From 75f3c61e6bfdc83d7c60ea5e45f615be7089a1c5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Oriol=20L=C3=B3pez-Doriga?= Date: Mon, 15 Apr 2024 21:03:39 +0200 Subject: [PATCH] filtering terms scopes fixed --- beacon/db/analyses.py | 2 +- beacon/db/biosamples.py | 2 +- beacon/db/cohorts.py | 2 +- beacon/db/datasets.py | 2 +- beacon/db/extract_filtering_terms.py | 16 ++++++++-------- beacon/db/filters.py | 8 ++++---- beacon/db/g_variants.py | 2 +- beacon/db/individuals.py | 2 +- beacon/db/runs.py | 2 +- beacon/request/cohorts.yml | 1 + beacon/request/datasets.yml | 1 + permissions/public_datasets.yml | 3 ++- 12 files changed, 23 insertions(+), 20 deletions(-) diff --git a/beacon/db/analyses.py b/beacon/db/analyses.py index dde3acf7..d22dd885 100644 --- a/beacon/db/analyses.py +++ b/beacon/db/analyses.py @@ -99,7 +99,7 @@ def get_variants_of_analysis(entry_id: Optional[str], qparams: RequestParams, da return schema, count, dataset_count, docs def get_filtering_terms_of_analyse(entry_id: Optional[str], qparams: RequestParams): - query = {'scope': 'analyses'} + query = {'scopes': 'analysis'} schema = DefaultSchemas.FILTERINGTERMS count = get_count(client.beacon.filtering_terms, query) remove_id={'_id':0} diff --git a/beacon/db/biosamples.py b/beacon/db/biosamples.py index 74360e1d..7837e8a8 100644 --- a/beacon/db/biosamples.py +++ b/beacon/db/biosamples.py @@ -136,7 +136,7 @@ def get_runs_of_biosample(entry_id: Optional[str], qparams: RequestParams, datas return schema, count, dataset_count, docs def get_filtering_terms_of_biosample(entry_id: Optional[str], qparams: RequestParams): - query = {'scope': 'biosamples'} + query = {'scopes': 'biosample'} schema = DefaultSchemas.FILTERINGTERMS count = get_count(client.beacon.filtering_terms, query) remove_id={'_id':0} diff --git a/beacon/db/cohorts.py b/beacon/db/cohorts.py index 7729b55c..d07d7fa0 100644 --- a/beacon/db/cohorts.py +++ b/beacon/db/cohorts.py @@ -173,7 +173,7 @@ def get_biosamples_of_cohort(entry_id: Optional[str], qparams: RequestParams, da def get_filtering_terms_of_cohort(entry_id: Optional[str], qparams: RequestParams): - query = {'scope': 'cohorts'} + query = {'scopes': 'cohort'} schema = DefaultSchemas.FILTERINGTERMS count = get_count(client.beacon.filtering_terms, query) remove_id={'_id':0} diff --git a/beacon/db/datasets.py b/beacon/db/datasets.py index da7b5d5b..2216aa5d 100644 --- a/beacon/db/datasets.py +++ b/beacon/db/datasets.py @@ -207,7 +207,7 @@ def filter_public_datasets(requested_datasets_ids): def get_filtering_terms_of_dataset(entry_id: Optional[str], qparams: RequestParams): - query = {'scope': 'datasets'} + query = {'scopes': 'dataset'} schema = DefaultSchemas.FILTERINGTERMS count = get_count(client.beacon.filtering_terms, query) docs = get_documents( diff --git a/beacon/db/extract_filtering_terms.py b/beacon/db/extract_filtering_terms.py index d18055d6..7fbeb334 100644 --- a/beacon/db/extract_filtering_terms.py +++ b/beacon/db/extract_filtering_terms.py @@ -283,7 +283,7 @@ def get_filtering_object(terms_ids: list, collection_name: str): 'label': ontology_label, # TODO: Use conf.py -> beaconGranularity to not disclouse counts in the filtering terms #'count': get_ontology_term_count(collection_name, onto), - 'scope': [collection_name[0:-1]] + 'scopes': [collection_name[0:-1]] }) terms.append({ @@ -291,14 +291,14 @@ def