Merge pull request #1836 from 4dn-dcic/wrr_schema

Jsonschema update

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
 =====
 

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 <support@4dnucleome.org>"]
 license = "MIT"
@@ -47,7 +47,7 @@ colorama = "0.3.3"
 # we get odd 'pyo3_runtime.PanicException: Python API call failed' error on import
 # of cryptography.hazmat.bindings._rust in cryptography package. 2023-04-21.
 cryptography = "39.0.2"
-dcicsnovault = "^9.1.1"
+dcicsnovault = "^10.0.2"
 dcicutils = "^7.5.0"
 elasticsearch = "7.13.4"
 elasticsearch-dsl = "^7.0.0"  # TODO: port code from cgap-portal to get rid of uses
@@ -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"

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)

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": [

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,

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" },

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,

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"],

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"],

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"],

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"],

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"],

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"],

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,

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"],

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"],

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"]
     },

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"],

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"],

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"],

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"],

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"],

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"],

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"],

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"]
     },

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"],

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"],