upgrade-validator

setup.py

@@ -5,7 +5,7 @@
 README = open(os.path.join(here, 'README.md')).read()
 CHANGES = open(os.path.join(here, 'CHANGES.rst')).read()
 # Edit Snovault version after the `@` here, can be a branch or tag
-SNOVAULT_DEP = "git+https://github.com/ENCODE-DCC/snovault.git@1.0.62"
+SNOVAULT_DEP = "git+https://github.com/ENCODE-DCC/snovault.git@upgrade-validator-sno2"
 
 INSTALL_REQUIRES = [
     "PasteDeploy==2.1.0",
@@ -21,7 +21,7 @@
     "elasticsearch==5.4.0",
     "future==0.18.2",
     "humanfriendly==6.1",
-    "jsonschema_serialize_fork==2.1.1",
+    "jsonschema[format]==4.4.0",
     "loremipsum==1.0.5",
     "passlib==1.7.2",
     "psutil==5.6.7",
@@ -32,7 +32,7 @@
     "pyramid==1.10.4",
     "python-magic==0.4.15",
     "pytz==2019.3",
-    "rdflib-jsonld==0.4.0",
+    "rdflib-jsonld==0.6.0",
     "rdflib==4.2.2",
     "repoze.debug==1.1",
     "rfc3987==1.3.8",

src/encoded/auth0.py

@@ -7,7 +7,7 @@
 from snovault.schema_utils import validate_request
 from pyramid.authentication import CallbackAuthenticationPolicy
 from encoded.types.user import User
-from jsonschema_serialize_fork.exceptions import ValidationError
+from jsonschema.exceptions import ValidationError
 from pyramid.httpexceptions import (
     HTTPBadRequest,
     HTTPInternalServerError,

src/encoded/schema_formats.py

@@ -1,6 +1,6 @@
 import re
 import rfc3987
-from jsonschema_serialize_fork import FormatChecker
+from jsonschema import FormatChecker
 from pyramid.threadlocal import get_current_request
 from uuid import UUID
 

src/encoded/schemas/access_key.json

@@ -1,7 +1,7 @@
 {
     "title": "Admin access key",
-    "id": "/profiles/access_key_admin.json",
-    "$schema": "http://json-schema.org/draft-04/schema#",
+    "$id": "/profiles/access_key_admin.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "required": [],
     "additionalProperties": false,
     "mixinProperties": [

src/encoded/schemas/aggregate_series.json

@@ -1,8 +1,8 @@
 {
     "title": "Aggregate series",
     "description": "Schema for submitting metadata for an aggregate series.",
-    "id": "/profiles/aggregate_series.json",
-    "$schema": "http://json-schema.org/draft-04/schema#",
+    "$id": "/profiles/aggregate_series.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "type": "object",
     "required": [ "award", "lab"],
     "identifyingProperties": ["uuid", "accession" , "aliases"],
@@ -21,7 +21,7 @@
         { "$ref": "series.json#/properties" },
         { "$ref": "mixins.json#/submitter_comment" }
     ],
-    "dependencies": {
+    "dependentSchemas": {
         "status": {
             "oneOf": [
                 {

src/encoded/schemas/analysis.json

@@ -2,8 +2,8 @@
     "title": "Analysis",
     "description": "Schema for grouping files into one analysis.",
     "comment": "An analysis is typically performed on one experiments and is initially designed to group only files from a single experiment.",
-    "id": "/profiles/analysis.json",
-    "$schema": "http://json-schema.org/draft-04/schema#",
+    "$id": "/profiles/analysis.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "type": "object",
     "required": ["files"],
     "identifyingProperties": ["uuid", "accession", "aliases"],
@@ -18,7 +18,6 @@
         { "$ref": "mixins.json#/notes" },
         { "$ref": "mixins.json#/documents" }
     ],
-    "dependencies": {},
     "properties": {
         "schema_version": {
             "default": "1"

src/encoded/schemas/analysis_step.json

@@ -1,8 +1,8 @@
 { 
     "title": "Analysis step",
     "description": "Schema for submitting a computational analysis steps as a subobject of pipeline that transforms input files to output files.",
-    "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": ["step_label", "title", "analysis_step_types", "input_file_types", "major_version"],
     "additionalProperties": false,