get_filtering_object(terms_ids: list, collection_name: str): 'id': field, # TODO: Use conf.py -> beaconGranularity to not disclouse counts in the filtering terms #'count': get_ontology_term_count(collection_name, onto), - 'scope': [collection_name[0:-1]] + 'scopes': [collection_name[0:-1]] }) terms.append({ 'type': 'custom', 'id': '{}:{}'.format(field,label), # TODO: Use conf.py -> beaconGranularity to not disclouse counts in the filtering terms #'count': get_ontology_term_count(collection_name, onto), - 'scope': [collection_name[0:-1]] + 'scopes': [collection_name[0:-1]] }) if value_id is not None: terms.append({ @@ -306,7 +306,7 @@ def get_filtering_object(terms_ids: list, collection_name: str): 'id': value_id, # TODO: Use conf.py -> beaconGranularity to not disclouse counts in the filtering terms #'count': get_ontology_term_count(collection_name, onto), - 'scope': [collection_name[0:-1]] + 'scopes': [collection_name[0:-1]] }) print(terms) @@ -369,9 +369,9 @@ def merge_terms(): #print(repeated_term) id=repeated_term["id"] label=repeated_term["label"] - if repeated_term['scope'] != []: - if repeated_term['scope'][0] not in array_of_scopes: - array_of_scopes.append(repeated_term['scope'][0]) + if repeated_term['scopes'] != []: + if repeated_term['scopes'][0] not in array_of_scopes: + array_of_scopes.append(repeated_term['scopes'][0]) if array_of_scopes != []: new_terms.append({ 'type': 'ontology', @@ -379,7 +379,7 @@ def merge_terms(): 'label': label, # TODO: Use conf.py -> beaconGranularity to not disclouse counts in the filtering terms #'count': get_ontology_term_count(collection_name, onto), - 'scope': array_of_scopes + 'scopes': array_of_scopes }) client.beacon.filtering_terms.delete_many({"id": repeated_id}) client.beacon.filtering_terms.insert_many(new_terms) diff --git a/beacon/db/filters.py b/beacon/db/filters.py index c8408830..d2c7e6e1 100644 --- a/beacon/db/filters.py +++ b/beacon/db/filters.py @@ -439,7 +439,7 @@ def apply_ontology_filter(query: dict, filter: OntologyFilter, collection: str, final_term_list.append(filter.id) query_filtering={} query_filtering['$and']=[] - dict_scope['scope']=scope + dict_scope['scopes']=scope query_filtering['$and'].append(dict_scope) dict_id={} dict_id['id']=filter.id @@ -514,7 +514,7 @@ def apply_ontology_filter(query: dict, filter: OntologyFilter, collection: str, query_filtering['$and']=[] dict_scope={} - dict_scope['scope']=scope + dict_scope['scopes']=scope dict_id={} dict_id['id']=filter.id query_filtering['$and'].append(dict_id) @@ -540,7 +540,7 @@ def apply_ontology_filter(query: dict, filter: OntologyFilter, collection: str, dict_id={} dict_id['id']=dict_regex dict_scope={} - dict_scope['scope']=scope + dict_scope['scopes']=scope query_filtering['$and'].append(dict_id) query_filtering['$and'].append(dict_scope) docs_2 = get_documents( @@ -573,7 +573,7 @@ def apply_ontology_filter(query: dict, filter: OntologyFilter, collection: str, query_filtering={} query_filtering['$and']=[] dict_scope={} - dict_scope['scope']=scope + dict_scope['scopes']=scope query_filtering['$and'].append(dict_scope) dict_id={} dict_id['id']=filter.id diff --git a/beacon/db/g_variants.py b/beacon/db/g_variants.py index 8d1dcfd3..9479d524 100644 --- a/beacon/db/g_variants.py +++ b/beacon/db/g_variants.py @@ -360,7 +360,7 @@ def get_analyses_of_variant(entry_id: Optional[str], qparams: RequestParams, dat return schema, count, dataset_count, docs def get_filtering_terms_of_genomicvariation(entry_id: Optional[str], qparams: RequestParams): - query = {'scope': 'genomicVariations'} + query = {'scopes': 'genomicVariation'} schema = DefaultSchemas.FILTERINGTERMS count = get_count(client.beacon.filtering_terms, query) remove_id={'_id':0} diff --git a/beacon/db/individuals.py b/beacon/db/individuals.py index e23c770c..f2a28464 100644 --- a/beacon/db/individuals.py +++ b/beacon/db/individuals.py @@ -297,7 +297,7 @@ def get_biosamples_of_individual(entry_id: Optional[str], qparams: RequestParams def get_filtering_terms_of_individual(entry_id: Optional[str], qparams: RequestParams): - query = {'scope': 'individuals'} + query = {'scopes': 'individual'} schema = DefaultSchemas.FILTERINGTERMS count = get_count(client.beacon.filtering_terms, query) remove_id={'_id':0} diff --git a/beacon/db/runs.py b/beacon/db/runs.py index 7b027bc9..dcc2cbee 100644 --- a/beacon/db/runs.py +++ b/beacon/db/runs.py @@ -228,7 +228,7 @@ def get_analyses_of_run(entry_id: Optional[str], qparams: RequestParams, dataset return schema, count, dataset_count, docs def get_filtering_terms_of_run(entry_id: Optional[str], qparams: RequestParams): - query = {'scope': 'runs'} + query = {'scopes': 'run'} schema = DefaultSchemas.FILTERINGTERMS count = get_count(client.beacon.filtering_terms, query) remove_id={'_id':0} diff --git a/beacon/request/cohorts.yml b/beacon/request/cohorts.yml index 06a5e46c..0c6ac538 100644 --- a/beacon/request/cohorts.yml +++ b/beacon/request/cohorts.yml @@ -1,5 +1,6 @@ rd_connect_synthetic_cohort: ['Case1F', 'Case1C', 'Case1M', 'Case2F', 'Case2C', 'Case2M', 'Case3F', 'Case3C', 'Case3M', 'Case4F', 'Case4C', 'Case4M', 'Case5F', 'Case5C', 'Case5M', 'Case6F', 'Case6C', 'Case6M'] AV_Dataset: ["AV0101", "AV0102"] +EOSC4Cancer_Synthetic_Colorectal_Cancer_Genomic_data: ['186_case', '186_control', '186', '185_case', '185_control', '185', '187_case', '187_control', '187', '187_case', '187_control', '187'] coadread_tcga_pan_can_atlas_2018: ['TCGA-AF-2687-01', 'TCGA-AF-2689-01', 'TCGA-AF-2690-01', 'TCGA-AF-2691-01', 'TCGA-AF-2692-01', 'TCGA-AF-2693-01', 'TCGA-AF-3400-01', 'TCGA-AF-3911-01', 'TCGA-AF-4110-01', 'TCGA-AF-5654-01', 'TCGA-AF-6136-01', 'TCGA-AF-6655-01', 'TCGA-AF-6672-01', 'TCGA-AF-A56K-01', 'TCGA-AF-A56L-01', 'TCGA-AF-A56N-01', 'TCGA-AG-3574-01', 'TCGA-AG-3575-01', 'TCGA-AG-3578-01', 'TCGA-AG-3580-01', 'TCGA-AG-3581-01', 'TCGA-AG-3582-01', 'TCGA-AG-3583-01', 'TCGA-AG-3584-01', 'TCGA-AG-3586-01', 'TCGA-AG-3587-01', 'TCGA-AG-3591-01', 'TCGA-AG-3592-01', 'TCGA-AG-3593-01', 'TCGA-AG-3594-01', 'TCGA-AG-3598-01', 'TCGA-AG-3599-01', 'TCGA-AG-3600-01', 'TCGA-AG-3601-01', 'TCGA-AG-3602-01', 'TCGA-AG-3605-01', 'TCGA-AG-3608-01', 'TCGA-AG-3609-01', 'TCGA-AG-3725-01', 'TCGA-AG-3726-01', 'TCGA-AG-3727-01', 'TCGA-AG-3728-01', 'TCGA-AG-3731-01', 'TCGA-AG-3732-01', 'TCGA-AG-3742-01', 'TCGA-AG-3878-01', 'TCGA-AG-3881-01', 'TCGA-AG-3882-01', 'TCGA-AG-3883-01', 'TCGA-AG-3885-01', 'TCGA-AG-3887-01', 'TCGA-AG-3890-01', 'TCGA-AG-3892-01', 'TCGA-AG-3893-01', 'TCGA-AG-3894-01', 'TCGA-AG-3896-01', 'TCGA-AG-3898-01', 'TCGA-AG-3901-01', 'TCGA-AG-3902-01', 'TCGA-AG-3909-01', 'TCGA-AG-3999-01', 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'TCGA-CA-6715', 'TCGA-CA-6716', 'TCGA-CA-6717', 'TCGA-CA-6718', 'TCGA-CA-6719', 'TCGA-CI-6619', 