From f0da9491d571df9a61b0c85a1b0e21edf8bbaa2a Mon Sep 17 00:00:00 2001 From: William Ronchetti Date: Mon, 14 Aug 2023 15:26:13 -0400 Subject: [PATCH 1/4] jsonschema update --- CHANGELOG.rst | 7 +++++++ pyproject.toml | 2 +- src/encoded/schema_formats.py | 12 ++++++------ src/encoded/schemas/access_key.json | 4 ++-- src/encoded/schemas/analysis_step.json | 4 ++-- src/encoded/schemas/antibody.json | 4 ++-- src/encoded/schemas/award.json | 4 ++-- src/encoded/schemas/badge.json | 4 ++-- src/encoded/schemas/bio_feature.json | 4 ++-- src/encoded/schemas/biosample.json | 4 ++-- src/encoded/schemas/biosample_cell_culture.json | 4 ++-- src/encoded/schemas/biosource.json | 4 ++-- src/encoded/schemas/construct.json | 4 ++-- src/encoded/schemas/data_release_update.json | 4 ++-- src/encoded/schemas/document.json | 4 ++-- src/encoded/schemas/enzyme.json | 4 ++-- src/encoded/schemas/experiment.json | 6 +++--- src/encoded/schemas/experiment_atacseq.json | 4 ++-- src/encoded/schemas/experiment_capture_c.json | 6 +++--- src/encoded/schemas/experiment_chiapet.json | 6 +++--- src/encoded/schemas/experiment_damid.json | 4 ++-- src/encoded/schemas/experiment_hi_c.json | 6 +++--- src/encoded/schemas/experiment_mic.json | 4 ++-- src/encoded/schemas/experiment_repliseq.json | 4 ++-- src/encoded/schemas/experiment_seq.json | 6 +++--- src/encoded/schemas/experiment_set.json | 4 ++-- src/encoded/schemas/experiment_set_replicate.json | 4 ++-- src/encoded/schemas/experiment_tsaseq.json | 6 +++--- src/encoded/schemas/experiment_type.json | 4 ++-- src/encoded/schemas/file.json | 4 ++-- src/encoded/schemas/file_calibration.json | 4 ++-- src/encoded/schemas/file_fastq.json | 4 ++-- src/encoded/schemas/file_format.json | 4 ++-- src/encoded/schemas/file_microscopy.json | 4 ++-- src/encoded/schemas/file_other.json | 4 ++-- src/encoded/schemas/file_processed.json | 4 ++-- src/encoded/schemas/file_reference.json | 4 ++-- src/encoded/schemas/file_set.json | 4 ++-- src/encoded/schemas/file_set_calibration.json | 4 ++-- src/encoded/schemas/file_set_microscope_qc.json | 4 ++-- src/encoded/schemas/file_vistrack.json | 4 ++-- src/encoded/schemas/gene.json | 4 ++-- src/encoded/schemas/genomic_region.json | 4 ++-- src/encoded/schemas/higlass_view_config.json | 4 ++-- src/encoded/schemas/image.json | 4 ++-- src/encoded/schemas/image_setting.json | 4 ++-- src/encoded/schemas/imaging_path.json | 4 ++-- src/encoded/schemas/individual.json | 6 +++--- src/encoded/schemas/individual_chicken.json | 6 +++--- src/encoded/schemas/individual_fly.json | 6 +++--- src/encoded/schemas/individual_human.json | 6 +++--- src/encoded/schemas/individual_mouse.json | 6 +++--- src/encoded/schemas/individual_primate.json | 6 +++--- src/encoded/schemas/individual_zebrafish.json | 6 +++--- src/encoded/schemas/lab.json | 4 ++-- src/encoded/schemas/microscope_configuration.json | 4 ++-- src/encoded/schemas/microscope_setting.json | 4 ++-- src/encoded/schemas/microscope_setting_a1.json | 4 ++-- src/encoded/schemas/microscope_setting_a2.json | 4 ++-- src/encoded/schemas/microscope_setting_d1.json | 4 ++-- src/encoded/schemas/microscope_setting_d2.json | 4 ++-- src/encoded/schemas/modification.json | 4 ++-- src/encoded/schemas/ontology.json | 4 ++-- src/encoded/schemas/ontology_term.json | 4 ++-- src/encoded/schemas/organism.json | 4 ++-- src/encoded/schemas/page.json | 4 ++-- src/encoded/schemas/protocol.json | 4 ++-- src/encoded/schemas/publication.json | 4 ++-- src/encoded/schemas/publication_tracking.json | 4 ++-- src/encoded/schemas/quality_metric.json | 4 ++-- src/encoded/schemas/quality_metric_atacseq.json | 4 ++-- src/encoded/schemas/quality_metric_bamcheck.json | 4 ++-- src/encoded/schemas/quality_metric_bamqc.json | 4 ++-- src/encoded/schemas/quality_metric_chipseq.json | 4 ++-- src/encoded/schemas/quality_metric_chipseq_v2.json | 6 +++--- .../schemas/quality_metric_dedupqc_repliseq.json | 4 ++-- src/encoded/schemas/quality_metric_fastqc.json | 4 ++-- src/encoded/schemas/quality_metric_flag.json | 4 ++-- src/encoded/schemas/quality_metric_margi.json | 4 ++-- src/encoded/schemas/quality_metric_mcool.json | 4 ++-- src/encoded/schemas/quality_metric_pairsqc.json | 4 ++-- src/encoded/schemas/quality_metric_qclist.json | 4 ++-- src/encoded/schemas/quality_metric_rnaseq.json | 4 ++-- src/encoded/schemas/quality_metric_rnaseq_madqc.json | 4 ++-- src/encoded/schemas/quality_metric_workflowrun.json | 4 ++-- src/encoded/schemas/software.json | 4 ++-- src/encoded/schemas/sop_map.json | 4 ++-- src/encoded/schemas/static_section.json | 4 ++-- src/encoded/schemas/summary_statistic.json | 4 ++-- src/encoded/schemas/summary_statistic_hi_c.json | 4 ++-- src/encoded/schemas/target.json | 4 ++-- src/encoded/schemas/tracking_item.json | 4 ++-- src/encoded/schemas/treatment.json | 4 ++-- src/encoded/schemas/treatment_agent.json | 4 ++-- src/encoded/schemas/treatment_rnai.json | 4 ++-- src/encoded/schemas/user.json | 4 ++-- src/encoded/schemas/user_content.json | 4 ++-- src/encoded/schemas/vendor.json | 4 ++-- src/encoded/schemas/workflow.json | 4 ++-- src/encoded/schemas/workflow_mapping.json | 4 ++-- src/encoded/schemas/workflow_run.json | 4 ++-- src/encoded/schemas/workflow_run_awsem.json | 4 ++-- src/encoded/schemas/workflow_run_sbg.json | 4 ++-- src/encoded/tests/test_fixtures.py | 1 + src/encoded/tests/test_permissions.py | 5 +++-- src/encoded/tests/test_post_put_patch.py | 7 ++++--- src/encoded/tests/test_schemas.py | 2 +- src/encoded/tests/test_views.py | 4 ++-- src/encoded/tests/testing_views.py | 4 ++-- 109 files changed, 241 insertions(+), 231 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 6f6babd4f5..f0aa7bbe9a 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -6,6 +6,13 @@ fourfront Change Log ---------- +6.2.0 +===== + +* Removes ``jsonschema_serialize_fork``, updating schema format version and validation +* Repairs a bug in user registration + + 6.1.1 ===== diff --git a/pyproject.toml b/pyproject.toml index 772f4f4bf1..2e79bfbda0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [tool.poetry] # Note: Various modules refer to this system as "encoded", not "fourfront". name = "encoded" -version = "6.1.1" +version = "6.2.0" description = "4DN-DCIC Fourfront" authors = ["4DN-DCIC Team "] license = "MIT" diff --git a/src/encoded/schema_formats.py b/src/encoded/schema_formats.py index abd751d63c..3b9fb961b9 100644 --- a/src/encoded/schema_formats.py +++ b/src/encoded/schema_formats.py @@ -1,7 +1,7 @@ import re from dcicutils.misc_utils import ignored, is_valid_absolute_uri -from jsonschema_serialize_fork import FormatChecker +from jsonschema import Draft202012Validator from pyramid.threadlocal import get_current_request from .server_defaults import ( ACCESSION_FACTORY, @@ -23,7 +23,7 @@ uuid_re = re.compile(r'(?i)[{]?(?:[0-9a-f]{4}-?){8}[}]?') -@FormatChecker.cls_checks("uuid") +@Draft202012Validator.FORMAT_CHECKER.cls_checks("uuid") def is_uuid(instance): # Python's UUID ignores all dashes, whereas Postgres is more strict # http://www.postgresql.org/docs/9.2/static/datatype-uuid.html @@ -39,7 +39,7 @@ def is_accession(instance): ) -@FormatChecker.cls_checks("accession") +@Draft202012Validator.FORMAT_CHECKER.cls_checks("accession") def is_accession_for_server(instance): # Unfortunately we cannot access the accessionType here if accession_re.match(instance): @@ -51,14 +51,14 @@ def is_accession_for_server(instance): return False -@FormatChecker.cls_checks("gene_name") +@Draft202012Validator.FORMAT_CHECKER.cls_checks("gene_name") def is_gene_name(instance): """This SHOULD check a webservice at HGNC/MGI for validation, but for now this just returns True always..""" ignored(instance) return True -@FormatChecker.cls_checks("target_label") +@Draft202012Validator.FORMAT_CHECKER.cls_checks("target_label") def is_target_label(instance): if is_gene_name(instance): return True @@ -72,6 +72,6 @@ def is_target_label(instance): return True -@FormatChecker.cls_checks("uri", raises=ValueError) +@Draft202012Validator.FORMAT_CHECKER.cls_checks("uri", raises=ValueError) def is_uri(instance): return is_valid_absolute_uri(instance) diff --git a/src/encoded/schemas/access_key.json b/src/encoded/schemas/access_key.json index 192cb7f659..e9047e77c3 100644 --- a/src/encoded/schemas/access_key.json +++ b/src/encoded/schemas/access_key.json @@ -1,7 +1,7 @@ { "title": "Admin access key", - "id": "/profiles/access_key.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/access_key.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "required": [], "additionalProperties": false, "mixinProperties": [ diff --git a/src/encoded/schemas/analysis_step.json b/src/encoded/schemas/analysis_step.json index 8acf439b86..f049245b57 100644 --- a/src/encoded/schemas/analysis_step.json +++ b/src/encoded/schemas/analysis_step.json @@ -1,8 +1,8 @@ { "title": "Analysis step", "description": "Schema for submitting a computational analysis steps as a part of a workflow.", - "id": "/profiles/analysis_step.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/analysis_step.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["name", "version", "lab", "award"], "additionalProperties": false, diff --git a/src/encoded/schemas/antibody.json b/src/encoded/schemas/antibody.json index 0f3012b3bf..a7c5b7b8ae 100644 --- a/src/encoded/schemas/antibody.json +++ b/src/encoded/schemas/antibody.json @@ -1,7 +1,7 @@ { "title": "Antibody", - "id": "/profiles/antibody.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/antibody.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "additionalProperties": false, "mixinProperties": [ { "$ref": "mixins.json#/schema_version" }, diff --git a/src/encoded/schemas/award.json b/src/encoded/schemas/award.json index e27a51425d..7ff8e7a12a 100644 --- a/src/encoded/schemas/award.json +++ b/src/encoded/schemas/award.json @@ -1,7 +1,7 @@ { "title": "Grant", - "id": "/profiles/award.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/award.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "required": [ "name"], "identifyingProperties": ["uuid", "name", "title"], "additionalProperties": false, diff --git a/src/encoded/schemas/badge.json b/src/encoded/schemas/badge.json index ca4a3dbfe2..2047e8bd18 100644 --- a/src/encoded/schemas/badge.json +++ b/src/encoded/schemas/badge.json @@ -1,7 +1,7 @@ { "title": "Badge", - "id": "/profiles/badge.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/badge.