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1.6.3
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@mbaudis
mbaudis committed Mar 8, 2024
1 parent a45c831 commit 34ca3ed
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2 changes: 1 addition & 1 deletion bin/collationsCreator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ def main():

def collations_creator():
initialize_bycon_service(byc, "collations_creator")

if len(byc["dataset_ids"]) > 1:
print("Please give only one dataset using -d")
exit()
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8 changes: 8 additions & 0 deletions bin/frequencymapsCreator.py
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Expand Up @@ -34,6 +34,14 @@ def frequencymaps_creator():
initialize_bycon_service(byc, "frequencymaps_creator")
generate_genome_bins(byc)

# avoiding pagination default ...
limit = BYC_PARS.get("limit")

if limit > 0 and limit < 10000:
proceed = input(f'Do you want to really want to process max. `--limit {limit}` samples per subset?\n(Y|n): ')
if "n" in proceed.lower():
exit()

if len(byc["dataset_ids"]) > 1:
print("Please give only one dataset using -d")
exit()
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16 changes: 0 additions & 16 deletions bin/local/beacon_defaults.yaml
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Expand Up @@ -9,33 +9,19 @@ defaults:
# mappings and aliases #########################################################
################################################################################

# map path id flavours to canonical entry_type_path_id #########################
# the aliases here are for non-standard speling or additional entry types

service_path_aliases:
filteringTerms: filtering_terms # just for speling variations
entryTypes: entry_types # just for speling variations
variants: genomicVariations # just for speling variations
genomicVariations: genomicVariations # just for speling variations
phenopackets: phenopackets # Beacon+ specific example


################################################################################
# here you can map additional path values to the corresponding (additional)
# entry type
################################################################################

path_entry_type_mappings:
phenopackets: phenopacket # Beacon+ specific example

################################################################################
# her you can add additional path ids to the data query aggregation pipeline
# that usually mapps/reduces queries against biosamples, genomicVariations,
# individuals ...
################################################################################

data_pipeline_path_ids:
- phenopackets # Beacon+ specific example

################################################################################
# Beacon entry type defaults - please adjust esp. info and schema paths...
Expand All @@ -45,7 +31,6 @@ data_pipeline_path_ids:

entity_defaults:
info:
is_entry_type: False
collection: Null
response_schema: beaconInfoResponse
beacon_schema:
Expand Down Expand Up @@ -99,7 +84,6 @@ entity_defaults:
##############################################################################

phenopacket:
is_entry_type: True
request_entity_path_id: phenopackets
response_entity_id: phenopacket
collection: individuals
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70 changes: 70 additions & 0 deletions bin/local/beacon_entity_defaults.yaml
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@@ -0,0 +1,70 @@
################################################################################
# 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 ...
################################################################################

info:
collection: Null
response_schema: beaconInfoResponse
beacon_schema:
entity_type: configuration
schema: https://progenetix.org/services/schemas/beaconInfoResults/
# TODO: move `content` to `local` file.
content:
beacon_id: org.progenetix
name: Progenetix Cancer Genomics Beacon+
api_version: v2.1.0-beaconplus
version: v2.1.0-beaconplus
id: org.progenetix.beacon
environment: prod
description: >-
Beacon+ provides a forward looking implementation of the Beacon v2 API, with
focus on structural genome variants and metadata based on the cancer and reference
genome profiling data in the Progenetix oncogenomic data resource (https://progenetix.org).
type:
group: org.ga4gh
artifact: beacon
version: v2.1.0-beaconplus
documentation_url: http://docs.progenetix.org
service_url: http://progenetix.org/beacon/
welcome_url: https://progenetix.org/biosamples/
alternative_url: https://progenetix.org
contact_url: mailto:[email protected]
created_at: 2015-11-13T00:00:00
updated_at: 2023-02-16T12:45:00
organization:
id: org.baudisgroup.info
name: Theoretical Cytogenetics and Oncogenomics group at UZH and SIB
description: >
The *Theoretical Cytogenetics and Oncogenomics* group at the University of
Zurich (UZH) and the Swiss Institute of Bioinformatics (SIB) performs research
in cancer genomics and provides bioinformatics tools and cancer genome data
resources to the scientific community.
address: >-
Department of Molecular Life Sciences
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich
Switzerland
welcome_url: https://progenetix.org/biosamples/
contact_url: mailto:[email protected]
logoUrl: https://progenetix.org/img/progenetix-logo.png
info:
update_date_time: 2023-01-16T12:45:00
create_date_time: 2015-11-13T00:00:00
update_date_time: 2023-01-16T12:45:00