'TCGA-CI-6620', 'TCGA-CI-6621', 'TCGA-CI-6622', 'TCGA-CI-6623', 'TCGA-CI-6624', 'TCGA-CK-4947', 'TCGA-CK-4948', 'TCGA-CK-4950', 'TCGA-CK-4951', 'TCGA-CK-4952', 'TCGA-CK-5912', 'TCGA-CK-5913', 'TCGA-CK-5914', 'TCGA-CK-5915', 'TCGA-CK-5916', 'TCGA-CK-6746', 'TCGA-CK-6747', 'TCGA-CK-6748', 'TCGA-CK-6751', 'TCGA-CL-4957', 'TCGA-CL-5917', 'TCGA-CL-5918', 'TCGA-CM-4743', 'TCGA-CM-4744', 'TCGA-CM-4746', 'TCGA-CM-4747', 'TCGA-CM-4748', 'TCGA-CM-4750', 'TCGA-CM-4751', 'TCGA-CM-4752', 'TCGA-CM-5341', 'TCGA-CM-5344', 'TCGA-CM-5348', 'TCGA-CM-5349', 'TCGA-CM-5860', 'TCGA-CM-5861', 'TCGA-CM-5862', 'TCGA-CM-5863', 'TCGA-CM-5864', 'TCGA-CM-5868', 'TCGA-CM-6161', 'TCGA-CM-6162', 'TCGA-CM-6163', 'TCGA-CM-6164', 'TCGA-CM-6165', 'TCGA-CM-6166', 'TCGA-CM-6167', 'TCGA-CM-6168', 'TCGA-CM-6169', 'TCGA-CM-6170', 'TCGA-CM-6171', 'TCGA-CM-6172', 'TCGA-CM-6674', 'TCGA-CM-6675', 'TCGA-CM-6676', 'TCGA-CM-6677', 'TCGA-CM-6678', 'TCGA-CM-6679', 'TCGA-CM-6680', 'TCGA-D5-5537', 'TCGA-D5-5538', 'TCGA-D5-5539', 'TCGA-D5-5540', 'TCGA-D5-5541', 'TCGA-D5-6529', 'TCGA-D5-6530', 'TCGA-D5-6531', 'TCGA-D5-6532', 'TCGA-D5-6533', 'TCGA-D5-6534', 'TCGA-D5-6535', 'TCGA-D5-6536', 'TCGA-D5-6537', 'TCGA-D5-6538', 'TCGA-D5-6539', 'TCGA-D5-6540', 'TCGA-D5-6541', 'TCGA-D5-6898', 'TCGA-D5-6920', 'TCGA-D5-6922', 'TCGA-D5-6923', 'TCGA-D5-6924', 'TCGA-D5-6926', 'TCGA-D5-6927', 'TCGA-D5-6928', 'TCGA-D5-6929', 'TCGA-D5-6930', 'TCGA-D5-6931', 'TCGA-D5-6932', 'TCGA-D5-7000', 'TCGA-DC-4745', 'TCGA-DC-4749', 'TCGA-DC-5337', 'TCGA-DC-5869', 'TCGA-DC-6154', 'TCGA-DC-6155', 'TCGA-DC-6156', 'TCGA-DC-6157', 'TCGA-DC-6158', 'TCGA-DC-6160', 'TCGA-DC-6681', 'TCGA-DC-6682', 'TCGA-DC-6683', 'TCGA-DM-A0X9', 'TCGA-DM-A0XD', 'TCGA-DM-A0XF', 'TCGA-DM-A1D0', 'TCGA-DM-A1D4', 'TCGA-DM-A1D6', 'TCGA-DM-A1D7', 'TCGA-DM-A1D8', 'TCGA-DM-A1D9', 'TCGA-DM-A1DA', 'TCGA-DM-A1DB', 'TCGA-DM-A1HA', 'TCGA-DM-A1HB', 'TCGA-DM-A280', 'TCGA-DM-A282', 'TCGA-DM-A285', 'TCGA-DM-A288', 'TCGA-DM-A28A', 'TCGA-DM-A28C', 'TCGA-DM-A28E', 'TCGA-DM-A28F', 'TCGA-DM-A28G', 'TCGA-DM-A28H', 'TCGA-DM-A28K', 'TCGA-DM-A28M', 'TCGA-DT-5265', 'TCGA-DY-A0XA', 'TCGA-DY-A1DC', 'TCGA-DY-A1DD', 'TCGA-DY-A1DE', 'TCGA-DY-A1DF', 'TCGA-DY-A1DG', 'TCGA-DY-A1H8', 'TCGA-EF-5830', 'TCGA-EF-5831', 'TCGA-EI-6506', 'TCGA-EI-6507', 'TCGA-EI-6508', 'TCGA-EI-6509', 'TCGA-EI-6510', 'TCGA-EI-6511', 'TCGA-EI-6512', 'TCGA-EI-6513', 'TCGA-EI-6514', 'TCGA-EI-6881', 'TCGA-EI-6882', 'TCGA-EI-6883', 'TCGA-EI-6884', 'TCGA-EI-6885', 'TCGA-EI-6917', 'TCGA-EI-7002', 'TCGA-EI-7004', 'TCGA-F4-6459', 'TCGA-F4-6460', 'TCGA-F4-6461', 'TCGA-F4-6463', 'TCGA-F4-6569', 'TCGA-F4-6570', 'TCGA-F4-6703', 'TCGA-F4-6704', 'TCGA-F4-6805', 'TCGA-F4-6806', 'TCGA-F4-6807', 'TCGA-F4-6808', 'TCGA-F4-6809', 'TCGA-F4-6854', 'TCGA-F4-6855', 'TCGA-F4-6856', 'TCGA-F5-6464', 'TCGA-F5-6465', 'TCGA-F5-6571', 'TCGA-F5-6702', 'TCGA-F5-6810', 'TCGA-F5-6811', 'TCGA-F5-6812', 'TCGA-F5-6813', 'TCGA-F5-6814', 'TCGA-F5-6861', 'TCGA-F5-6863', 'TCGA-F5-6864', 'TCGA-G4-6293', 'TCGA-G4-6294', 'TCGA-G4-6295', 'TCGA-G4-6297', 'TCGA-G4-6298', 'TCGA-G4-6299', 'TCGA-G4-6302', 'TCGA-G4-6303', 'TCGA-G4-6304', 'TCGA-G4-6306', 'TCGA-G4-6307', 'TCGA-G4-6309', 'TCGA-G4-6311', 'TCGA-G4-6315', 'TCGA-G4-6317', 'TCGA-G4-6320', 'TCGA-G4-6321', 'TCGA-G4-6322', 'TCGA-G4-6323', 'TCGA-G4-6586', 'TCGA-G4-6588', 'TCGA-G4-6626', 'TCGA-G4-6627', 'TCGA-G4-6628', 'TCGA-G5-6641', 'TCGA-NH-A50T', 'TCGA-NH-A50U', 