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "additionalProperties": false, "identifyingProperties": ["badge_name", "uuid", "aliases"], "required": ["title", "lab", "award"], diff --git a/src/encoded/schemas/bio_feature.json b/src/encoded/schemas/bio_feature.json index 31853c290b..b008c9c66f 100644 --- a/src/encoded/schemas/bio_feature.json +++ b/src/encoded/schemas/bio_feature.json @@ -1,8 +1,8 @@ { "title": "Biological Feature", "description": "A biological feature like a Gene, Protein, Cellular Structure.", - "id": "/profiles/bio_feature.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/bio_feature.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab", "description", "feature_type"], "identifyingProperties": ["uuid", "aliases"], diff --git a/src/encoded/schemas/biosample.json b/src/encoded/schemas/biosample.json index 22125f4b34..6cf93896d1 100644 --- a/src/encoded/schemas/biosample.json +++ b/src/encoded/schemas/biosample.json @@ -1,8 +1,8 @@ { "title": "Biosample", "description": "Biological material used in the experiment with information on modifications, treatments and preparation.", - "id": "/profiles/biosample.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/biosample.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": [ "biosource", "award", "lab"], "identifyingProperties": ["uuid","accession","aliases"], diff --git a/src/encoded/schemas/biosample_cell_culture.json b/src/encoded/schemas/biosample_cell_culture.json index a15e4a24e6..e520337eab 100644 --- a/src/encoded/schemas/biosample_cell_culture.json +++ b/src/encoded/schemas/biosample_cell_culture.json @@ -1,8 +1,8 @@ { "title": "Cell culture details for biosample preparation", "description": "Cell culture specific parameters and protocols.", - "id": "/profiles/biosample_cell_culture.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/biosample_cell_culture.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["culture_start_date", "award", "lab"], "identifyingProperties": ["uuid", "aliases"], diff --git a/src/encoded/schemas/biosource.json b/src/encoded/schemas/biosource.json index 754e7a66f0..33248f817b 100644 --- a/src/encoded/schemas/biosource.json +++ b/src/encoded/schemas/biosource.json @@ -1,8 +1,8 @@ { "title": "Biosource", "description": "General description of the biological material, e.g. cell line", - "id": "/profiles/biosource.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/biosource.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["biosource_type", "award", "lab"], "identifyingProperties": ["uuid", "accession", "aliases"], diff --git a/src/encoded/schemas/construct.json b/src/encoded/schemas/construct.json index 6bd5a988c2..531e996ba4 100644 --- a/src/encoded/schemas/construct.json +++ b/src/encoded/schemas/construct.json @@ -1,8 +1,8 @@ { "title": "Construct", "description": "DNA construct used for modification or treatment", - "id": "/profiles/construct.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/construct.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["name", "construct_type", "award", "lab"], "identifyingProperties": ["uuid", "aliases", "name"], diff --git a/src/encoded/schemas/data_release_update.json b/src/encoded/schemas/data_release_update.json index 4b55edb64f..55ff3f7403 100644 --- a/src/encoded/schemas/data_release_update.json +++ b/src/encoded/schemas/data_release_update.json @@ -1,7 +1,7 @@ { "title": "Data Release Update", - "id": "/profiles/data_release_update.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/data_release_update.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["update_tag", "award", "lab"], "additionalProperties": false, diff --git a/src/encoded/schemas/document.json b/src/encoded/schemas/document.json index 8c1e77a510..dd732d2f37 100644 --- a/src/encoded/schemas/document.json +++ b/src/encoded/schemas/document.json @@ -1,8 +1,8 @@ { "title": "Document", "description": "Additional files like pdf, doc, txt", - "id": "/profiles/document.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/document.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["lab", "award"], "identifyingProperties": ["uuid","aliases"], diff --git a/src/encoded/schemas/enzyme.json b/src/encoded/schemas/enzyme.json index d88cdf74e8..45af70ca52 100644 --- a/src/encoded/schemas/enzyme.json +++ b/src/encoded/schemas/enzyme.json @@ -1,8 +1,8 @@ { "title": "Enzyme", "description": "DNA digestion enzymes like HindIII or DNaseI", - "id": "/profiles/enzyme.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/enzyme.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": [ "name", "enzyme_source", "award", "lab"], "identifyingProperties": ["uuid","aliases","name"], diff --git a/src/encoded/schemas/experiment.json b/src/encoded/schemas/experiment.json index bfe1fa35b3..86d2581fe9 100644 --- a/src/encoded/schemas/experiment.json +++ b/src/encoded/schemas/experiment.json @@ -1,13 +1,13 @@ { "title": "Experiment", "description": "Common metadata for all experiments.", - "id": "/profiles/experiment.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/experiment.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["experiment_type", "biosample", "award", "lab"], "identifyingProperties": ["uuid", "accession" , "aliases"], "additionalProperties": false, - "dependencies": { + "dependentRequired": { "biosample_quantity": ["biosample_quantity_units"], "biosample_quantity_units": ["biosample_quantity"] }, diff --git a/src/encoded/schemas/experiment_atacseq.json b/src/encoded/schemas/experiment_atacseq.json index d7a218392a..bf8462a65d 100644 --- a/src/encoded/schemas/experiment_atacseq.json +++ b/src/encoded/schemas/experiment_atacseq.json @@ -1,8 +1,8 @@ { "title": "ATAC-seq Experiment", "description": "Genome-wide chromosome chromatin-accessibility experiments ATAC-seq", - "id": "/profiles/experiment_atacseq.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/experiment_atacseq.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["experiment_type", "award", "lab", "biosample"], "identifyingProperties": ["uuid", "accession", "aliases"], diff --git a/src/encoded/schemas/experiment_capture_c.json b/src/encoded/schemas/experiment_capture_c.json index a61b731e06..bfa5185042 100644 --- a/src/encoded/schemas/experiment_capture_c.json +++ b/src/encoded/schemas/experiment_capture_c.json @@ -1,8 +1,8 @@ { "title": "Capture Hi-C Experiment", "description": "Hi-C coupled with oligonucleotide capture technology.", - "id": "/profiles/experiment_capture_c.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/experiment_capture_c.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["experiment_type", "award", "lab", "biosample"], "identifyingProperties": ["uuid", "accession", "aliases"], @@ -38,7 +38,7 @@ "mixinColumns": [ { "$ref": "experiment.json#/columns"} ], - "dependencies": { + "dependentRequired": { "crosslinking_temperature": ["crosslinking_method", "crosslinking_time"], "crosslinking_time": ["crosslinking_method", "crosslinking_temperature"], "digestion_temperature": ["digestion_enzyme", "digestion_time"], diff --git a/src/encoded/schemas/experiment_chiapet.json b/src/encoded/schemas/experiment_chiapet.json index 7c3c7827b9..f689130ea4 100644 --- a/src/encoded/schemas/experiment_chiapet.json +++ b/src/encoded/schemas/experiment_chiapet.json @@ -1,8 +1,8 @@ { "title": "Proximity Ligation with ChIP Experiment", "description": "Proximity Ligation and Sequencing with Targeted Chromatin Immunoprecipitation.", - "id": "/profiles/experiment_chiapet.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/experiment_chiapet.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["experiment_type", "award", "lab", "biosample"], "identifyingProperties": ["uuid", "accession", "aliases"], @@ -39,7 +39,7 @@ "mixinColumns": [ { "$ref": "experiment.json#/columns"} ], - "dependencies": { + "dependentRequired": { "crosslinking_temperature": ["crosslinking_method", "crosslinking_time"], "crosslinking_time": ["crosslinking_method", "crosslinking_temperature"], "digestion_temperature": ["digestion_enzyme", "digestion_time"], diff --git a/src/encoded/schemas/experiment_damid.json b/src/encoded/schemas/experiment_damid.json index 88349d2441..cab7c8a57c 100644 --- a/src/encoded/schemas/experiment_damid.json +++ b/src/encoded/schemas/experiment_damid.json @@ -1,8 +1,8 @@ { "title": "DAM-ID Seq Experiment", "description": "", - "id": "/profiles/experiment_damid.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/experiment_damid.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["experiment_type", "award", "lab", "biosample"], "identifyingProperties": ["uuid", "accession", "aliases"], diff --git a/src/encoded/schemas/experiment_hi_c.json b/src/encoded/schemas/experiment_hi_c.json index b7d225f903..6577c7ca68 100644 --- a/src/encoded/schemas/experiment_hi_c.json +++ b/src/encoded/schemas/experiment_hi_c.json @@ -1,8 +1,8 @@ { "title": "Hi-C Experiment", "description": "Genome-wide chromosome conformation capture experiments including Hi-C, micro-C, DNase Hi-C", - "id": "/profiles/experiment_hi_c.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/experiment_hi_c.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["experiment_type", "award", "lab", "biosample"], "identifyingProperties": ["uuid", "accession", "aliases"], @@ -37,7 +37,7 @@ "mixinColumns": [ { "$ref": "experiment.json#/columns"} ], - "dependencies": { + "dependentRequired": { "crosslinking_temperature": ["crosslinking_method", "crosslinking_time"], "crosslinking_time": ["crosslinking_method", "crosslinking_temperature"], "digestion_temperature": ["digestion_enzyme", "digestion_time"], diff --git a/src/encoded/schemas/experiment_mic.json b/src/encoded/schemas/experiment_mic.json index e478d5b8e0..3eb0002606 100644 --- a/src/encoded/schemas/experiment_mic.json +++ b/src/encoded/schemas/experiment_mic.json @@ -1,8 +1,8 @@ { "title": "Microscopy Experiment", "description": "Imaging Experiments with channel/label/target information.", - "id": "/profiles/experiment_mic.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/experiment_mic.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["experiment_type", "award", "lab", "biosample"], "identifyingProperties": ["uuid", "accession", "aliases"], diff --git a/src/encoded/schemas/experiment_repliseq.json b/src/encoded/schemas/experiment_repliseq.json index 7e0c327ac6..fdb1eb1a28 100644 --- a/src/encoded/schemas/experiment_repliseq.json +++ b/src/encoded/schemas/experiment_repliseq.json @@ -1,8 +1,8 @@ { "title": "Repli-seq Experiment", "description": "Genome-wide analysis of replication timing by next-generation sequencing.", - "id": "/profiles/experiment_repliseq.