build!: updating to vrs 2.0 models

README.md

@@ -30,7 +30,7 @@ source venv/bin/activate
 python3 -m pip install -e ".[dev,tests]"  # make sure to include the extra dependencies!
 ```
 
-Acquire two sets of static assets and place all of them within the `server/curation/data` directory:
+Acquire two sets of static assets and place all of them within the `server/src/curfu/data` directory:
 
 1. Gene autocomplete files, providing legal gene search terms to the client autocomplete component. One file each is used for entity types `aliases`, `assoc_with`, `xrefs`, `prev_symbols`, `labels`, and `symbols`. Each should be named according to the pattern `gene_<type>_<YYYYMMDD>.tsv`. These can be regenerated with the shell command `curfu_devtools genes`.
 
@@ -39,7 +39,7 @@ Acquire two sets of static assets and place all of them within the `server/curat
 Your data/directory should look something like this:
 
 ```
-server/curfu/data
+server/src/curfu/data
 ├── domain_lookup_2022-01-20.tsv
 ├── gene_aliases_suggest_20211025.tsv
 ├── gene_assoc_with_suggest_20211025.tsv

client/src/services/ResponseModels.ts

@@ -94,27 +94,13 @@ export interface RegulatoryElement {
   type?: "RegulatoryElement";
   regulatory_class: RegulatoryClass;
   feature_id?: string;
-  associated_gene?: GeneDescriptor;
-  feature_location?: LocationDescriptor;
-}
-/**
- * This descriptor is intended to reference VRS Gene value objects.
- */
-export interface GeneDescriptor {
-  id: CURIE;
-  type?: "GeneDescriptor";
-  label?: string;
-  description?: string;
-  xrefs?: CURIE[];
-  alternate_labels?: string[];
-  extensions?: Extension[];
-  gene_id?: CURIE;
-  gene?: Gene;
+  associated_gene?: Gene;
+  feature_location?: SequenceLocation;
 }
 /**
  * The Extension class provides VODs with a means to extend descriptions
  * with other attributes unique to a content provider. These extensions are
- * not expected to be natively understood under VRSATILE, but may be used
+ * not expected to be natively understood under VRS, but may be used
  * for pre-negotiated exchange of message attributes when needed.
  */
 export interface Extension {
@@ -129,57 +115,33 @@ export interface Extension {
  */
 export interface Gene {
   type?: "Gene";
-  /**
-   * A CURIE reference to a Gene concept
-   */
-  gene_id: CURIE;
+  id: string;
+  label: string;
 }
 /**
- * This descriptor is intended to reference VRS Location value objects.
+ * A referenced Sequence
  */
-export interface LocationDescriptor {
-  id: CURIE;
-  type?: "LocationDescriptor";
-  label?: string;
-  description?: string;
-  xrefs?: CURIE[];
-  alternate_labels?: string[];
-  extensions?: Extension[];
-  location_id?: CURIE;
-  location?: SequenceLocation | ChromosomeLocation;
+export interface SequenceReference {
+  // refseq id of the referenced sequence
+  id?: CURIE;
+  type?: "SequenceReference";
+  // VRS computed identifier for the sequence accession
+  refgetAccession: string;
 }
 /**
- * A Location defined by an interval on a referenced Sequence.
+ * A Location defined by the start/end coordinates on a referenced Sequence.
  */
 export interface SequenceLocation {
   /**
-   * Variation Id. MUST be unique within document.
+   * A VRS Computed Identifier for the Sequence location.
    */
-  _id?: CURIE;
+  id?: CURIE;
   type?: "SequenceLocation";
-  /**
-   * A VRS Computed Identifier for the reference Sequence.
-   */
-  sequence_id: CURIE;
-  /**
-   * Reference sequence region defined by a SequenceInterval.
-   */
-  interval: SequenceInterval | SimpleInterval;
-}
-/**
- * A SequenceInterval represents a span on a Sequence. Positions are always
- * represented by contiguous spans using interbase coordinates or coordinate ranges.
- */
-export interface SequenceInterval {
-  type?: "SequenceInterval";
-  /**
-   * The start coordinate or range of the interval. The minimum value of this coordinate or range is 0. MUST represent a coordinate or range less than the value of `end`.
-   */
-  start: DefiniteRange | IndefiniteRange | Number;
-  /**
-   * The end coordinate or range of the interval. The minimum value of this coordinate or range is 0. MUST represent a coordinate or range greater than the value of `start`.
-   */
-  end: DefiniteRange | IndefiniteRange | Number;
+  sequenceReference: SequenceReference;
+  // start coordinate of the sequence location