'TCGA-NH-A50V', 'TCGA-NH-A5IV', 'TCGA-NH-A6GA', 'TCGA-NH-A6GB', 'TCGA-NH-A6GC', 'TCGA-NH-A8F7', 'TCGA-NH-A8F8', 'TCGA-QG-A5YV', 'TCGA-QG-A5YW', 'TCGA-QG-A5YX', 'TCGA-QG-A5Z1', 'TCGA-QG-A5Z2', 'TCGA-QL-A97D', 'TCGA-RU-A8FL', 'TCGA-SS-A7HO', 'TCGA-T9-A92H', 'TCGA-WS-AB45'] CINECA_synthetic_cohort_UK1: [ "HG00096", diff --git a/beacon/request/datasets.yml b/beacon/request/datasets.yml index e46f7ce6..a93b9a5b 100644 --- a/beacon/request/datasets.yml +++ b/beacon/request/datasets.yml @@ -1,5 +1,6 @@ rd-connect_dataset: ['Case1_IC', 'Case1_F', 'Case1_M', 'Case2_IC', 'Case2_F', 'Case2_M', 'Case3_IC', 'Case2_F', 'Case2_M', 'Case4_IC', 'Case4_F', 'Case4_M', 'Case5_IC', 'Case5_F', 'Case5_M', 'Case6_IC', 'Case6_F', 'Case6_M','Case1F', 'Case1C', 'Case1M', 'Case2F', 'Case2C', 'Case2M', 'Case3F', 'Case3C', 'Case3M', 'Case4F', 'Case4C', 'Case4M', 'Case5F', 'Case5C', 'Case5M', 'Case6F', 'Case6C', 'Case6M'] AV_Dataset: ["AV0101", "AV0102"] +B1MG-COADREAD: ['186_case', '186_control', '186', '185_case', '185_control', '185', '187_case', '187_control', '187', '187_case', '187_control', '187'] coadread_tcga_pan_can_atlas_2018: ['TCGA-AF-2687-01', 'TCGA-AF-2689-01', 'TCGA-AF-2690-01', 'TCGA-AF-2691-01', 'TCGA-AF-2692-01', 'TCGA-AF-2693-01', 'TCGA-AF-3400-01', 'TCGA-AF-3911-01', 'TCGA-AF-4110-01', 'TCGA-AF-5654-01', 'TCGA-AF-6136-01', 'TCGA-AF-6655-01', 'TCGA-AF-6672-01', 'TCGA-AF-A56K-01', 'TCGA-AF-A56L-01', 'TCGA-AF-A56N-01', 'TCGA-AG-3574-01', 'TCGA-AG-3575-01', 'TCGA-AG-3578-01', 'TCGA-AG-3580-01', 'TCGA-AG-3581-01', 'TCGA-AG-3582-01', 'TCGA-AG-3583-01', 'TCGA-AG-3584-01', 'TCGA-AG-3586-01', 'TCGA-AG-3587-01', 'TCGA-AG-3591-01', 'TCGA-AG-3592-01', 'TCGA-AG-3593-01', 'TCGA-AG-3594-01', 'TCGA-AG-3598-01', 'TCGA-AG-3599-01', 'TCGA-AG-3600-01', 'TCGA-AG-3601-01', 'TCGA-AG-3602-01', 'TCGA-AG-3605-01', 'TCGA-AG-3608-01', 'TCGA-AG-3609-01', 'TCGA-AG-3725-01', 'TCGA-AG-3726-01', 'TCGA-AG-3727-01', 'TCGA-AG-3728-01', 'TCGA-AG-3731-01', 'TCGA-AG-3732-01', 'TCGA-AG-3742-01', 'TCGA-AG-3878-01', 'TCGA-AG-3881-01', 'TCGA-AG-3882-01', 'TCGA-AG-3883-01', 'TCGA-AG-3885-01', 'TCGA-AG-3887-01', 'TCGA-AG-3890-01', 'TCGA-AG-3892-01', 'TCGA-AG-3893-01', 'TCGA-AG-3894-01', 'TCGA-AG-3896-01', 'TCGA-AG-3898-01', 'TCGA-AG-3901-01', 'TCGA-AG-3902-01', 'TCGA-AG-3909-01', 'TCGA-AG-3999-01', 'TCGA-AG-4001-01', 'TCGA-AG-4005-01', 'TCGA-AG-4007-01', 'TCGA-AG-4008-01', 'TCGA-AG-4015-01', 'TCGA-AG-4021-01', 'TCGA-AG-4022-01', 'TCGA-AG-A002-01', 'TCGA-AG-A008-01', 'TCGA-AG-A00C-01', 'TCGA-AG-A00Y-01', 'TCGA-AG-A011-01', 'TCGA-AG-A015-01', 'TCGA-AG-A016-01', 'TCGA-AG-A01J-01', 'TCGA-AG-A01L-01', 'TCGA-AG-A01N-01', 'TCGA-AG-A01W-01', 'TCGA-AG-A01Y-01', 'TCGA-AG-A020-01', 'TCGA-AG-A025-01', 'TCGA-AG-A026-01', 'TCGA-AG-A02G-01', 'TCGA-AG-A02N-01', 'TCGA-AG-A02X-01', 'TCGA-AG-A032-01', 'TCGA-AH-6544-01', 'TCGA-AH-6547-01', 'TCGA-AH-6643-01', 'TCGA-AH-6644-01', 'TCGA-AH-6897-01', 'TCGA-AH-6903-01', 'TCGA-CI-6619-01', 'TCGA-CI-6620-01', 'TCGA-CI-6621-01', 'TCGA-CI-6622-01', 'TCGA-CI-6623-01', 'TCGA-CI-6624-01', 'TCGA-CL-4957-01', 'TCGA-CL-5917-01', 'TCGA-CL-5918-01', 'TCGA-DC-4745-01', 'TCGA-DC-4749-01', 'TCGA-DC-5337-01', 'TCGA-DC-5869-01', 'TCGA-DC-6154-01', 'TCGA-DC-6155-01', 'TCGA-DC-6156-01', 'TCGA-DC-6157-01', 'TCGA-DC-6158-01', 'TCGA-DC-6160-01', 'TCGA-DC-6681-01', 'TCGA-DC-6682-01', 'TCGA-DC-6683-01', 'TCGA-DT-5265-01', 'TCGA-DY-A0XA-01', 'TCGA-DY-A1DC-01', 