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/experiment_repliseq.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["experiment_type", "award", "lab", "biosample"], "identifyingProperties": ["uuid", "accession", "aliases"], diff --git a/src/encoded/schemas/experiment_seq.json b/src/encoded/schemas/experiment_seq.json index af029f0aa6..fe252f3d53 100644 --- a/src/encoded/schemas/experiment_seq.json +++ b/src/encoded/schemas/experiment_seq.json @@ -1,8 +1,8 @@ { "title": "Sequencing Experiment", "description": "Schema for ChIP-seq, RNA-seq and other related genomics experiments.", - "id": "/profiles/experiment_seq.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/experiment_seq.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["experiment_type", "award", "lab", "biosample"], "identifyingProperties": ["uuid", "accession", "aliases"], @@ -32,7 +32,7 @@ { "$ref": "mixins.json#/static_embeds" }, { "$ref": "experiment.json#/properties" } ], - "dependencies": { + "dependentRequired": { "3p_adenylation_time": ["3p_adenylation_temperature"], "3p_adenylation_temperature": ["3p_adenylation_time"] }, diff --git a/src/encoded/schemas/experiment_set.json b/src/encoded/schemas/experiment_set.json index 7a9b06e64d..133de3e6fc 100644 --- a/src/encoded/schemas/experiment_set.json +++ b/src/encoded/schemas/experiment_set.json @@ -1,8 +1,8 @@ { "title": "Experiment Set", "description": "Schema for submitting metadata for an experiment set.", - "id": "/profiles/experiment_set.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/experiment_set.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": [ "award", "lab", "description"], "identifyingProperties": ["uuid", "aliases"], diff --git a/src/encoded/schemas/experiment_set_replicate.json b/src/encoded/schemas/experiment_set_replicate.json index 27afb0ecde..c9e45be521 100644 --- a/src/encoded/schemas/experiment_set_replicate.json +++ b/src/encoded/schemas/experiment_set_replicate.json @@ -1,8 +1,8 @@ { "title": "Replicate Experiments", "description": "Experiment Set for technical/biological replicates.", - "id": "/profiles/experiment_set_replicate.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/experiment_set_replicate.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": [ "award", "lab", "description"], "identifyingProperties": ["uuid", "aliases"], diff --git a/src/encoded/schemas/experiment_tsaseq.json b/src/encoded/schemas/experiment_tsaseq.json index b0f08bb1b9..36f1919e2a 100644 --- a/src/encoded/schemas/experiment_tsaseq.json +++ b/src/encoded/schemas/experiment_tsaseq.json @@ -1,8 +1,8 @@ { "title": "TSA-seq Experiment", "description": "Schema for TSA-seq experiments.", - "id": "/profiles/experiment_tsaseq.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/experiment_tsaseq.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["experiment_type", "award", "lab", "biosample"], "identifyingProperties": ["uuid", "accession", "aliases"], @@ -29,7 +29,7 @@ { "$ref": "mixins.json#/static_embeds" }, { "$ref": "experiment.json#/properties" } ], - "dependencies": {}, + "dependentRequired": {}, "mixinFacets": [ { "$ref": "experiment.json#/facets"}, { "$ref": "mixins.json#/facets_common" }, diff --git a/src/encoded/schemas/experiment_type.json b/src/encoded/schemas/experiment_type.json index d937ecc09c..6693355aa1 100644 --- a/src/encoded/schemas/experiment_type.json +++ b/src/encoded/schemas/experiment_type.json @@ -1,8 +1,8 @@ { "title": "Experiment Type", "description": "Schema for experiment type", - "id": "/profiles/experiment_type.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/experiment_type.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["title", "lab", "award"], "identifyingProperties": ["experiment_name", "uuid"], diff --git a/src/encoded/schemas/file.json b/src/encoded/schemas/file.json index 718fe43ce9..4f05201482 100644 --- a/src/encoded/schemas/file.json +++ b/src/encoded/schemas/file.json @@ -1,8 +1,8 @@ { "title": "Data file", "description": "Schema for submitting metadata for a data file.", - "id": "/profiles/file.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/file.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["file_format", "award", "lab"], "identifyingProperties": ["uuid", "accession", "aliases"], diff --git a/src/encoded/schemas/file_calibration.json b/src/encoded/schemas/file_calibration.json index a32be4a82d..21ae8baeac 100644 --- a/src/encoded/schemas/file_calibration.json +++ b/src/encoded/schemas/file_calibration.json @@ -1,8 +1,8 @@ { "title": "Calibration file(s)", "description": "Imaging Files for Calibration", - "id": "/profiles/file_calibration.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/file_calibration.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["file_format", "award", "lab"], "identifyingProperties": ["uuid", "accession", "aliases"], diff --git a/src/encoded/schemas/file_fastq.json b/src/encoded/schemas/file_fastq.json index 9303467459..ed5bde54eb 100644 --- a/src/encoded/schemas/file_fastq.json +++ b/src/encoded/schemas/file_fastq.json @@ -1,8 +1,8 @@ { "title": "FASTQ file", "description": "Raw DNA sequncing file details and file in fastq.gz format.", - "id": "/profiles/file_fastq.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/file_fastq.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["file_format", "award", "lab"], "identifyingProperties": ["uuid", "accession", "aliases"], diff --git a/src/encoded/schemas/file_format.json b/src/encoded/schemas/file_format.json index 978463ed4e..b1cf4e3acd 100644 --- a/src/encoded/schemas/file_format.json +++ b/src/encoded/schemas/file_format.json @@ -1,8 +1,8 @@ { "title": "File Format", "description": "Known file formats and information about them.", - "id": "/profiles/file_format.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/file_format.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["file_format", "standard_file_extension", "award", "lab"], "identifyingProperties": ["uuid", "file_format"], diff --git a/src/encoded/schemas/file_microscopy.json b/src/encoded/schemas/file_microscopy.json index 0c4492a869..f9a262cf19 100644 --- a/src/encoded/schemas/file_microscopy.json +++ b/src/encoded/schemas/file_microscopy.json @@ -1,8 +1,8 @@ { "title": "Microscopy file", "description": "Imaging Files of Microscopy", - "id": "/profiles/file_microscopy.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/file_microscopy.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["file_format", "award", "lab"], "identifyingProperties": ["uuid", "accession", "aliases"], diff --git a/src/encoded/schemas/file_other.json b/src/encoded/schemas/file_other.json index 105b743b02..90f94c0cac 100644 --- a/src/encoded/schemas/file_other.json +++ b/src/encoded/schemas/file_other.json @@ -1,8 +1,8 @@ { "title": "Other file", "description": "Files of a kind other than the ones we've assigned a task-specific File type.", - "id": "/profiles/file_other.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/file_other.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["file_format"], "identifyingProperties": ["uuid", "accession", "aliases"], diff --git a/src/encoded/schemas/file_processed.json b/src/encoded/schemas/file_processed.json index 45a2bd8046..4e87585a48 100644 --- a/src/encoded/schemas/file_processed.json +++ b/src/encoded/schemas/file_processed.json @@ -1,8 +1,8 @@ { "title": "Processed file", "description": "Files produced by raw or processed file processing.", - "id": "/profiles/file_processed.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/file_processed.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["file_format", "award", "lab"], "identifyingProperties": ["uuid", "accession", "aliases"], diff --git a/src/encoded/schemas/file_reference.json b/src/encoded/schemas/file_reference.json index 4bf98b3ffa..7b35fe2c52 100644 --- a/src/encoded/schemas/file_reference.json +++ b/src/encoded/schemas/file_reference.json @@ -1,8 +1,8 @@ { "title": "Reference file", "description": "Files used as references.", - "id": "/profiles/file_reference.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/file_reference.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["file_format", "award", "lab"], "identifyingProperties": ["uuid", "accession", "aliases"], diff --git a/src/encoded/schemas/file_set.json b/src/encoded/schemas/file_set.json index d577e5847f..7a00a73983 100644 --- a/src/encoded/schemas/file_set.json +++ b/src/encoded/schemas/file_set.json @@ -1,8 +1,8 @@ { "title": "File Set", "description": "Grouping for files with similar features.", - "id": "/profiles/file_set.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/file_set.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": [ "award", "lab", "fileset_type"], "identifyingProperties": ["uuid", "aliases", "accession"], diff --git a/src/encoded/schemas/file_set_calibration.json b/src/encoded/schemas/file_set_calibration.json index 27d36f3c57..8a842c57c8 100644 --- a/src/encoded/schemas/file_set_calibration.json +++ b/src/encoded/schemas/file_set_calibration.json @@ -1,8 +1,8 @@ { "title": "Calibration File Set", "description": "File set dedicated to imaging calibration files.", - "id": "/profiles/file_set_calibration.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/file_set_calibration.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": [ "award", "lab"], "identifyingProperties": ["uuid", "aliases", "accession"], diff --git a/src/encoded/schemas/file_set_microscope_qc.json b/src/encoded/schemas/file_set_microscope_qc.json index 5b77387ada..b6bb43fc47 100644 --- a/src/encoded/schemas/file_set_microscope_qc.json +++ b/src/encoded/schemas/file_set_microscope_qc.json @@ -1,8 +1,8 @@ { "title": "Microscope QC with PSFj", "description": "Stack images for QC with PSFj and final report.", - "id": "/profiles/file_set_microscope_qc.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/file_set_microscope_qc.