src/encoded/schemas/analysis_step_run.json

@@ -1,8 +1,8 @@
 {
     "title": "Analysis step run",
     "description": "Schema for reporting the specific calculation of an analysis_step",
-    "id": "/profiles/analysis_step_run.json",
-    "$schema": "http://json-schema.org/draft-04/schema#",
+    "$id": "/profiles/analysis_step_run.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "type": "object",
     "required": ["analysis_step_version"],
     "additionalProperties": false,

src/encoded/schemas/analysis_step_version.json

@@ -1,8 +1,8 @@
 {
     "title": "Analysis step version",
     "description": "A compatible version of an analysis step.",
-    "id": "/profiles/analysis_step_version.json",
-    "$schema": "http://json-schema.org/draft-04/schema#",
+    "$id": "/profiles/analysis_step_version.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "type": "object",
     "required": ["software_versions", "analysis_step", "minor_version"],
     "additionalProperties": false,

src/encoded/schemas/annotation.json

@@ -1,8 +1,8 @@
 {
     "title": "Annotation",
     "description": "Schema for submitting metadata for an annotation set.",
-    "id": "/profiles/annotation.json",
-    "$schema": "http://json-schema.org/draft-04/schema#",
+    "$id": "/profiles/annotation.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "type": "object",
     "required": [ "award", "lab", "annotation_type"],
     "identifyingProperties": ["uuid", "accession" , "aliases"],
@@ -21,7 +21,11 @@
         { "$ref": "dataset.json#/properties" },
         { "$ref": "file_set.json#/properties" }
     ],
-    "dependencies": {
+    "dependentRequired": {
+	"relevant_timepoint": ["relevant_timepoint_units"],
+	"relevant_timepoint_units": ["relevant_timepoint"]
+    },
+    "dependentSchemas": {
         "biosample_ontology": {
             "not": {
                 "properties": {
@@ -41,8 +45,6 @@
                 }
             }
         },
-        "relevant_timepoint": ["relevant_timepoint_units"],
-        "relevant_timepoint_units": ["relevant_timepoint"],
         "status": {
             "oneOf": [
                 {

src/encoded/schemas/antibody_characterization.json

@@ -1,8 +1,8 @@
- {
+{
     "title": "Antibody characterization",
     "description": "Schema for submitting antibody characterization data.",
-    "id": "/profiles/antibody_characterization.json",
-    "$schema": "http://json-schema.org/draft-04/schema#",
+    "$id": "/profiles/antibody_characterization.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "type": "object",
     "required": [ "award", "lab", "characterizes", "target", "attachment"],
     "identifyingProperties": ["uuid", "aliases"],
@@ -20,8 +20,10 @@
         { "$ref": "mixins.json#/documents" },
         { "$ref": "mixins.json#/submitter_comment" }
     ],
-    "dependencies": {
-        "characterization_reviews": ["primary_characterization_method"],
+    "dependentRequired": {
+	"characterization_reviews": ["primary_characterization_method"]
+    },
+    "dependentSchemas": {
         "primary_characterization_method": {
             "oneOf": [
                 {

src/encoded/schemas/antibody_lot.json

@@ -1,8 +1,8 @@
 {
     "title": "Antibody lot",
     "description": "Schema for submitting an antibody lot (not including target or characterization information).",
-    "id": "/profiles/antibody_lot.json",
-    "$schema": "http://json-schema.org/draft-04/schema#",
+    "$id": "/profiles/antibody_lot.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "type": "object",
     "required": [ "award", "lab", "product_id", "source", "lot_id", "host_organism"],
     "identifyingProperties": ["uuid","accession","aliases"],

src/encoded/schemas/atac_alignment_enrichment_quality_metric.json

@@ -1,8 +1,8 @@
 {
     "title": "ATAC-seq alignment enrichment quality metric",
     "description": "Schema for ATAC-seq alignment enrichment quality metrics",
-    "id": "/profiles/atac_alignment_enrichment_quality_metric.json",
-    "$schema": "http://json-schema.org/draft-04/schema#",
+    "$id": "/profiles/atac_alignment_enrichment_quality_metric.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "type": "object",
     "required": ["step_run","quality_metric_of", "award", "lab"],
     "additionalProperties": false,