'TCGA-DY-A1DD-01', 'TCGA-DY-A1DE-01', 'TCGA-DY-A1DF-01', 'TCGA-DY-A1DG-01', 'TCGA-DY-A1H8-01', 'TCGA-EF-5830-01', 'TCGA-EF-5831-01', 'TCGA-EI-6506-01', 'TCGA-EI-6507-01', 'TCGA-EI-6508-01', 'TCGA-EI-6509-01', 'TCGA-EI-6510-01', 'TCGA-EI-6511-01', 'TCGA-EI-6512-01', 'TCGA-EI-6513-01', 'TCGA-EI-6514-01', 'TCGA-EI-6881-01', 'TCGA-EI-6882-01', 'TCGA-EI-6883-01', 'TCGA-EI-6884-01', 'TCGA-EI-6885-01', 'TCGA-EI-6917-01', 'TCGA-EI-7002-01', 'TCGA-EI-7004-01', 'TCGA-F5-6464-01', 'TCGA-F5-6465-01', 'TCGA-F5-6571-01', 'TCGA-F5-6702-01', 'TCGA-F5-6810-01', 'TCGA-F5-6811-01', 'TCGA-F5-6812-01', 'TCGA-F5-6813-01', 'TCGA-F5-6814-01', 'TCGA-F5-6861-01', 'TCGA-F5-6863-01', 'TCGA-F5-6864-01', 'TCGA-G5-6641-01', 'TCGA-3L-AA1B-01', 'TCGA-4N-A93T-01', 'TCGA-4T-AA8H-01', 'TCGA-5M-AAT4-01', 'TCGA-5M-AAT6-01', 'TCGA-5M-AATE-01', 'TCGA-A6-2671-01', 'TCGA-A6-2672-01', 'TCGA-A6-2674-01', 'TCGA-A6-2675-01', 'TCGA-A6-2676-01', 'TCGA-A6-2677-01', 'TCGA-A6-2678-01', 'TCGA-A6-2679-01', 'TCGA-A6-2680-01', 'TCGA-A6-2681-01', 'TCGA-A6-2682-01', 'TCGA-A6-2683-01', 'TCGA-A6-2684-01', 'TCGA-A6-2685-01', 'TCGA-A6-2686-01', 'TCGA-A6-3807-01', 'TCGA-A6-3808-01', 'TCGA-A6-3809-01', 'TCGA-A6-3810-01', 'TCGA-A6-4105-01', 'TCGA-A6-4107-01', 'TCGA-A6-5656-01', 'TCGA-A6-5657-01', 'TCGA-A6-5659-01', 'TCGA-A6-5660-01', 'TCGA-A6-5661-01', 'TCGA-A6-5662-01', 'TCGA-A6-5664-01', 'TCGA-A6-5665-01', 'TCGA-A6-5666-01', 'TCGA-A6-5667-01', 'TCGA-A6-6137-01', 'TCGA-A6-6138-01', 'TCGA-A6-6140-01', 'TCGA-A6-6141-01', 'TCGA-A6-6142-01', 'TCGA-A6-6648-01', 'TCGA-A6-6649-01', 'TCGA-A6-6650-01', 'TCGA-A6-6651-01', 'TCGA-A6-6652-01', 'TCGA-A6-6653-01', 'TCGA-A6-6654-01', 'TCGA-A6-6780-01', 'TCGA-A6-6781-01', 'TCGA-A6-6782-01', 'TCGA-A6-A565-01', 'TCGA-A6-A566-01', 'TCGA-A6-A567-01', 'TCGA-A6-A56B-01', 'TCGA-A6-A5ZU-01', 'TCGA-AA-3488-01', 'TCGA-AA-3489-01', 'TCGA-AA-3492-01', 'TCGA-AA-3494-01', 'TCGA-AA-3495-01', 'TCGA-AA-3496-01', 'TCGA-AA-3502-01', 'TCGA-AA-3506-01', 'TCGA-AA-3510-01', 'TCGA-AA-3511-01', 'TCGA-AA-3514-01', 'TCGA-AA-3517-01', 'TCGA-AA-3518-01', 'TCGA-AA-3519-01', 'TCGA-AA-3520-01', 'TCGA-AA-3521-01', 'TCGA-AA-3522-01', 'TCGA-AA-3524-01', 'TCGA-AA-3525-01', 'TCGA-AA-3526-01', 'TCGA-AA-3527-01', 'TCGA-AA-3529-01', 'TCGA-AA-3530-01', 'TCGA-AA-3531-01', 'TCGA-AA-3532-01', 'TCGA-AA-3534-01', 'TCGA-AA-3538-01', 'TCGA-AA-3542-01', 'TCGA-AA-3543-01', 'TCGA-AA-3544-01', 'TCGA-AA-3548-01', 'TCGA-AA-3549-01', 'TCGA-AA-3552-01', 'TCGA-AA-3553-01', 'TCGA-AA-3555-01', 'TCGA-AA-3558-01', 'TCGA-AA-3560-01', 'TCGA-AA-3561-01', 'TCGA-AA-3655-01', 'TCGA-AA-3660-01', 'TCGA-AA-3663-01', 'TCGA-AA-3664-01', 'TCGA-AA-3666-01', 'TCGA-AA-3667-01', 'TCGA-AA-3673-01', 'TCGA-AA-3675-01', 'TCGA-AA-3678-01', 'TCGA-AA-3679-01', 'TCGA-AA-3680-01', 'TCGA-AA-3681-01', 'TCGA-AA-3684-01', 'TCGA-AA-3685-01', 'TCGA-AA-3688-01', 'TCGA-AA-3692-01', 'TCGA-AA-3693-01', 'TCGA-AA-3695-01', 'TCGA-AA-3696-01', 'TCGA-AA-3710-01', 'TCGA-AA-3712-01', 'TCGA-AA-3713-01', 'TCGA-AA-3715-01', 'TCGA-AA-3811-01', 'TCGA-AA-3812-01', 'TCGA-AA-3814-01', 'TCGA-AA-3818-01', 'TCGA-AA-3819-01', 'TCGA-AA-3821-01', 'TCGA-AA-3831-01', 'TCGA-AA-3833-01', 'TCGA-AA-3837-01', 'TCGA-AA-3841-01', 'TCGA-AA-3842-01', 'TCGA-AA-3844-01', 'TCGA-AA-3845-01', 'TCGA-AA-3846-01', 'TCGA-AA-3848-01', 'TCGA-AA-3850-01', 'TCGA-AA-3851-01', 'TCGA-AA-3852-01', 'TCGA-AA-3854-01', 'TCGA-AA-3855-01', 'TCGA-AA-3856-01', 'TCGA-AA-3858-01', 