##############################################################################

phenopacket:
request_entity_path_id: phenopackets
response_entity_id: phenopacket
collection: individuals
response_schema: beaconResultsetsResponse
beacon_schema:
entity_type: phenopacket
schema: https://progenetix.org/services/schemas/phenopacket/
h->o_access_key: individuals._id


70 changes: 70 additions & 0 deletions bin/local/entity_defaults.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,70 @@
################################################################################
# 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 ...
################################################################################

info:
collection: Null
response_schema: beaconInfoResponse
beacon_schema:
entity_type: configuration
schema: https://progenetix.org/services/schemas/beaconInfoResults/
# TODO: move `content` to `local` file.
content:
beacon_id: org.progenetix
name: Progenetix Cancer Genomics Beacon+
api_version: v2.1.0-beaconplus
version: v2.1.0-beaconplus
id: org.progenetix.beacon
environment: prod
description: >-
Beacon+ provides a forward looking implementation of the Beacon v2 API, with
focus on structural genome variants and metadata based on the cancer and reference
genome profiling data in the Progenetix oncogenomic data resource (https://progenetix.org).
type:
group: org.ga4gh
artifact: beacon
version: v2.1.0-beaconplus
documentation_url: http://docs.progenetix.org
service_url: http://progenetix.org/beacon/
welcome_url: https://progenetix.org/biosamples/
alternative_url: https://progenetix.org
contact_url: mailto:[email protected]
created_at: 2015-11-13T00:00:00
updated_at: 2023-02-16T12:45:00
organization:
id: org.baudisgroup.info
name: Theoretical Cytogenetics and Oncogenomics group at UZH and SIB
description: >
The *Theoretical Cytogenetics and Oncogenomics* group at the University of
Zurich (UZH) and the Swiss Institute of Bioinformatics (SIB) performs research
in cancer genomics and provides bioinformatics tools and cancer genome data
resources to the scientific community.
address: >-
Department of Molecular Life Sciences
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich
Switzerland
welcome_url: https://progenetix.org/biosamples/
contact_url: mailto:[email protected]
logoUrl: https://progenetix.org/img/progenetix-logo.png
info:
update_date_time: 2023-01-16T12:45:00
create_date_time: 2015-11-13T00:00:00
update_date_time: 2023-01-16T12:45:00

##############################################################################

phenopacket:
request_entity_path_id: phenopackets
response_entity_id: phenopacket
collection: individuals
response_schema: beaconResultsetsResponse
beacon_schema:
entity_type: phenopacket
schema: https://progenetix.org/services/schemas/phenopacket/
h->o_access_key: individuals._id


134 changes: 105 additions & 29 deletions bin/local/instance_overrides.yaml
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Original file line number Diff line number Diff line change
@@ -1,3 +1,79 @@
################################################################################
# general override for site installation #######################################
################################################################################