+  start: number;
+  // end coordinate of the sequence location
+  end: number;
 }
 /**
  * A bounded, inclusive range of numbers.
@@ -222,22 +184,6 @@ export interface Number {
    */
   value: number;
 }
-/**
- * DEPRECATED: A SimpleInterval represents a span of sequence. Positions are always
- * represented by contiguous spans using interbase coordinates.
- * This class is deprecated. Use SequenceInterval instead.
- */
-export interface SimpleInterval {
-  type?: "SimpleInterval";
-  /**
-   * The start coordinate
-   */
-  start: number;
-  /**
-   * The end coordinate
-   */
-  end: number;
-}
 /**
  * A Location on a chromosome defined by a species and chromosome name.
  */
@@ -286,16 +232,16 @@ export interface TranscriptSegmentElement {
   exon_start_offset?: number;
   exon_end?: number;
   exon_end_offset?: number;
-  gene_descriptor: GeneDescriptor;
-  element_genomic_start?: LocationDescriptor;
-  element_genomic_end?: LocationDescriptor;
+  gene: Gene;
+  element_genomic_start?: SequenceLocation;
+  element_genomic_end?: SequenceLocation;
 }
 /**
  * Define Gene Element class.
  */
 export interface GeneElement {
   type?: "GeneElement";
-  gene_descriptor: GeneDescriptor;
+  gene: Gene;
 }
 /**
  * Define Templated Sequence Element class.
@@ -304,7 +250,7 @@ export interface GeneElement {
  */
 export interface TemplatedSequenceElement {
   type?: "TemplatedSequenceElement";
-  region: LocationDescriptor;
+  region: SequenceLocation;
   strand: Strand;
 }
 /**
@@ -314,21 +260,6 @@ export interface LinkerElement {
   type?: "LinkerSequenceElement";
   linker_sequence: SequenceDescriptor;
 }
-/**
- * This descriptor is intended to reference VRS Sequence value objects.
- */
-export interface SequenceDescriptor {
-  id: CURIE;
-  type?: "SequenceDescriptor";
-  label?: string;
-  description?: string;
-  xrefs?: CURIE[];
-  alternate_labels?: string[];
-  extensions?: Extension[];
-  sequence_id?: CURIE;
-  sequence?: Sequence;
-  residue_type?: CURIE;
-}
 /**
  * Define UnknownGene class. This is primarily intended to represent a
  * partner in the result of a fusion partner-agnostic assay, which identifies
@@ -417,10 +348,10 @@ export interface MultiplePossibleGenesElement {
 export interface FunctionalDomain {
   type?: "FunctionalDomain";
   status: DomainStatus;
-  associated_gene: GeneDescriptor;
+  associated_gene: Gene;
   _id?: CURIE;
   label?: string;
-  sequence_location?: LocationDescriptor;
+  sequence_location?: SequenceLocation;
 }
 /**
  * Assayed fusion with client-oriented structural element models. Used in
@@ -446,8 +377,8 @@ export interface ClientRegulatoryElement {
   type?: "RegulatoryElement";
   regulatory_class: RegulatoryClass;
   feature_id?: string;
-  associated_gene?: GeneDescriptor;
-  feature_location?: LocationDescriptor;
+  associated_gene?: Gene;
+  feature_location?: SequenceLocation;
   display_class: string;
   nomenclature: string;
 }
@@ -463,9 +394,9 @@ export interface ClientTranscriptSegmentElement {
   exon_start_offset?: number;
   exon_end?: number;
   exon_end_offset?: number;
-  gene_descriptor: GeneDescriptor;
-  element_genomic_start?: LocationDescriptor;
-  element_genomic_end?: LocationDescriptor;
+  gene: Gene;
+  element_genomic_start?: SequenceLocation;
+  element_genomic_end?: SequenceLocation;
   input_type: "genomic_coords_gene" | "genomic_coords_tx" | "exon_coords_tx";
   input_tx?: string;
   input_strand?: Strand;
@@ -485,7 +416,7 @@ export interface ClientGeneElement {
   element_id: string;
   nomenclature: string;
   type?: "GeneElement";
-  gene_descriptor: GeneDescriptor;
+  gene: Gene;
 }
 /**
  * Templated sequence element used client-side.
@@ -494,7 +425,7 @@ export interface ClientTemplatedSequenceElement {
   element_id: string;
   nomenclature: string;
   type?: "TemplatedSequenceElement";
-  region: LocationDescriptor;
+  region: SequenceLocation;
   strand: Strand;
   input_chromosome?: string;
   input_start?: string;
@@ -548,10 +479,10 @@ export interface ClientMultiplePossibleGenesElement {
 export interface ClientFunctionalDomain {
   type?: "FunctionalDomain";
   status: DomainStatus;
-  associated_gene: GeneDescriptor;
+  associated_gene: Gene;
   _id?: CURIE;
   label?: string;
-  sequence_location?: LocationDescriptor;
+  sequence_location?: SequenceLocation;
   domain_id: string;
 }
 /**