'TCGA-AA-3864-01', 'TCGA-AA-3866-01', 'TCGA-AA-3867-01', 'TCGA-AA-3869-01', 'TCGA-AA-3870-01', 'TCGA-AA-3872-01', 'TCGA-AA-3875-01', 'TCGA-AA-3877-01', 'TCGA-AA-3930-01', 'TCGA-AA-3939-01', 'TCGA-AA-3941-01', 'TCGA-AA-3947-01', 'TCGA-AA-3949-01', 'TCGA-AA-3950-01', 'TCGA-AA-3952-01', 'TCGA-AA-3955-01', 'TCGA-AA-3956-01', 'TCGA-AA-3966-01', 'TCGA-AA-3968-01', 'TCGA-AA-3971-01', 'TCGA-AA-3973-01', 'TCGA-AA-3975-01', 'TCGA-AA-3976-01', 'TCGA-AA-3977-01', 'TCGA-AA-3979-01', 'TCGA-AA-3980-01', 'TCGA-AA-3982-01', 'TCGA-AA-3984-01', 'TCGA-AA-3986-01', 'TCGA-AA-3989-01', 'TCGA-AA-3994-01', 'TCGA-AA-A004-01', 'TCGA-AA-A00A-01', 'TCGA-AA-A00D-01', 'TCGA-AA-A00E-01', 'TCGA-AA-A00F-01', 'TCGA-AA-A00J-01', 'TCGA-AA-A00K-01', 'TCGA-AA-A00L-01', 'TCGA-AA-A00N-01', 'TCGA-AA-A00O-01', 'TCGA-AA-A00Q-01', 'TCGA-AA-A00R-01', 'TCGA-AA-A00U-01', 'TCGA-AA-A00W-01', 'TCGA-AA-A00Z-01', 'TCGA-AA-A010-01', 'TCGA-AA-A017-01', 'TCGA-AA-A01C-01', 'TCGA-AA-A01D-01', 'TCGA-AA-A01F-01', 'TCGA-AA-A01G-01', 'TCGA-AA-A01I-01', 'TCGA-AA-A01K-01', 'TCGA-AA-A01P-01', 'TCGA-AA-A01Q-01', 'TCGA-AA-A01R-01', 'TCGA-AA-A01S-01', 'TCGA-AA-A01T-01', 'TCGA-AA-A01V-01', 'TCGA-AA-A01X-01', 'TCGA-AA-A01Z-01', 'TCGA-AA-A022-01', 'TCGA-AA-A024-01', 'TCGA-AA-A029-01', 'TCGA-AA-A02E-01', 'TCGA-AA-A02F-01', 'TCGA-AA-A02H-01', 'TCGA-AA-A02J-01', 'TCGA-AA-A02O-01', 'TCGA-AA-A02R-01', 'TCGA-AA-A02W-01', 'TCGA-AA-A02Y-01', 'TCGA-AA-A03F-01', 'TCGA-AA-A03J-01', 'TCGA-AD-5900-01', 'TCGA-AD-6548-01', 'TCGA-AD-6888-01', 'TCGA-AD-6889-01', 'TCGA-AD-6890-01', 'TCGA-AD-6895-01', 'TCGA-AD-6899-01', 'TCGA-AD-6901-01', 'TCGA-AD-6963-01', 'TCGA-AD-6964-01', 'TCGA-AD-6965-01', 'TCGA-AD-A5EJ-01', 'TCGA-AD-A5EK-01', 'TCGA-AM-5820-01', 'TCGA-AM-5821-01', 'TCGA-AU-3779-01', 'TCGA-AU-6004-01', 'TCGA-AY-4070-01', 'TCGA-AY-4071-01', 'TCGA-AY-5543-01', 'TCGA-AY-6196-01', 'TCGA-AY-6197-01', 'TCGA-AY-6386-01', 'TCGA-AY-A54L-01', 'TCGA-AY-A69D-01', 'TCGA-AY-A71X-01', 'TCGA-AY-A8YK-01', 'TCGA-AZ-4308-01', 'TCGA-AZ-4313-01', 'TCGA-AZ-4315-01', 'TCGA-AZ-4323-01', 'TCGA-AZ-4614-01', 'TCGA-AZ-4615-01', 'TCGA-AZ-4616-01', 'TCGA-AZ-4681-01', 'TCGA-AZ-4682-01', 'TCGA-AZ-4684-01', 'TCGA-AZ-5403-01', 'TCGA-AZ-5407-01', 'TCGA-AZ-6598-01', 'TCGA-AZ-6599-01', 'TCGA-AZ-6600-01', 'TCGA-AZ-6603-01', 'TCGA-AZ-6605-01', 'TCGA-AZ-6606-01', 'TCGA-AZ-6607-01', 'TCGA-CA-5254-01', 'TCGA-CA-5255-01', 'TCGA-CA-5256-01', 'TCGA-CA-5796-01', 'TCGA-CA-5797-01', 'TCGA-CA-6715-01', 'TCGA-CA-6716-01', 'TCGA-CA-6717-01', 'TCGA-CA-6718-01', 'TCGA-CA-6719-01', 'TCGA-CK-4947-01', 'TCGA-CK-4948-01', 'TCGA-CK-4950-01', 'TCGA-CK-4951-01', 'TCGA-CK-4952-01', 'TCGA-CK-5912-01', 'TCGA-CK-5913-01', 'TCGA-CK-5914-01', 'TCGA-CK-5915-01', 'TCGA-CK-5916-01', 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'TCGA-CK-4948', 'TCGA-CK-4950', 'TCGA-CK-4951', 'TCGA-CK-4952', 'TCGA-CK-5912', 'TCGA-CK-5913', 'TCGA-CK-5914', 'TCGA-CK-5915', 'TCGA-CK-5916', 'TCGA-CK-6746', 'TCGA-CK-6747', 'TCGA-CK-6748', 'TCGA-CK-6751', 'TCGA-CL-4957', 'TCGA-CL-5917', 'TCGA-CL-5918', 'TCGA-CM-4743', 'TCGA-CM-4744', 'TCGA-CM-4746', 'TCGA-CM-4747', 'TCGA-CM-4748', 'TCGA-CM-4750', 'TCGA-CM-4751', 'TCGA-CM-4752', 'TCGA-CM-5341', 'TCGA-CM-5344', 'TCGA-CM-5348', 'TCGA-CM-5349', 'TCGA-CM-5860', 'TCGA-CM-5861', 'TCGA-CM-5862', 'TCGA-CM-5863', 'TCGA-CM-5864', 'TCGA-CM-5868', 'TCGA-CM-6161', 'TCGA-CM-6162', 'TCGA-CM-6163', 'TCGA-CM-6164', 'TCGA-CM-6165', 'TCGA-CM-6166', 