local:
beacon_defaults:
defaults:
default_dataset_id: progenetix
entity_defaults:
info:
collection: Null
response_schema: beaconInfoResponse
beacon_schema:
entity_type: configuration
schema: https://progenetix.org/services/schemas/beaconInfoResults/
# TODO: move `content` to `local` file.
content:
beacon_id: org.progenetix
name: Progenetix Cancer Genomics Beacon+
api_version: v2.1.0-beaconplus
version: v2.1.0-beaconplus
id: org.progenetix.beacon
environment: prod
description: >-
Beacon+ provides a forward looking implementation of the Beacon v2 API, with
focus on structural genome variants and metadata based on the cancer and reference
genome profiling data in the Progenetix oncogenomic data resource (https://progenetix.org).
type:
group: org.ga4gh
artifact: beacon
version: v2.1.0-beaconplus
documentation_url: http://docs.progenetix.org
service_url: http://progenetix.org/beacon/
welcome_url: https://progenetix.org/biosamples/
alternative_url: https://progenetix.org
contact_url: mailto:[email protected]
created_at: 2015-11-13T00:00:00
updated_at: 2023-02-16T12:45:00
organization:
id: org.baudisgroup.info
name: Theoretical Cytogenetics and Oncogenomics group at UZH and SIB
description: >
The *Theoretical Cytogenetics and Oncogenomics* group at the University of
Zurich (UZH) and the Swiss Institute of Bioinformatics (SIB) performs research
in cancer genomics and provides bioinformatics tools and cancer genome data
resources to the scientific community.
address: >-
Department of Molecular Life Sciences
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich
Switzerland
welcome_url: https://progenetix.org/biosamples/
contact_url: mailto:[email protected]
logoUrl: https://progenetix.org/img/progenetix-logo.png
info:
update_date_time: 2023-01-16T12:45:00
create_date_time: 2015-11-13T00:00:00
update_date_time: 2023-01-16T12:45:00

############################################################################

phenopacket:
request_entity_path_id: phenopackets
response_entity_id: phenopacket
collection: individuals
response_schema: beaconResultsetsResponse
beacon_schema:
entity_type: phenopacket
schema: https://progenetix.org/services/schemas/phenopacket/
h->o_access_key: individuals._id

################################################################################
# domain specific ##############################################################
################################################################################

progenetix:
domains:
- progenetix.org
Expand Down Expand Up @@ -29,34 +105,34 @@ cancercelllines:
default_dataset_id: cellz
test_domains:
- cancercelllines.test
entity_defaults:
info:
content:
beacon_id: org.cancercelllines
name: Cancer Cell Line Genomics Beacon+
id: org.cancercelllines.beacon
environment: prod
description: >-
The cancercelllines.org Beacon is a specific instance of the Progenetix
Beacon+ environment providing information about genommic variations in
cancer cell lines.
type:
group: org.ga4gh
artifact: beacon
version: v2.1.0-beaconplus
documentation_url: http://docs.cancercelllines.org
service_url: http://cancercelllines.org/beacon/
welcome_url: https://cancercelllines.org/biosamples/
alternative_url: https://cancercelllines.org
entity_defaults:
info:
content:
beacon_id: org.cancercelllines
name: Cancer Cell Line Genomics Beacon+
id: org.cancercelllines.beacon
environment: prod
description: >-
The cancercelllines.org Beacon is a specific instance of the Progenetix
Beacon+ environment providing information about genommic variations in
cancer cell lines.
type:
group: org.ga4gh
artifact: beacon
version: v2.1.0-beaconplus
documentation_url: http://docs.cancercelllines.org
service_url: http://cancercelllines.org/beacon/
welcome_url: https://cancercelllines.org/biosamples/
alternative_url: https://cancercelllines.org
contact_url: mailto:[email protected]
created_at: 2023-07-01T00:00:00
updated_at: 2024-02-24T13:00:00
organization:
welcome_url: https://cancercelllines.org/
contact_url: mailto:[email protected]
created_at: 2023-07-01T00:00:00
updated_at: 2024-02-24T13:00:00
organization:
welcome_url: https://cancercelllines.org/
contact_url: mailto:[email protected]
logoUrl: https://cancercelllines.org/img/cancercelllines-icon-400x300.png
info:
update_date_time: 2024-02-24T12:45:00
create_date_time: 2023-07-01T00:00:00
update_date_time: 2024-02-24T13:00:00
logoUrl: https://cancercelllines.org/img/cancercelllines-icon-400x300.png
info:
update_date_time: 2024-02-24T12:45:00
create_date_time: 2023-07-01T00:00:00
update_date_time: 2024-02-24T13:00:00

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