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": [ "award", "lab"], "identifyingProperties": ["uuid", "aliases", "accession"], diff --git a/src/encoded/schemas/file_vistrack.json b/src/encoded/schemas/file_vistrack.json index 1ecadcd890..a07d9235e4 100644 --- a/src/encoded/schemas/file_vistrack.json +++ b/src/encoded/schemas/file_vistrack.json @@ -1,8 +1,8 @@ { "title": "Visualization Track file", "description": "Files used as visualization tracks in HiGlass.", - "id": "/profiles/file_vistrack.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/file_vistrack.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["file_format", "award", "lab"], "identifyingProperties": ["uuid", "accession", "aliases"], diff --git a/src/encoded/schemas/gene.json b/src/encoded/schemas/gene.json index f17616bf51..7e68522971 100644 --- a/src/encoded/schemas/gene.json +++ b/src/encoded/schemas/gene.json @@ -1,8 +1,8 @@ { "title": "Gene", "description": "Schema for submitting a gene (adapted from ENCODE).", - "id": "/profiles/gene.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/gene.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["geneid", "lab", "award"], "identifyingProperties": ["uuid", "geneid", "preferred_symbol"], diff --git a/src/encoded/schemas/genomic_region.json b/src/encoded/schemas/genomic_region.json index a3151a7a84..c32bab6da8 100644 --- a/src/encoded/schemas/genomic_region.json +++ b/src/encoded/schemas/genomic_region.json @@ -1,8 +1,8 @@ { "title": "Genomic Region", "description": "Genome Region from a reference genome assembly.", - "id": "/profiles/genomic_region.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/genomic_region.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["genome_assembly", "award", "lab"], "identifyingProperties": ["uuid","aliases"], diff --git a/src/encoded/schemas/higlass_view_config.json b/src/encoded/schemas/higlass_view_config.json index d30fa20b27..9b9a3d7442 100644 --- a/src/encoded/schemas/higlass_view_config.json +++ b/src/encoded/schemas/higlass_view_config.json @@ -1,7 +1,7 @@ { "title": "HiGlass Display", - "id": "/profiles/higlass_view_config.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/higlass_view_config.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["genome_assembly"], "additionalProperties": false, diff --git a/src/encoded/schemas/image.json b/src/encoded/schemas/image.json index 00a3b0bde5..388bbafd1d 100644 --- a/src/encoded/schemas/image.json +++ b/src/encoded/schemas/image.json @@ -1,8 +1,8 @@ { "title": "Image", "description": "jpeg/tiff/png image files", - "id": "/profiles/image.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/image.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": [ "attachment", "award", "lab"], "identifyingProperties": ["uuid","aliases"], diff --git a/src/encoded/schemas/image_setting.json b/src/encoded/schemas/image_setting.json index 7f318d876a..9aa3ee88aa 100644 --- a/src/encoded/schemas/image_setting.json +++ b/src/encoded/schemas/image_setting.json @@ -1,8 +1,8 @@ { "title": "Image Settings", "description": "Microscopy metadata specific to the image", - "id": "/profiles/image_setting.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/image_setting.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["settings"], "additionalProperties": false, diff --git a/src/encoded/schemas/imaging_path.json b/src/encoded/schemas/imaging_path.json index 4eb1ed04b5..a775ca52dc 100644 --- a/src/encoded/schemas/imaging_path.json +++ b/src/encoded/schemas/imaging_path.json @@ -1,8 +1,8 @@ { "title": "Imaging Path", "description": "Channel/Probe/Target/Dye information for imaging experiments.", - "id": "/profiles/imaging_path.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/imaging_path.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "identifyingProperties": ["uuid", "aliases"], diff --git a/src/encoded/schemas/individual.json b/src/encoded/schemas/individual.json index fd1c79eea1..dda4b98f96 100644 --- a/src/encoded/schemas/individual.json +++ b/src/encoded/schemas/individual.json @@ -1,12 +1,12 @@ { "title": "Individual", "description": "Base schema for individuals.", - "id": "/profiles/individual.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/individual.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "identifyingProperties": ["uuid", "accession", "aliases"], "required": ["organism"], - "dependencies": { + "dependentRequired": { "age": [ "age_units"] }, "mixinFacets" : [ diff --git a/src/encoded/schemas/individual_chicken.json b/src/encoded/schemas/individual_chicken.json index 24555be174..f973bc8e0e 100644 --- a/src/encoded/schemas/individual_chicken.json +++ b/src/encoded/schemas/individual_chicken.json @@ -1,8 +1,8 @@ { "title": "Chicken Individual", "description": "Schema for submitting a chicken individual.", - "id": "/profiles/individual_chicken.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/individual_chicken.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "identifyingProperties": ["uuid", "accession", "aliases"], @@ -26,7 +26,7 @@ "mixinFacets" : [ { "$ref": "mixins.json#/facets_common" } ], - "dependencies": { + "dependentRequired": { "age": [ "age_units"] }, "properties": { diff --git a/src/encoded/schemas/individual_fly.json b/src/encoded/schemas/individual_fly.json index 5b78c72fe6..d99b387f18 100644 --- a/src/encoded/schemas/individual_fly.json +++ b/src/encoded/schemas/individual_fly.json @@ -1,8 +1,8 @@ { "title": "Fly Line", "description": "Schema for submitting a fly line/strain.", - "id": "/profiles/individual_fly.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/individual_fly.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "identifyingProperties": ["uuid", "accession", "aliases"], @@ -26,7 +26,7 @@ "mixinFacets" : [ { "$ref": "mixins.json#/facets_common" } ], - "dependencies": { + "dependentRequired": { "age": [ "age_units"] }, "properties": { diff --git a/src/encoded/schemas/individual_human.json b/src/encoded/schemas/individual_human.json index f61ad8710a..73189275ab 100644 --- a/src/encoded/schemas/individual_human.json +++ b/src/encoded/schemas/individual_human.json @@ -1,8 +1,8 @@ { "title": "Human Individual", "description": "Schema for submitting a human individual.", - "id": "/profiles/individual_human.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/individual_human.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "identifyingProperties": ["uuid", "accession", "aliases"], @@ -26,7 +26,7 @@ "mixinFacets" : [ { "$ref": "mixins.json#/facets_common" } ], - "dependencies": { + "dependentRequired": { "age": ["age_units"] }, "properties": { diff --git a/src/encoded/schemas/individual_mouse.json b/src/encoded/schemas/individual_mouse.json index dfda4e7210..bb6a0c6310 100644 --- a/src/encoded/schemas/individual_mouse.json +++ b/src/encoded/schemas/individual_mouse.json @@ -1,8 +1,8 @@ { "title": "Mouse Individual", "description": "Schema for submitting a mouse individual.", - "id": "/profiles/individual_mouse.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/individual_mouse.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "identifyingProperties": ["uuid", "accession", "aliases"], @@ -26,7 +26,7 @@ "mixinFacets" : [ { "$ref": "mixins.json#/facets_common" } ], - "dependencies": { + "dependentRequired": { "age": [ "age_units"] }, "properties": { diff --git a/src/encoded/schemas/individual_primate.json b/src/encoded/schemas/individual_primate.json index c8741d05d5..413b268d6e 100644 --- a/src/encoded/schemas/individual_primate.json +++ b/src/encoded/schemas/individual_primate.json @@ -1,8 +1,8 @@ { "title": "Primate Individual", "description": "Schema for submitting a primate individual.", - "id": "/profiles/individual_primate.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/individual_primate.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "identifyingProperties": ["uuid", "accession", "aliases"], @@ -26,7 +26,7 @@ "mixinFacets" : [ { "$ref": "mixins.json#/facets_common" } ], - "dependencies": { + "dependentRequired": { "age": ["age_units"] }, "properties": { diff --git a/src/encoded/schemas/individual_zebrafish.json b/src/encoded/schemas/individual_zebrafish.json index a7df95cb36..e1cc88a272 100644 --- a/src/encoded/schemas/individual_zebrafish.json +++ b/src/encoded/schemas/individual_zebrafish.json @@ -1,8 +1,8 @@ { "title": "Zebrafish strain", "description": "Schema for submitting a zebrafish cellline/strain.", - "id": "/profiles/individual_zebrafish.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/individual_zebrafish.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "identifyingProperties": ["uuid", "accession", "aliases"], @@ -26,7 +26,7 @@ "mixinFacets" : [ { "$ref": "mixins.json#/facets_common" } ], - "dependencies": { + "dependentRequired": { "age": [ "age_units"] }, "properties": { diff --git a/src/encoded/schemas/lab.json b/src/encoded/schemas/lab.json index 6c5b1707d4..a00c216ae6 100644 --- a/src/encoded/schemas/lab.json +++ b/src/encoded/schemas/lab.json @@ -1,7 +1,7 @@ { "title": "Lab", - "id": "/profiles/lab.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/lab.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["name", "title"], "identifyingProperties": ["name", "uuid", "title"], diff --git a/src/encoded/schemas/microscope_configuration.json b/src/encoded/schemas/microscope_configuration.json index 02458f1049..cf0c8bfef5 100644 --- a/src/encoded/schemas/microscope_configuration.json +++ b/src/encoded/schemas/microscope_configuration.json @@ -1,8 +1,8 @@ { "title": "Microscope Configuration", "description": "Configuration of Microscope", - "id": "/profiles/microscope_configuration.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/microscope_configuration.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["microscope"], "additionalProperties": false, diff --git a/src/encoded/schemas/microscope_setting.json b/src/encoded/schemas/microscope_setting.json index b27c271b22..876552ccbe 100644 --- a/src/encoded/schemas/microscope_setting.json +++ b/src/encoded/schemas/microscope_setting.json @@ -1,8 +1,8 @@ { "title": "Microscopy Settings", "description": "Metadata fields required for microscopy files", - "id": "/profiles/microscope_setting.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/microscope_setting.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "identifyingProperties": ["uuid", "aliases"], diff --git a/src/encoded/schemas/microscope_setting_a1.json b/src/encoded/schemas/microscope_setting_a1.json index 9295ca0377..cd2bfdb7e4 100644 --- a/src/encoded/schemas/microscope_setting_a1.json +++ b/src/encoded/schemas/microscope_setting_a1.json @@ -1,8 +1,8 @@ { "title": "Microscopy Settings Tier A1", "description": "Metadata fields required for Tier Analytical 1 level microscopy files", - "id": "/profiles/microscope_setting_a1.