'TCGA-CM-6167', 'TCGA-CM-6168', 'TCGA-CM-6169', 'TCGA-CM-6170', 'TCGA-CM-6171', 'TCGA-CM-6172', 'TCGA-CM-6674', 'TCGA-CM-6675', 'TCGA-CM-6676', 'TCGA-CM-6677', 'TCGA-CM-6678', 'TCGA-CM-6679', 'TCGA-CM-6680', 'TCGA-D5-5537', 'TCGA-D5-5538', 'TCGA-D5-5539', 'TCGA-D5-5540', 'TCGA-D5-5541', 'TCGA-D5-6529', 'TCGA-D5-6530', 'TCGA-D5-6531', 'TCGA-D5-6532', 'TCGA-D5-6533', 'TCGA-D5-6534', 'TCGA-D5-6535', 'TCGA-D5-6536', 'TCGA-D5-6537', 'TCGA-D5-6538', 'TCGA-D5-6539', 'TCGA-D5-6540', 'TCGA-D5-6541', 'TCGA-D5-6898', 'TCGA-D5-6920', 'TCGA-D5-6922', 'TCGA-D5-6923', 'TCGA-D5-6924', 'TCGA-D5-6926', 'TCGA-D5-6927', 'TCGA-D5-6928', 'TCGA-D5-6929', 'TCGA-D5-6930', 'TCGA-D5-6931', 'TCGA-D5-6932', 'TCGA-D5-7000', 'TCGA-DC-4745', 'TCGA-DC-4749', 'TCGA-DC-5337', 'TCGA-DC-5869', 'TCGA-DC-6154', 'TCGA-DC-6155', 'TCGA-DC-6156', 'TCGA-DC-6157', 'TCGA-DC-6158', 'TCGA-DC-6160', 'TCGA-DC-6681', 'TCGA-DC-6682', 'TCGA-DC-6683', 'TCGA-DM-A0X9', 'TCGA-DM-A0XD', 'TCGA-DM-A0XF', 'TCGA-DM-A1D0', 'TCGA-DM-A1D4', 'TCGA-DM-A1D6', 'TCGA-DM-A1D7', 'TCGA-DM-A1D8', 'TCGA-DM-A1D9', 'TCGA-DM-A1DA', 'TCGA-DM-A1DB', 'TCGA-DM-A1HA', 'TCGA-DM-A1HB', 'TCGA-DM-A280', 'TCGA-DM-A282', 'TCGA-DM-A285', 'TCGA-DM-A288', 'TCGA-DM-A28A', 'TCGA-DM-A28C', 'TCGA-DM-A28E', 'TCGA-DM-A28F', 'TCGA-DM-A28G', 'TCGA-DM-A28H', 'TCGA-DM-A28K', 'TCGA-DM-A28M', 'TCGA-DT-5265', 'TCGA-DY-A0XA', 'TCGA-DY-A1DC', 'TCGA-DY-A1DD', 'TCGA-DY-A1DE', 'TCGA-DY-A1DF', 'TCGA-DY-A1DG', 'TCGA-DY-A1H8', 'TCGA-EF-5830', 'TCGA-EF-5831', 'TCGA-EI-6506', 'TCGA-EI-6507', 'TCGA-EI-6508', 'TCGA-EI-6509', 'TCGA-EI-6510', 'TCGA-EI-6511', 'TCGA-EI-6512', 'TCGA-EI-6513', 'TCGA-EI-6514', 'TCGA-EI-6881', 'TCGA-EI-6882', 'TCGA-EI-6883', 'TCGA-EI-6884', 'TCGA-EI-6885', 'TCGA-EI-6917', 'TCGA-EI-7002', 'TCGA-EI-7004', 'TCGA-F4-6459', 'TCGA-F4-6460', 'TCGA-F4-6461', 'TCGA-F4-6463', 'TCGA-F4-6569', 'TCGA-F4-6570', 'TCGA-F4-6703', 'TCGA-F4-6704', 'TCGA-F4-6805', 'TCGA-F4-6806', 'TCGA-F4-6807', 'TCGA-F4-6808', 'TCGA-F4-6809', 'TCGA-F4-6854', 'TCGA-F4-6855', 'TCGA-F4-6856', 'TCGA-F5-6464', 'TCGA-F5-6465', 'TCGA-F5-6571', 'TCGA-F5-6702', 'TCGA-F5-6810', 'TCGA-F5-6811', 'TCGA-F5-6812', 'TCGA-F5-6813', 'TCGA-F5-6814', 'TCGA-F5-6861', 'TCGA-F5-6863', 'TCGA-F5-6864', 'TCGA-G4-6293', 'TCGA-G4-6294', 'TCGA-G4-6295', 'TCGA-G4-6297', 'TCGA-G4-6298', 'TCGA-G4-6299', 'TCGA-G4-6302', 'TCGA-G4-6303', 'TCGA-G4-6304', 'TCGA-G4-6306', 'TCGA-G4-6307', 'TCGA-G4-6309', 'TCGA-G4-6311', 'TCGA-G4-6315', 'TCGA-G4-6317', 'TCGA-G4-6320', 'TCGA-G4-6321', 'TCGA-G4-6322', 'TCGA-G4-6323', 'TCGA-G4-6586', 'TCGA-G4-6588', 'TCGA-G4-6626', 'TCGA-G4-6627', 'TCGA-G4-6628', 'TCGA-G5-6641', 'TCGA-NH-A50T', 'TCGA-NH-A50U', 'TCGA-NH-A50V', 'TCGA-NH-A5IV', 'TCGA-NH-A6GA', 'TCGA-NH-A6GB', 'TCGA-NH-A6GC', 'TCGA-NH-A8F7', 'TCGA-NH-A8F8', 'TCGA-QG-A5YV', 'TCGA-QG-A5YW', 'TCGA-QG-A5YX', 'TCGA-QG-A5Z1', 'TCGA-QG-A5Z2', 'TCGA-QL-A97D', 'TCGA-RU-A8FL', 'TCGA-SS-A7HO', 'TCGA-T9-A92H', 'TCGA-WS-AB45'] CINECA_synthetic_cohort_EUROPE_UK1: [ "HG00096", diff --git a/permissions/public_datasets.yml b/permissions/public_datasets.yml index a6ca5924..d4714d80 100644 --- a/permissions/public_datasets.yml +++ b/permissions/public_datasets.yml @@ -3,4 +3,5 @@ public_datasets: - CINECA_dataset - AV_Dataset - rd-connect_dataset -- coadread_tcga_pan_can_atlas_2018 \ No newline at end of file +- coadread_tcga_pan_can_atlas_2018 +- B1MG-COADREAD \ No newline at end of file