_m["definitions"][ r_t ]["parameters"]
+        io_params = dt_m["$defs"][ r_t ]["parameters"]
 
         for p_k, p_v in io_params.items():
             if (i_t := p_v.get("indexed", False)) is False:

importers/importTablesGenerator.py

@@ -16,7 +16,7 @@
 ################################################################################
 
 def main():
-    dt_m = BYC["datatable_mappings"].get("definitions", {})
+    dt_m = BYC["datatable_mappings"].get("$defs", {})
     ordered_mcs = BYC["datatable_mappings"].get("ordered_metadata_core", [])
     ordered_vcs = BYC["datatable_mappings"].get("ordered_variants_core", [])
     rsrc_p = path.join(pkg_path, "rsrc", "templates")

rsrc/templates/analyses.tsv

@@ -0,0 +1 @@
+analysis_id	biosample_id	individual_id	platform_id	platform_label	pipeline_name	pipeline_ref	analysis_operation_id	analysis_operation_label	experiment_id	series_id	experiment_title	data_provenance

rsrc/templates/biosamples.tsv

@@ -0,0 +1 @@
+biosample_id	individual_id	biosample_name	notes	histological_diagnosis_id	histological_diagnosis_label	pathological_stage_id	pathological_stage_label	biosample_status_id	biosample_status_label	sample_origin_type_id	sample_origin_type_label	sampled_tissue_id	sampled_tissue_label	tnm	tumor_grade_id	tumor_grade_label	age_iso	icdo_morphology_id	icdo_morphology_label	icdo_topography_id	icdo_topography_label	pubmed_id	pubmed_label	cellosaurus_id	cellosaurus_label	cbioportal_id	cbioportal_label	tcgaproject_id	tcgaproject_label	cohorts	geoprov_id	geoprov_city	geoprov_country	geoprov_iso_alpha3	geoprov_long_lat	group_id	group_label

rsrc/templates/individuals.tsv

@@ -0,0 +1 @@
+individual_id	individual_name	sex_id	sex_label	age_iso	age_days	external_references	data_use_conditions_id	data_use_conditions_label	histological_diagnosis_id	histological_diagnosis_label	notes	index_disease_followup_time	index_disease_followup_state_id	index_disease_followup_state_label	auxiliary_disease_id	auxiliary_disease_label	auxiliary_disease_notes	ethnicity_id	ethnicity_label

rsrc/templates/metadata.tsv

@@ -0,0 +1 @@
+analysis_id	biosample_id	individual_id	experiment_title	biosample_name	notes	histological_diagnosis_id	histological_diagnosis_label	experiment_id	series_id	pubmed_id	sex_id	sex_label	age_iso	icdo_morphology_id	icdo_morphology_label	icdo_topography_id	icdo_topography_label	sampled_tissue_id	sampled_tissue_label	biosample_status_id	biosample_status_label	sample_origin_type_id	sample_origin_type_label	tnm	pathological_stage_id	pathological_stage_label	tumor_grade_id	tumor_grade_label	ethnicity_id	ethnicity_label	index_disease_followup_time	index_disease_followup_state_id	index_disease_followup_state_label	platform_id	platform_label	pipeline_name	pipeline_ref	analysis_operation_id	analysis_operation_label	geoprov_id

rsrc/templates/metadata_all.tsv

@@ -0,0 +1 @@
+analysis_id	biosample_id	individual_id	experiment_title	biosample_name	notes	histological_diagnosis_id	histological_diagnosis_label	experiment_id	series_id	pubmed_id	sex_id	sex_label	age_iso	icdo_morphology_id	icdo_morphology_label	icdo_topography_id	icdo_topography_label	sampled_tissue_id	sampled_tissue_label	biosample_status_id	biosample_status_label	sample_origin_type_id	sample_origin_type_label	tnm	pathological_stage_id	pathological_stage_label	tumor_grade_id	tumor_grade_label	ethnicity_id	ethnicity_label	index_disease_followup_time	index_disease_followup_state_id	index_disease_followup_state_label	platform_id	platform_label	pipeline_name	pipeline_ref	analysis_operation_id	analysis_operation_label	geoprov_id	data_provenance	pubmed_label	cellosaurus_id	cellosaurus_label	cbioportal_id	cbioportal_label	tcgaproject_id	tcgaproject_label	cohorts	geoprov_city	geoprov_country	geoprov_iso_alpha3	geoprov_long_lat	group_id	group_label	individual_name	age_days	external_references	data_use_conditions_id	data_use_conditions_label	auxiliary_disease_id	auxiliary_disease_label	auxiliary_disease_notes

rsrc/templates/variants.tsv

@@ -0,0 +1 @@
+analysis_id	biosample_id	individual_id	reference_name	start	end	variant_state_id	variant_state_label	reference_sequence	sequence

rsrc/templates/variants_all.tsv

@@ -0,0 +1 @@
+variant_id	variant_internal_id	analysis_id	biosample_id	individual_id	sequence_id	reference_name	start	end	adjoined_sequences	variant_state_id	variant_state_label	reference_sequence	sequence	annotation_derived	aminoacid_changes	genomic_hgvs_id	var_length	variant_fusion_id	updated	log2	variant_type