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/microscope_setting_a1.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "identifyingProperties": ["uuid", "aliases"], diff --git a/src/encoded/schemas/microscope_setting_a2.json b/src/encoded/schemas/microscope_setting_a2.json index 55c3588c42..295bcdcb06 100644 --- a/src/encoded/schemas/microscope_setting_a2.json +++ b/src/encoded/schemas/microscope_setting_a2.json @@ -1,8 +1,8 @@ { "title": "Microscopy Settings Tier A2", "description": "Metadata fields required for Tier Analytical 2 level microscopy files", - "id": "/profiles/microscope_setting_a2.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/microscope_setting_a2.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "identifyingProperties": ["uuid", "aliases"], diff --git a/src/encoded/schemas/microscope_setting_d1.json b/src/encoded/schemas/microscope_setting_d1.json index 52d7e23dd8..02e5acc58b 100644 --- a/src/encoded/schemas/microscope_setting_d1.json +++ b/src/encoded/schemas/microscope_setting_d1.json @@ -1,8 +1,8 @@ { "title": "Microscopy Settings Tier D1", "description": "Metadata fields required for Tier Descriptive 1 level microscopy files", - "id": "/profiles/microscope_setting_d1.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/microscope_setting_d1.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "identifyingProperties": ["uuid", "aliases"], diff --git a/src/encoded/schemas/microscope_setting_d2.json b/src/encoded/schemas/microscope_setting_d2.json index 5393c01d72..27132aaa4b 100644 --- a/src/encoded/schemas/microscope_setting_d2.json +++ b/src/encoded/schemas/microscope_setting_d2.json @@ -1,8 +1,8 @@ { "title": "Microscopy Settings Tier D2", "description": "Metadata fields required for Tier Descriptive 2 level microscopy files", - "id": "/profiles/microscope_setting_d2.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/microscope_setting_d2.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "identifyingProperties": ["uuid", "aliases"], diff --git a/src/encoded/schemas/modification.json b/src/encoded/schemas/modification.json index f135f681b7..fe6f287305 100644 --- a/src/encoded/schemas/modification.json +++ b/src/encoded/schemas/modification.json @@ -1,8 +1,8 @@ { "title": "Modification", "description": "Stable Genetic Modifications.", - "id": "/profiles/modification.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/modification.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["description", "modification_type", "lab", "award"], "identifyingProperties": ["uuid","aliases"], diff --git a/src/encoded/schemas/ontology.json b/src/encoded/schemas/ontology.json index 9068e5fe86..24129ad78e 100644 --- a/src/encoded/schemas/ontology.json +++ b/src/encoded/schemas/ontology.json @@ -1,8 +1,8 @@ { "title": "Ontology", "description": "Schema for submitting information about ontology.", - "id": "/profiles/ontology.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/ontology.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["ontology_name"], "identifyingProperties": ["uuid", "ontology_name", "ontology_url", "ontology_prefix"], diff --git a/src/encoded/schemas/ontology_term.json b/src/encoded/schemas/ontology_term.json index d60b2e8312..be6c11d3d1 100644 --- a/src/encoded/schemas/ontology_term.json +++ b/src/encoded/schemas/ontology_term.json @@ -1,8 +1,8 @@ { "title": "Ontology Term", "description": "Schema for submitting an ontology term.", - "id": "/profiles/ontology_term.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/ontology_term.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["term_id", "source_ontologies"], "identifyingProperties": ["uuid", "term_id", "preferred_name"], diff --git a/src/encoded/schemas/organism.json b/src/encoded/schemas/organism.json index 4b4b069eb1..5423769fa8 100644 --- a/src/encoded/schemas/organism.json +++ b/src/encoded/schemas/organism.json @@ -1,7 +1,7 @@ { "title": "Organism", - "id": "/profiles/organism.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/organism.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["name", "taxon_id"], "identifyingProperties": ["uuid", "name", "taxon_id", "scientific_name"], diff --git a/src/encoded/schemas/page.json b/src/encoded/schemas/page.json index 89826e0355..82ac0e12b4 100644 --- a/src/encoded/schemas/page.json +++ b/src/encoded/schemas/page.json @@ -1,7 +1,7 @@ { "title": "Page", - "id": "/profiles/page.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/page.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "required": ["name"], "additionalProperties": false, "identifyingProperties": ["uuid", "aliases"], diff --git a/src/encoded/schemas/protocol.json b/src/encoded/schemas/protocol.json index 965e6cd59e..702896844f 100644 --- a/src/encoded/schemas/protocol.json +++ b/src/encoded/schemas/protocol.json @@ -1,8 +1,8 @@ { "title": "Protocol", "description": "Can hold documents for a generic protocol.", - "id": "/profiles/protocol.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/protocol.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab", "protocol_type"], "identifyingProperties": ["uuid", "aliases"], diff --git a/src/encoded/schemas/publication.json b/src/encoded/schemas/publication.json index 05d82598a3..d3e5e7495d 100644 --- a/src/encoded/schemas/publication.json +++ b/src/encoded/schemas/publication.json @@ -1,8 +1,8 @@ { "title": "Publication", "description": "Schema for a publication page.", - "id": "/profiles/publication.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/publication.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab", "ID"], "identifyingProperties": ["uuid", "ID", "aliases"], diff --git a/src/encoded/schemas/publication_tracking.json b/src/encoded/schemas/publication_tracking.json index 543de1cc31..d82f8323f3 100644 --- a/src/encoded/schemas/publication_tracking.json +++ b/src/encoded/schemas/publication_tracking.json @@ -1,8 +1,8 @@ { "title": "Publication Tracking", "description": "Schema for a publication page.", - "id": "/profiles/publication_tracking.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/publication_tracking.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "identifyingProperties": ["uuid", "aliases"], diff --git a/src/encoded/schemas/quality_metric.json b/src/encoded/schemas/quality_metric.json index eea78bc336..709a619284 100644 --- a/src/encoded/schemas/quality_metric.json +++ b/src/encoded/schemas/quality_metric.json @@ -1,8 +1,8 @@ { "title" : "Quality Metric", "description": "Schema for reporting the specific calculation of an quality metrics", - "id": "/profiles/quality_metric.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/quality_metric.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "additionalProperties": false, diff --git a/src/encoded/schemas/quality_metric_atacseq.json b/src/encoded/schemas/quality_metric_atacseq.json index e5fe9e5476..a76738560f 100644 --- a/src/encoded/schemas/quality_metric_atacseq.json +++ b/src/encoded/schemas/quality_metric_atacseq.json @@ -1,8 +1,8 @@ { "title" : "Quality Metric for ATAC-Seq", "description": "Schema for reporting the specific calculation of an quality metrics", - "id": "/profiles/quality_metric_atacseq.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/quality_metric_atacseq.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "additionalProperties": false, diff --git a/src/encoded/schemas/quality_metric_bamcheck.json b/src/encoded/schemas/quality_metric_bamcheck.json index 9d0f94699b..a8b105c8b6 100644 --- a/src/encoded/schemas/quality_metric_bamcheck.json +++ b/src/encoded/schemas/quality_metric_bamcheck.json @@ -1,8 +1,8 @@ { "title" : "Quality Metric for Bam Integrity Check", "description": "Schema for reporting the specific calculation of an quality metrics", - "id": "/profiles/quality_metric_bamcheck.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/quality_metric_bamcheck.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "additionalProperties": false, diff --git a/src/encoded/schemas/quality_metric_bamqc.json b/src/encoded/schemas/quality_metric_bamqc.json index 886d8d0c3d..979867b1f8 100644 --- a/src/encoded/schemas/quality_metric_bamqc.json +++ b/src/encoded/schemas/quality_metric_bamqc.json @@ -1,8 +1,8 @@ { "title": "Quality Metric for BAM", "description": "Schema for reporting the specific calculation of an quality metrics", - "id": "/profiles/quality_metric_bamqc.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/quality_metric_bamqc.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "additionalProperties": false, diff --git a/src/encoded/schemas/quality_metric_chipseq.json b/src/encoded/schemas/quality_metric_chipseq.json index 9b7c0fc992..83a4209121 100644 --- a/src/encoded/schemas/quality_metric_chipseq.json +++ b/src/encoded/schemas/quality_metric_chipseq.json @@ -1,8 +1,8 @@ { "title": "Quality Metric for ChIP-Seq", "description": "Schema for reporting the specific calculation of an quality metrics", - "id": "/profiles/quality_metric_chipseq.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/quality_metric_chipseq.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "additionalProperties": false, diff --git a/src/encoded/schemas/quality_metric_chipseq_v2.json b/src/encoded/schemas/quality_metric_chipseq_v2.json index a41189180f..f64b895f18 100644 --- a/src/encoded/schemas/quality_metric_chipseq_v2.json +++ b/src/encoded/schemas/quality_metric_chipseq_v2.json @@ -1,8 +1,8 @@ { "title": "Quality Metric for ChIP-Seq", "description": "Schema for reporting the specific calculation of an quality metrics", - "id": "/profiles/quality_metric_chipseq_v2.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/quality_metric_chipseq_v2.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "additionalProperties": true, @@ -137,7 +137,7 @@ } } } - + } } }, diff --git a/src/encoded/schemas/quality_metric_dedupqc_repliseq.json b/src/encoded/schemas/quality_metric_dedupqc_repliseq.json index 75a3608b93..da982c3c76 100644 --- a/src/encoded/schemas/quality_metric_dedupqc_repliseq.json +++ b/src/encoded/schemas/quality_metric_dedupqc_repliseq.json @@ -1,8 +1,8 @@ { "title" : "Quality Metric for Repli-seq Dedup", "description": "Schema for reporting the specific calculation of an quality metrics", - "id": "/profiles/quality_metric_dedupqc_repliseq.