requirements.txt

@@ -18,17 +18,16 @@ charset-normalizer==3.2.0
 click==8.1.6
 coloredlogs==15.0.1
 configparser==6.0.0
-cool-seq-tool==0.1.14.dev0
+cool-seq-tool==0.5.1
 cssselect==1.2.0
 Cython==3.0.0
 decorator==5.1.1
 executing==1.2.0
 fake-useragent==1.1.3
 fastapi==0.100.0
-fusor==0.0.30.dev1
-ga4gh.vrs==0.8.4
-ga4gh.vrsatile.pydantic==0.0.13
-gene-normalizer==0.1.39
+# TODO: add this back once new release is out fusor==0.0.30.dev1
+ga4gh.vrs==2.0.0a10
+gene-normalizer==0.4.0
 h11==0.14.0
 hgvs==1.5.4
 humanfriendly==10.0
@@ -55,7 +54,7 @@ prompt-toolkit==3.0.39
 psycopg2==2.9.6
 ptyprocess==0.7.0
 pure-eval==0.2.2
-pydantic==1.10.12
+pydantic==2.4.2
 pyee==8.2.2
 Pygments==2.15.1
 pyliftover==0.4

server/pyproject.toml

@@ -25,7 +25,6 @@ dependencies = [
     "fastapi >= 0.72.0",
     "aiofiles",
     "asyncpg",
-    "fusor ~= 0.0.30-dev1",
     "sqlparse >= 0.4.2",
     "urllib3 >= 1.26.5",
     "click",
@@ -47,7 +46,7 @@ dev = [
     "ruff",
     "black",
     "pre-commit>=3.7.1",
-    "gene-normalizer ~= 0.1.39",
+    "gene-normalizer ~= 0.4.0",
     "pydantic-to-typescript",
 ]
 

server/src/curfu/devtools/build_client_types.py

@@ -7,7 +7,7 @@
 
 def build_client_types() -> None:
     """Construct type definitions for front-end client."""
-    client_dir = Path(__file__).resolve().parents[3] / "client"
+    client_dir = Path(__file__).resolve().parents[4] / "client"
     generate_typescript_defs(
         "curfu.schemas",
         str((client_dir / "src" / "services" / "ResponseModels.ts").absolute()),

server/src/curfu/gene_services.py

@@ -3,7 +3,6 @@
 import csv
 from pathlib import Path
 
-from ga4gh.vrsatile.pydantic.vrsatile_models import CURIE
 from gene.query import QueryHandler
 from gene.schemas import MatchType
 
@@ -50,7 +49,7 @@ def __init__(self, suggestions_file: Path | None = None) -> None:
     @staticmethod
     def get_normalized_gene(
         term: str, normalizer: QueryHandler
-    ) -> tuple[CURIE, str, str | CURIE | None]:
+    ) -> tuple[str, str, str | str | None]:
         """Get normalized ID given gene symbol/label/alias.
         :param str term: user-entered gene term
         :param QueryHandler normalizer:  gene normalizer instance

server/src/curfu/routers/meta.py

@@ -1,6 +1,6 @@
 """Provide service meta information"""
 
-from cool_seq_tool.version import __version__ as cool_seq_tool_version
+from cool_seq_tool import __version__ as cool_seq_tool_version
 from fastapi import APIRouter
 from fusor import __version__ as fusor_version
 

server/src/curfu/schemas.py

@@ -18,14 +18,13 @@
     TranscriptSegmentElement,
     UnknownGeneElement,
 )
-from ga4gh.vrsatile.pydantic.vrsatile_models import CURIE
 from pydantic import BaseModel, Extra, Field, StrictInt, StrictStr, validator
 
 ResponseWarnings = list[StrictStr] | None
 
 ResponseDict = dict[
     str,
-    str | int | CURIE | list[str] | list[tuple[str, str, str, str]] | FunctionalDomain,
+    str | int | str | list[str] | list[tuple[str, str, str, str]] | FunctionalDomain,
 ]
 Warnings = list[str]
 
@@ -134,7 +133,7 @@ class NormalizeGeneResponse(Response):
     """Response model for gene normalization endpoint."""
 
     term: StrictStr
-    concept_id: CURIE | None
+    concept_id: StrictStr | None
     symbol: StrictStr | None
     cased: StrictStr | None
 
@@ -154,7 +153,7 @@ class SuggestGeneResponse(Response):
 class DomainParams(BaseModel):
     """Fields for individual domain suggestion entries"""
 
-    interpro_id: CURIE
+    interpro_id: StrictStr
     domain_name: StrictStr
     start: int
     end: int