src/encoded/schemas/atac_alignment_quality_metric.json

@@ -1,8 +1,8 @@
 {
     "title": "ATAC-seq alignment quality metric",
     "description": "Schema for reporting ATAC-seq alignment quality metrics",
-    "id": "/profiles/atac_alignment_quality_metric.json",
-    "$schema": "http://json-schema.org/draft-04/schema#",
+    "$id": "/profiles/atac_alignment_quality_metric.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "type": "object",
     "required": ["step_run","quality_metric_of", "award", "lab"],
     "additionalProperties": false,

src/encoded/schemas/atac_library_complexity_quality_metric.json

@@ -1,8 +1,8 @@
 {
     "title": "ATAC-seq library quality metric",
     "description": "Schema for reporting ATAC-seq library quality metrics",
-    "id": "/profiles/atac_library_complexity_quality_metric.json",
-    "$schema": "http://json-schema.org/draft-04/schema#",
+    "$id": "/profiles/atac_library_complexity_quality_metric.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "type": "object",
     "required": ["step_run","quality_metric_of", "award", "lab"],
     "additionalProperties": false,

src/encoded/schemas/atac_peak_enrichment_quality_metric.json

@@ -1,8 +1,8 @@
 {
     "title": "ATAC-seq peak enrichment quality metric",
     "description": "Schema for reporting ATAC-seq peak enrichment quality metrics",
-    "id": "/profiles/atac_peak_enrichment_quality_metric.json",
-    "$schema": "http://json-schema.org/draft-04/schema#",
+    "$id": "/profiles/atac_peak_enrichment_quality_metric.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "type": "object",
     "required": ["step_run","quality_metric_of", "award", "lab"],
     "additionalProperties": false,

src/encoded/schemas/atac_replication_quality_metric.json

@@ -1,8 +1,8 @@
 {
     "title": "ATAC-seq replication quality metric",
     "description": "Schema for reporting ATAC-seq replication quality metrics",
-    "id": "/profiles/atac_replication_quality_metric.json",
-    "$schema": "http://json-schema.org/draft-04/schema#",
+    "$id": "/profiles/atac_replication_quality_metric.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "type": "object",
     "required": ["step_run","quality_metric_of", "award", "lab"],
     "additionalProperties": false,

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", "project", "rfa", "title"],
     "identifyingProperties": ["uuid", "name", "title"],
     "additionalProperties": false,

src/encoded/schemas/biosample.json

@@ -2,8 +2,8 @@
     "title": "Biosample",
     "description": "Schema for submitting a biosample.",
     "comment": "For cultured samples this object represents unique growths or culture harvests.",
-    "id": "/profiles/biosample.json",
-    "$schema": "http://json-schema.org/draft-04/schema#",
+    "$id": "/profiles/biosample.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "type": "object",
     "required": [ "award", "lab", "source", "organism", "biosample_ontology"],
     "identifyingProperties": ["uuid", "accession", "aliases"],
@@ -27,7 +27,7 @@
         {"$ref": "mixins.json#/accession"},
         {"$ref": "mixins.json#/uuid"}
     ],
-    "dependencies": {
+    "dependentSchemas": {
         "biosample_ontology": {
             "not": {
                 "properties": {
@@ -976,9 +976,11 @@
                         "maximum": 100
                     }
                 },
-                "dependencies": {
-                    "expression_range_minimum": ["expression_range_maximum"],
-                    "expression_range_maximum": ["expression_range_minimum"],
+		"dependentRequired": {
+		    "expression_range_minimum": ["expression_range_maximum"],
+		    "expression_range_maximum": ["expression_range_minimum"]
+		},
+                "dependentSchemas": {
                     "expression_percentile": {
                         "not": {
                             "anyOf": [