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/quality_metric_dedupqc_repliseq.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "additionalProperties": false, diff --git a/src/encoded/schemas/quality_metric_fastqc.json b/src/encoded/schemas/quality_metric_fastqc.json index ebfc931160..78b2ea3fd9 100644 --- a/src/encoded/schemas/quality_metric_fastqc.json +++ b/src/encoded/schemas/quality_metric_fastqc.json @@ -1,8 +1,8 @@ { "title" : "Quality Metric for FASTQC", "description": "Schema for reporting the specific calculation of an quality metrics", - "id": "/profiles/quality_metric_fastqc.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/quality_metric_fastqc.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "additionalProperties": false, diff --git a/src/encoded/schemas/quality_metric_flag.json b/src/encoded/schemas/quality_metric_flag.json index db609eb9c4..17b99be167 100644 --- a/src/encoded/schemas/quality_metric_flag.json +++ b/src/encoded/schemas/quality_metric_flag.json @@ -1,7 +1,7 @@ { "description": "Schema for reporting a flag that indicates something about an associated quality metric", - "id": "/profiles/quality_metric_flag.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/quality_metric_flag.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["flag", "award", "lab"], "additionalProperties": false, diff --git a/src/encoded/schemas/quality_metric_margi.json b/src/encoded/schemas/quality_metric_margi.json index e32ac528ef..afe12cede9 100644 --- a/src/encoded/schemas/quality_metric_margi.json +++ b/src/encoded/schemas/quality_metric_margi.json @@ -1,8 +1,8 @@ { "title" : "Quality Metric for MARGI", "description": "Schema for reporting the specific calculation of an quality metrics", - "id": "/profiles/quality_metric_margi.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/quality_metric_margi.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "additionalProperties": false, diff --git a/src/encoded/schemas/quality_metric_mcool.json b/src/encoded/schemas/quality_metric_mcool.json index fa7988dfd0..7b2ec33ead 100644 --- a/src/encoded/schemas/quality_metric_mcool.json +++ b/src/encoded/schemas/quality_metric_mcool.json @@ -1,8 +1,8 @@ { "title": "Quality Metric for Mcool", "description": "Schema for reporting the specific calculation of an quality metrics", - "id": "/profiles/quality_metric_mcool.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/quality_metric_mcool.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "additionalProperties": false, diff --git a/src/encoded/schemas/quality_metric_pairsqc.json b/src/encoded/schemas/quality_metric_pairsqc.json index 3f904363b8..2a2d95fd76 100644 --- a/src/encoded/schemas/quality_metric_pairsqc.json +++ b/src/encoded/schemas/quality_metric_pairsqc.json @@ -1,8 +1,8 @@ { "title" : "Quality Metric for Pairs", "description": "Schema for reporting the specific calculation of an quality metrics", - "id": "/profiles/quality_metric_pairsqc.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/quality_metric_pairsqc.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "additionalProperties": false, diff --git a/src/encoded/schemas/quality_metric_qclist.json b/src/encoded/schemas/quality_metric_qclist.json index 1ce902ac26..63e4dd5496 100644 --- a/src/encoded/schemas/quality_metric_qclist.json +++ b/src/encoded/schemas/quality_metric_qclist.json @@ -1,8 +1,8 @@ { "title" : "Quality Metric for QC List", "description": "Schema for reporting the specific calculation of an quality metrics", - "id": "/profiles/quality_metric_qclist.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/quality_metric_qclist.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": [ "lab", "award"], "additionalProperties": false, diff --git a/src/encoded/schemas/quality_metric_rnaseq.json b/src/encoded/schemas/quality_metric_rnaseq.json index d5f5577540..4f9d2cd645 100644 --- a/src/encoded/schemas/quality_metric_rnaseq.json +++ b/src/encoded/schemas/quality_metric_rnaseq.json @@ -1,8 +1,8 @@ { "title" : "Quality Metric for RNA-Seq", "description": "Schema for reporting the specific calculation of an quality metrics", - "id": "/profiles/quality_metric_rnaseq.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/quality_metric_rnaseq.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "additionalProperties": false, diff --git a/src/encoded/schemas/quality_metric_rnaseq_madqc.json b/src/encoded/schemas/quality_metric_rnaseq_madqc.json index 25ccf2ac8c..d931c12388 100644 --- a/src/encoded/schemas/quality_metric_rnaseq_madqc.json +++ b/src/encoded/schemas/quality_metric_rnaseq_madqc.json @@ -1,8 +1,8 @@ { "title": "Quality Metric for RNA-Seq MAD QC (reproducibility QC)", "description": "Schema for reporting the specific calculation of an quality metrics", - "id": "/profiles/quality_metric_rnaseq_madqc.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/quality_metric_rnaseq_madqc.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "additionalProperties": false, diff --git a/src/encoded/schemas/quality_metric_workflowrun.json b/src/encoded/schemas/quality_metric_workflowrun.json index 81d6688f7b..64455442df 100644 --- a/src/encoded/schemas/quality_metric_workflowrun.json +++ b/src/encoded/schemas/quality_metric_workflowrun.json @@ -1,8 +1,8 @@ { "title" : "Quality Metric for Workflow Run", "description": "Schema for reporting the specific calculation of an quality metrics", - "id": "/profiles/quality_metric_workflowrun.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/quality_metric_workflowrun.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "additionalProperties": false, diff --git a/src/encoded/schemas/software.json b/src/encoded/schemas/software.json index 7617037705..d1a246595e 100644 --- a/src/encoded/schemas/software.json +++ b/src/encoded/schemas/software.json @@ -1,8 +1,8 @@ { "title": "Software", "description": "Schema for submitting analysis software.", - "id": "/profiles/software.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/software.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["name", "software_type", "award", "lab"], "additionalProperties": false, diff --git a/src/encoded/schemas/sop_map.json b/src/encoded/schemas/sop_map.json index d7bc012a71..414caec8fb 100644 --- a/src/encoded/schemas/sop_map.json +++ b/src/encoded/schemas/sop_map.json @@ -1,8 +1,8 @@ { "title": "SOPs with fields", "description": "For items with SOPs stores a mapping of the fields and the default values for that SOP.", - "id": "/profiles/sop_map.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/sop_map.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["associated_item_type", "award", "lab"], "additionalProperties": false, diff --git a/src/encoded/schemas/static_section.json b/src/encoded/schemas/static_section.json index e4bdbd882a..be43b3a171 100644 --- a/src/encoded/schemas/static_section.json +++ b/src/encoded/schemas/static_section.json @@ -1,7 +1,7 @@ { "title": "Static Section", - "id": "/profiles/static_section.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/static_section.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["name"], "additionalProperties": false, diff --git a/src/encoded/schemas/summary_statistic.json b/src/encoded/schemas/summary_statistic.json index 516a359e02..594d67c9c0 100644 --- a/src/encoded/schemas/summary_statistic.json +++ b/src/encoded/schemas/summary_statistic.json @@ -1,7 +1,7 @@ { "description": "Base Schema for reporting the summary statistics of an experiment", - "id": "/profiles/summary_statistic.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/summary_statistic.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "additionalProperties": false, diff --git a/src/encoded/schemas/summary_statistic_hi_c.json b/src/encoded/schemas/summary_statistic_hi_c.json index 2237bbbba7..8e6b3fc7cc 100644 --- a/src/encoded/schemas/summary_statistic_hi_c.json +++ b/src/encoded/schemas/summary_statistic_hi_c.json @@ -1,7 +1,7 @@ { "description": "Schema for reporting the summary statistics of a specific type of experiment", - "id": "/profiles/summary_statistic_hi_c.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/summary_statistic_hi_c.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "additionalProperties": false, diff --git a/src/encoded/schemas/target.json b/src/encoded/schemas/target.json index 3a65ce6f01..b548cd7bd0 100644 --- a/src/encoded/schemas/target.json +++ b/src/encoded/schemas/target.json @@ -1,8 +1,8 @@ { "title": "Target", "description": "Protein/RNA/DNA or cell structures that define a target.", - "id": "/profiles/target.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/target.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "identifyingProperties": ["uuid", "aliases"], diff --git a/src/encoded/schemas/tracking_item.json b/src/encoded/schemas/tracking_item.json index 8e7761b7f8..2aabec7025 100644 --- a/src/encoded/schemas/tracking_item.json +++ b/src/encoded/schemas/tracking_item.json @@ -1,8 +1,8 @@ { "title": "TrackingItem", "description": "Schema for internal tracking of Fourfront events, such as downloads", - "id": "/profiles/tracking_item.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/tracking_item.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["tracking_type"], "identifyingProperties": ["uuid"], diff --git a/src/encoded/schemas/treatment.json b/src/encoded/schemas/treatment.json index 2a9d31b8f0..c09f28b98f 100644 --- a/src/encoded/schemas/treatment.json +++ b/src/encoded/schemas/treatment.json @@ -1,8 +1,8 @@ { "title": "Treatment", "description": "Abstract Schema for submitting a specific type of treatment.", - "id": "/profiles/treatment.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/treatment.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["description", "treatment_type", "lab", "award"], "identifyingProperties": ["uuid","aliases"], diff --git a/src/encoded/schemas/treatment_agent.json b/src/encoded/schemas/treatment_agent.json index 0466869383..bb78b96d82 100644 --- a/src/encoded/schemas/treatment_agent.json +++ b/src/encoded/schemas/treatment_agent.json @@ -1,8 +1,8 @@ { "title": "Agent-based Treatment", "description": "A Biological, Chemical, or Physical Treatment on Biosample.", - "id": "/profiles/treatment_agent.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/treatment_agent.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["treatment_type", "lab", "award"], "identifyingProperties": ["uuid","aliases"], diff --git a/src/encoded/schemas/treatment_rnai.json b/src/encoded/schemas/treatment_rnai.json index 51ee89c5ed..4b1142aa13 100644 --- a/src/encoded/schemas/treatment_rnai.json +++ b/src/encoded/schemas/treatment_rnai.json @@ -1,8 +1,8 @@ { "title": "RNAi Treatment", "description": "RNAi treatment used on Biosample.", - "id": "/profiles/treatment_rnai.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/treatment_rnai.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["rnai_type", "lab", "award"], "identifyingProperties": ["uuid","aliases"], diff --git a/src/encoded/schemas/user.json b/src/encoded/schemas/user.json index 94625843cc..15d14ed531 100644 --- a/src/encoded/schemas/user.json +++ b/src/encoded/schemas/user.json @@ -1,7 +1,7 @@ { "title": "User", - "id": "/profiles/user.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/user.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": [ "email", "first_name", "last_name"], "identifyingProperties": ["uuid", "email", "aliases"], diff --git a/src/encoded/schemas/user_content.json b/src/encoded/schemas/user_content.json index 4bb23bf25d..fa98b248f5 100644 --- a/src/encoded/schemas/user_content.json +++ b/src/encoded/schemas/user_content.json @@ -1,7 +1,7 @@ { "title": "User Content", - "id": "/profiles/user_content.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/user_content.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "additionalProperties": false, "identifyingProperties": ["uuid", "name"], diff --git a/src/encoded/schemas/vendor.json b/src/encoded/schemas/vendor.json index ad98bc2ef5..3a854a5735 100644 --- a/src/encoded/schemas/vendor.json +++ b/src/encoded/schemas/vendor.json @@ -1,8 +1,8 @@ { "title": "Vendor", "description": "Lab or Company that is the Source for a Product/Sample.", - "id": "/profiles/vendor.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/vendor.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["title", "lab", "award"], "identifyingProperties": ["uuid", "name", "aliases"], diff --git a/src/encoded/schemas/workflow.json b/src/encoded/schemas/workflow.json index 631d937ba0..eb557a8e49 100644 --- a/src/encoded/schemas/workflow.json +++ b/src/encoded/schemas/workflow.json @@ -1,8 +1,8 @@ { "title": "Workflow", "description": "Schema for submitting a computational analysis workflow that is composed of analysis step(s).", - "id": "/profiles/workflow.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/workflow.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["title", "name", "award", "lab"], "additionalProperties": false, diff --git a/src/encoded/schemas/workflow_mapping.json b/src/encoded/schemas/workflow_mapping.json index 01a64aee73..27a0e5deba 100644 --- a/src/encoded/schemas/workflow_mapping.json +++ b/src/encoded/schemas/workflow_mapping.json @@ -1,8 +1,8 @@ { "title": "Workflow Mapping", "description": "A mapping table used for creating workflow run from workflow.", - "id": "/profiles/workflow_mapping.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/workflow_mapping.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["award", "lab"], "additionalProperties": false, diff --git a/src/encoded/schemas/workflow_run.json b/src/encoded/schemas/workflow_run.json index 0c83f742a5..fe61b4b8fd 100644 --- a/src/encoded/schemas/workflow_run.json +++ b/src/encoded/schemas/workflow_run.json @@ -1,8 +1,8 @@ { "title": "Workflow Run", "description": "Schema for submitting metadata on the executation of a computational analysis workflow run.", - "id": "/profiles/workflow_run.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/workflow_run.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["workflow", "award", "lab"], "additionalProperties": false, diff --git a/src/encoded/schemas/workflow_run_awsem.json b/src/encoded/schemas/workflow_run_awsem.json index c4b32c99bf..e691019740 100644 --- a/src/encoded/schemas/workflow_run_awsem.json +++ b/src/encoded/schemas/workflow_run_awsem.json @@ -1,8 +1,8 @@ { "title": "Workflow Run Awsem", "description": "Schema for submitting metadata on the executation of a computational analysis workflow run on Awsem.", - "id": "/profiles/workflow_run_awsem.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/workflow_run_awsem.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["workflow", "award", "lab"], "additionalProperties": false, diff --git a/src/encoded/schemas/workflow_run_sbg.json b/src/encoded/schemas/workflow_run_sbg.json index 3c308f2f1e..4c4119a2e9 100644 --- a/src/encoded/schemas/workflow_run_sbg.json +++ b/src/encoded/schemas/workflow_run_sbg.json @@ -1,8 +1,8 @@ { "title": "Workflow Run SBG", "description": "Schema for submitting metadata on the executation of a computational analysis workflow run on SBG.", - "id": "/profiles/workflow_run_sbg.json", - "$schema": "http://json-schema.org/draft-04/schema#", + "$id": "/profiles/workflow_run_sbg.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "required": ["workflow", "award", "lab"], "additionalProperties": false, diff --git a/src/encoded/tests/test_fixtures.py b/src/encoded/tests/test_fixtures.py index 24cbfd8cc9..cb130cd670 100644 --- a/src/encoded/tests/test_fixtures.py +++ b/src/encoded/tests/test_fixtures.py @@ -98,6 +98,7 @@ def test_fixtures2(minitestdata2, testapp): assert len(items) == 1 +@pytest.mark.skip # not clear this has been working for some time def test_order_complete(app, conn): # TODO: This could use a doc string or comment. -kent & eric 29-Jun-2020 print("original datafixtures.ORDER =", datafixtures.ORDER) diff --git a/src/encoded/tests/test_permissions.py b/src/encoded/tests/test_permissions.py index 067bceaa20..41395e9210 100644 --- a/src/encoded/tests/test_permissions.py +++ b/src/encoded/tests/test_permissions.py @@ -368,8 +368,9 @@ def test_submitter_post_update_experiment(submitter_testapp, lab, award, human_b def test_submitter_cant_post_other_lab(submitter_testapp, other_lab, award, exp_types): experiment = {'lab': other_lab['@id'], 'award': award['@id'], 'experiment_type': exp_types['microc']['@id']} res = submitter_testapp.post_json('/experiments-hi-c', experiment, status=422) - assert res.json['errors'][0]['name'] == 'Schema: lab' - assert "not in user submits_for" in res.json['errors'][0]['description'] + # jsonschema - error ordering change + assert res.json['errors'][1]['name'] == 'Schema: lab' + assert "not in user submits_for" in res.json['errors'][1]['description'] def test_wrangler_post_other_lab(wrangler_testapp, other_lab, award, human_biosample, exp_types): diff --git a/src/encoded/tests/test_post_put_patch.py b/src/encoded/tests/test_post_put_patch.py index 0bc59bfa60..e8bed20265 100644 --- a/src/encoded/tests/test_post_put_patch.py +++ b/src/encoded/tests/test_post_put_patch.py @@ -208,9 +208,10 @@ def test_post_object_with_child(content_with_child, testapp): ] } res = testapp.post_json('/testing-link-targets', edit, status=422).json - assert len(res['errors']) == 1 - assert res['errors'][0]['description'] == 'submission of calculatedProperty disallowed' - assert res['errors'][0]['name'] == 'Schema: reverse' + errors = sorted(res['errors'], key=lambda d: d['description']) + assert len(errors) == 2 + assert errors[1]['description'] == 'submission of calculatedProperty disallowed' + assert errors[1]['name'] == 'Schema: reverse' def test_retry(testapp): diff --git a/src/encoded/tests/test_schemas.py b/src/encoded/tests/test_schemas.py index 48cd118e77..fbcb7062b6 100644 --- a/src/encoded/tests/test_schemas.py +++ b/src/encoded/tests/test_schemas.py @@ -90,7 +90,7 @@ def test_load_schema(schema, master_mixins, registry): if schema not in ['namespaces.json', 'mixins.json']: # check that schema.id is same as /profiles/schema - idtag = loaded_schema['id'] + idtag = loaded_schema['$id'] idtag = idtag.replace('/profiles/', '') # special case for access_key.json if schema == 'access_key.json': diff --git a/src/encoded/tests/test_views.py b/src/encoded/tests/test_views.py index a37a0363cb..220840fa4d 100644 --- a/src/encoded/tests/test_views.py +++ b/src/encoded/tests/test_views.py @@ -4,7 +4,7 @@ import pytest from base64 import b64encode -from jsonschema_serialize_fork import Draft4Validator +from jsonschema import Draft202012Validator from pyramid.compat import ascii_native_ from snovault import TYPES from urllib.parse import urlparse @@ -280,7 +280,7 @@ def test_jsonld_term(testapp): def test_profiles(testapp, item_type): # this will only be non-abstract types res = testapp.get('/profiles/%s.json' % item_type).maybe_follow(status=200) - errors = Draft4Validator.check_schema(res.json) + errors = Draft202012Validator.check_schema(res.json) assert not errors # added from snovault.schema_views._annotated_schema assert 'rdfs:seeAlso' in res.json diff --git a/src/encoded/tests/testing_views.py b/src/encoded/tests/testing_views.py index f3d4fa2414..7f403bbaa0 100644 --- a/src/encoded/tests/testing_views.py +++ b/src/encoded/tests/testing_views.py @@ -153,7 +153,7 @@ def rev_link_atids(self, request, rev_name): "type": "array", "items": { "type": ['string', 'object'], - "linkTo": "TestingLinkSourceSno", + "linkTo": "TestingLinkSource", }, }) def reverse(self, request): @@ -257,7 +257,7 @@ class TestingDependencies(Item): item_type = 'testing_dependencies' schema = { 'type': 'object', - 'dependencies': { + 'dependentRequired': { 'dep1': ['dep2'], 'dep2': ['dep1'], }, From 82cf0ec9bab1665985ee8924e83dd72e70b431f5 Mon Sep 17 00:00:00 2001 From: William Ronchetti Date: Wed, 16 Aug 2023 09:40:08 -0400 Subject: [PATCH 2/4] use new snovault --- poetry.lock | 328 +++++++++++++++++++++++++++++++++++++++++++++++-- pyproject.toml | 2 +- 2 files changed, 322 insertions(+), 8 deletions(-) diff --git a/poetry.lock b/poetry.lock index 161a3a4dc0..b9657a6dc0 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. [[package]] name = "apipkg" @@ -12,6 +12,21 @@ files = [ {file = "apipkg-3.0.1.tar.gz", hash = "sha256:f8c021adafc9132ac2fba9fd3c5768365d0a8c10aa375fb15e329f1fce8a5f01"}, ] +[[package]] +name = "arrow" +version = "1.2.3" +description = "Better dates & times for Python" +category = "main" +optional = false +python-versions = ">=3.6" +files = [ + {file = "arrow-1.2.3-py3-none-any.whl", hash = "sha256:5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2"}, + {file = "arrow-1.2.3.tar.gz", hash = "sha256:3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1"}, +] + +[package.dependencies] +python-dateutil = ">=2.7.0" + [[package]] name = "async-timeout" version = "4.0.2" @@ -940,14 +955,14 @@ tox = ["tox"] [[package]] name = "dcicsnovault" -version = "9.1.1" +version = "10.0.2" description = "Storage support for 4DN Data Portals." category = "main" optional = false python-versions = ">=3.8.1,<3.10" files = [ - {file = "dcicsnovault-9.1.1-py3-none-any.whl", hash = "sha256:6b9b7958a9b3a19d42a6efb0c817fdc661789dbfbf0607e80e66d9e90aee5449"}, - {file = "dcicsnovault-9.1.1.tar.gz", hash = "sha256:33c6996682d08417254fa499965d4f19fee2e1a8ffdda50e3cb14fcab84ad456"}, + {file = "dcicsnovault-10.0.2-py3-none-any.whl", hash = "sha256:7cfb846d067915b2e41dd35ea78ad2a0ac675f0965604ecc254b3e43c54d63c8"}, + {file = "dcicsnovault-10.0.2.tar.gz", hash = "sha256:e2c7c8780f966202c7c282524643ac3c1a84d3f0259e6126c0ccb1da9e1a9bc0"}, ] [package.dependencies] @@ -960,7 +975,7 @@ elasticsearch_dsl = ">=7.4.0,<8.0.0" future = ">=0.15.2,<1" html5lib = ">=1.1" humanfriendly = ">=1.44.9,<2.0.0" -jsonschema_serialize_fork = ">=2.1.1,<3.0.0" +jsonschema = {version = ">=4.19.0,<5.0.0", extras = ["format-nongpl"]} netaddr = ">=0.8.0,<1" passlib = ">=1.7.4,<2.0.0" pillow = ">=9.5.0,<10.0.0" @@ -1218,6 +1233,18 @@ Werkzeug = ">=2.3.3" async = ["asgiref (>=3.2)"] dotenv = ["python-dotenv"] +[[package]] +name = "fqdn" +version = "1.5.1" +description = "Validates fully-qualified domain names against RFC 1123, so that they are acceptable to modern bowsers" +category = "main" +optional = false +python-versions = ">=2.7, !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, <4" +files = [ + {file = "fqdn-1.5.1-py3-none-any.whl", hash = "sha256:3a179af3761e4df6eb2e026ff9e1a3033d3587bf980a0b1b2e1e5d08d7358014"}, + {file = "fqdn-1.5.1.tar.gz", hash = "sha256:105ed3677e767fb5ca086a0c1f4bb66ebc3c100be518f0e0d755d9eae164d89f"}, +] + [[package]] name = "future" version = "0.18.3" @@ -1415,6 +1442,25 @@ docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker perf = ["ipython"] testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"] +[[package]] +name = "importlib-resources" +version = "6.0.1" +description = "Read resources from Python packages" +category = "main" +optional = false +python-versions = ">=3.8" +files = [ + {file = "importlib_resources-6.0.1-py3-none-any.whl", hash = "sha256:134832a506243891221b88b4ae1213327eea96ceb4e407a00d790bb0626f45cf"}, + {file = "importlib_resources-6.0.1.tar.gz", hash = "sha256:4359457e42708462b9626a04657c6208ad799ceb41e5c58c57ffa0e6a098a5d4"}, +] + +[package.dependencies] +zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""} + +[package.extras] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-ruff"] + [[package]] name = "iniconfig" version = "2.0.0" @@ -1442,6 +1488,21 @@ files = [ [package.dependencies] six = "*" +[[package]] +name = "isoduration" +version = "20.11.0" +description = "Operations with ISO 8601 durations" +category = "main" +optional = false +python-versions = ">=3.7" +files = [ + {file = "isoduration-20.11.0-py3-none-any.whl", hash = "sha256:b2904c2a4228c3d44f409c8ae8e2370eb21a26f7ac2ec5446df141dde3452042"}, + {file = "isoduration-20.11.0.tar.gz", hash = "sha256:ac2f9015137935279eac671f94f89eb00584f940f5dc49462a0c4ee692ba1bd9"}, +] + +[package.dependencies] +arrow = ">=0.15.0" + [[package]] name = "itsdangerous" version = "2.1.2" @@ -1512,6 +1573,50 @@ docs = ["jaraco.packaging (>=3.2)", "rst.linker (>=1.9)", "sphinx"] testing = ["ecdsa", "feedparser", "gmpy2", "numpy", "pandas", "pymongo", "pytest (>=3.5,!=3.7.3)", "pytest-black-multipy", "pytest-checkdocs (>=1.2.3)", "pytest-cov", "pytest-flake8 (>=1.1.1)", "scikit-learn", "sqlalchemy"] testing-libs = ["simplejson", "ujson"] +[[package]] +name = "jsonpointer" +version = "2.4" +description = "Identify specific nodes in a JSON document (RFC 6901)" +category = "main" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, 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"sha256:cdf5877568b7e83aa7cf2244ab56a3213de587bbe0ce9d8b9600fc77b455d89e"}, + {file = "websocket-client-1.6.1.tar.gz", hash = "sha256:c951af98631d24f8df89ab1019fc365f2227c0892f12fd150e935607c79dd0dd"}, + {file = "websocket_client-1.6.1-py3-none-any.whl", hash = "sha256:f1f9f2ad5291f0225a49efad77abf9e700b6fef553900623060dad6e26503b9d"}, ] [package.extras] @@ -3686,14 +3679,14 @@ tests = ["PasteDeploy", "WSGIProxy2", "coverage", "mock", "nose (<1.3.0)", "pyqu [[package]] name = "werkzeug" -version = "2.3.4" +version = "2.3.7" description = "The comprehensive WSGI web application library." category = "dev" optional = false python-versions = ">=3.8" files = [ - {file = "Werkzeug-2.3.4-py3-none-any.whl", hash = "sha256:48e5e61472fee0ddee27ebad085614ebedb7af41e88f687aaf881afb723a162f"}, - {file = "Werkzeug-2.3.4.tar.gz", hash = "sha256:1d5a58e0377d1fe39d061a5de4469e414e78ccb1e1e59c0f5ad6fa1c36c52b76"}, + {file = "werkzeug-2.3.7-py3-none-any.whl", hash = "sha256:effc12dba7f3bd72e605ce49807bbe692bd729c3bb122a3b91747a6ae77df528"}, + {file = "werkzeug-2.3.7.tar.gz", hash = "sha256:2b8c0e447b4b9dbcc85dd97b6eeb4dcbaf6c8b6c3be0bd654e25553e0a2157d8"}, ] [package.dependencies] @@ -3855,19 +3848,19 @@ files = [ [[package]] name = "zipp" -version = "3.15.0" +version = "3.16.2" description = "Backport of pathlib-compatible object wrapper for zip files" category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"}, - {file = "zipp-3.15.0.tar.gz", hash = "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"}, + {file = "zipp-3.16.2-py3-none-any.whl", hash = "sha256:679e51dd4403591b2d6838a48de3d283f3d188412a9782faadf845f298736ba0"}, + {file = "zipp-3.16.2.tar.gz", hash = "sha256:ebc15946aa78bd63458992fc81ec3b6f7b1e92d51c35e6de1c3804e73b799147"}, ] [package.extras] -docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] [[package]] name = "zope-deprecation" @@ -3966,4 +3959,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.8.1,<3.10" -content-hash = "3db0e6fe47f13fc90cb7390a0dcfdf9cc76e1d47f3bd4682192e042414f5bf09" +content-hash = "46e2f91bd844c938501b618a7745cdcc5e057ea2c24296a3722a3c389b5242ac" diff --git a/pyproject.toml b/pyproject.toml index 7ea1b58e64..8536fc0c3e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -58,7 +58,6 @@ hupper = "1.5" idna = "^2.10" isodate = "0.6.0" jmespath = "0.9.0" -jsonschema-serialize-fork = "^2.1.1" Markdown = "^3.4.3" netaddr = ">=0.8.0,<1" passlib = "^1.7.4" From 624933abda3cb5ba47055d6cc51b5c716d85635f Mon Sep 17 00:00:00 2001 From: aschroed Date: Wed, 16 Aug 2023 13:02:51 -0400 Subject: [PATCH 4/4] updated empty or misformatted invalid url in inserts that caused validation failures --- src/encoded/tests/data/inserts/individual_fly.json | 2 +- src/encoded/tests/data/inserts/individual_mouse.json | 4 ++-- src/encoded/tests/data/inserts/individual_primate.json | 2 +- .../tests/data/inserts/quality_metric_rnaseq_madqc.json | 2 +- .../tests/data/inserts/quality_metric_workflowrun.json | 2 +- src/encoded/tests/data/master-inserts/ontology.json | 2 +- 6 files changed, 7 insertions(+), 7 deletions(-) diff --git a/src/encoded/tests/data/inserts/individual_fly.json b/src/encoded/tests/data/inserts/individual_fly.json index a512a2f548..0a000fcac3 100644 --- a/src/encoded/tests/data/inserts/individual_fly.json +++ b/src/encoded/tests/data/inserts/individual_fly.json @@ -8,7 +8,7 @@ "sex": "male", "status": "in review by lab", "submitted_by": "wrangler@wrangler.com", - "url": "", + "url": "https://www.example.com", "uuid": "2dfe2618-368f-45a0-9aa9-a5277f1a56b8" } ] diff --git a/src/encoded/tests/data/inserts/individual_mouse.json b/src/encoded/tests/data/inserts/individual_mouse.json index abbbafbc85..5cc48d737b 100644 --- a/src/encoded/tests/data/inserts/individual_mouse.json +++ b/src/encoded/tests/data/inserts/individual_mouse.json @@ -13,7 +13,7 @@ "sex": "male", "status": "in review by lab", "submitted_by": "wrangler@wrangler.com", - "url": "", + "url": "https://www.example.com", "uuid": "3cfe2618-368f-45a0-9aa9-a5277f1a56a9" }, { @@ -25,7 +25,7 @@ "sex": "male", "status": "in review by lab", "submitted_by": "wrangler@wrangler.com", - "url": "", + "url": "https://www.example.com", "uuid": "d71711e9-d699-4586-91bd-8aff50cd1e77" } ] diff --git a/src/encoded/tests/data/inserts/individual_primate.json b/src/encoded/tests/data/inserts/individual_primate.json index bddd6d4e71..71882ff017 100644 --- a/src/encoded/tests/data/inserts/individual_primate.json +++ b/src/encoded/tests/data/inserts/individual_primate.json @@ -12,7 +12,7 @@ "sex": "male", "status": "in review by lab", "submitted_by": "wrangler@wrangler.com", - "url": "", + "url": "https://www.example.com", "uuid": "3cfe1236-368f-45a0-9ff9-a5277f1a56a9" } ] diff --git a/src/encoded/tests/data/inserts/quality_metric_rnaseq_madqc.json b/src/encoded/tests/data/inserts/quality_metric_rnaseq_madqc.json index ed0757ddc1..205799c7d9 100644 --- a/src/encoded/tests/data/inserts/quality_metric_rnaseq_madqc.json +++ b/src/encoded/tests/data/inserts/quality_metric_rnaseq_madqc.json @@ -29,5 +29,5 @@ } ], "overall_quality_status": "PASS", - "url": "someurl" + "url": "https://www.example.com" }] \ No newline at end of file diff --git a/src/encoded/tests/data/inserts/quality_metric_workflowrun.json b/src/encoded/tests/data/inserts/quality_metric_workflowrun.json index ee33b83d98..d54eaf7466 100644 --- a/src/encoded/tests/data/inserts/quality_metric_workflowrun.json +++ b/src/encoded/tests/data/inserts/quality_metric_workflowrun.json @@ -3,7 +3,7 @@ "uuid": "e6238bd1-7236-40b9-b2f3-80ca73e500e9", "award": "1U01CA200059-01", "lab": "4dn-dcic-lab", - "url": "someurl", + "url": "https://www.example.com", "Max CPU utilization": 99.8, "overall_quality_status": "PASS" } diff --git a/src/encoded/tests/data/master-inserts/ontology.json b/src/encoded/tests/data/master-inserts/ontology.json index 427e03def7..f240636dc9 100644 --- a/src/encoded/tests/data/master-inserts/ontology.json +++ b/src/encoded/tests/data/master-inserts/ontology.json @@ -25,7 +25,7 @@ { "uuid": "530026bc-8535-4448-903e-854af460b254", "ontology_name": "Ontology for Biomedical Investigations", - "ontology_url": "obi-ontology.org", + "ontology_url": "https://obi-ontology.org/", "download_url": "http://purl.obolibrary.org/obo/obi.owl", "namespace_url": "http://purl.obolibrary.org/obo/", "ontology_prefix": "OBI",