src/encoded/schemas/biosample_characterization.json

@@ -1,8 +1,8 @@
 {
     "title": "Biosample characterization",
     "description": "Schema for submitting biosample characterization data",
-    "id": "/profiles/biosample_characterization.json",
-    "$schema": "http://json-schema.org/draft-04/schema#",
+    "$id": "/profiles/biosample_characterization.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "type": "object",
     "required": [ "award", "lab", "characterizes", "attachment"],
     "identifyingProperties": ["uuid", "aliases"],

src/encoded/schemas/biosample_type.json

@@ -2,8 +2,8 @@
     "title": "Biosample Type",
     "description": "Schema for describing the type of a specific biosample.",
     "comment": "This object collects common properties of a group of similar biosamples to help reduce ambiguity and duplications. Do not submit. DCC personnel is responsible for creating and maintaining these objects",
-    "id": "/profiles/biosample_type.json",
-    "$schema": "http://json-schema.org/draft-04/schema#",
+    "$id": "/profiles/biosample_type.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "type": "object",
     "required": ["classification", "term_id", "term_name"],
     "identifyingProperties": ["aliases", "uuid"],
@@ -16,7 +16,7 @@
         {"$ref": "mixins.json#/standard_status"},
         {"$ref": "mixins.json#/uuid"}
     ],
-    "dependencies": {
+    "dependentSchemas": {
         "term_id":{
             "oneOf": [
                 { 

src/encoded/schemas/bismark_quality_metric.json

@@ -1,8 +1,8 @@
 {
     "title": "Bismark quality metric",
     "description": "Schema for reporting the specific calculation of an quality metrics",
-    "id": "/profiles/bismark_quality_metric.json",
-    "$schema": "http://json-schema.org/draft-04/schema#",
+    "$id": "/profiles/bismark_quality_metric.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "type": "object",
     "required": ["step_run", "quality_metric_of", "award", "lab"],
     "additionalProperties": false,

src/encoded/schemas/bru_library_quality_metric.json

@@ -1,8 +1,8 @@
 {
     "title": "Bru library quality metric",
     "description": "Schema for reporting Bru assay library quality metric",
-    "id": "/profiles/bru_library_quality_metric.json",
-    "$schema": "http://json-schema.org/draft-04/schema#",
+    "$id": "/profiles/bru_library_quality_metric.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "type": "object",
     "required": ["step_run", "award", "lab", "quality_metric_of"],
     "additionalProperties": false,

src/encoded/schemas/cart.json

@@ -2,8 +2,8 @@
     "title": "Cart",
     "description": "Cart of objects aka shopping cart.",
     "comment": "This object gets connected with user objects.",
-    "id": "/profiles/cart.json",
-    "$schema": "http://json-schema.org/draft-04/schema#",
+    "$id": "/profiles/cart.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "type": "object",
     "required": ["name"],
     "identifyingProperties": ["uuid", "identifier"],
@@ -13,7 +13,7 @@
         { "$ref": "mixins.json#/submitted" },
         { "$ref": "mixins.json#/uuid" }
     ],
-    "dependencies": {
+    "dependentSchemas": {
         "status":{
             "comment": "Listed, released, or revoked carts must have a description.",
             "oneOf": [

src/encoded/schemas/characterization.json

@@ -1,8 +1,8 @@
 {
     "title": "Base characterization",
     "description": "Schema for submitting a characterization of an object.",
-    "id": "/profiles/characterization.json",
-    "$schema": "http://json-schema.org/draft-04/schema#",
+    "$id": "/profiles/characterization.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "type": "object",
     "required": [ "award", "lab", "characterizes", "attachment"],
     "additionalProperties": false,

src/encoded/schemas/chia_pet_alignment_quality_metric.json

@@ -1,8 +1,8 @@
 {
     "title": "ChIA-PET alignment quality metric",
     "description": "Schema for reporting ChIA-PET alignment quality metric",
-    "id": "/profiles/chia_pet_alignment_quality_metric.json",
-    "$schema": "http://json-schema.org/draft-04/schema#",
+    "$id": "/profiles/chia_pet_alignment_quality_metric.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "type": "object",
     "required": ["step_run", "award", "lab", "quality_metric_of"],
     "additionalProperties": false,