Merge branch 'main' into fork-readme

Author: jsstevenson

.gitmodules

@@ -1,4 +1,4 @@
 [submodule "submodules/vrs"]
 	path = submodules/vrs
 	url = https://github.com/ga4gh/vrs.git
-	branch = 2.0.0-snapshot.2025-02
+	branch = 2.0

README.md

@@ -83,7 +83,7 @@ First, you must install a local [SeqRepo](https://github.com/biocommons/biocommo
 
 ```shell
 pip install seqrepo
-export SEQREPO_VERSION=2024-02-20  # or newer if available -- check `seqrepo list-remote-instances`
+export SEQREPO_VERSION=2024-12-20  # or newer if available -- check `seqrepo list-remote-instances`
 sudo mkdir -p /usr/local/share/seqrepo
 sudo chown $USER /usr/local/share/seqrepo
 seqrepo pull -i $SEQREPO_VERSION
@@ -93,7 +93,7 @@ seqrepo update-latest
 If you encounter a permission error similar to the one below:
 
 ```shell
-PermissionError: [Error 13] Permission denied: '/usr/local/share/seqrepo/2024-02-20._fkuefgd' -> '/usr/local/share/seqrepo/2024-02-20'
+PermissionError: [Error 13] Permission denied: '/usr/local/share/seqrepo/2024-12-20._fkuefgd' -> '/usr/local/share/seqrepo/2024-12-20'
 ```
 
 Try moving data manually with `sudo`:
@@ -131,7 +131,7 @@ Check that the containers are running, by running:
 $ docker ps
 CONTAINER ID        IMAGE                                    //  NAMES
 86e872ab0c69        biocommons/seqrepo-rest-service:latest   //  vrs-python_seqrepo-rest-service_1
-a40576b8cf1f        biocommons/uta:uta_20210129b              //  vrs-python_uta_1
+a40576b8cf1f        biocommons/uta:uta_20241220              //  vrs-python_uta_1
 ```
 
 Depending on your network and host, the _first_ run is likely to take 5-15
@@ -141,7 +141,7 @@ nearly instantaneous.
 You can test UTA and seqrepo installations like so:
 
 ```shell
-$ psql -XAt postgres://anonymous@localhost/uta -c 'select count(*) from uta_20210129b.transcript'
+$ psql -XAt postgres://anonymous@localhost/uta -c 'select count(*) from uta_20241220.transcript'
 314227
 ```
 
@@ -156,9 +156,9 @@ Here are some things to try.
   $ docker-compose up seqrepo-rest-service
   Starting vrs-python_seqrepo-rest-service_1 ... done
   Attaching to vrs-python_seqrepo-rest-service_1
-  seqrepo-rest-service_1  | 2022-07-26 15:59:59 seqrepo_rest_service.__main__[1] INFO Using seqrepo_dir='/usr/local/share/seqrepo/2024-02-20' from command line
+  seqrepo-rest-service_1  | 2022-07-26 15:59:59 seqrepo_rest_service.__main__[1] INFO Using seqrepo_dir='/usr/local/share/seqrepo/2024-12-20' from command line
   ⋮
-  seqrepo-rest-service_1  | OSError: Unable to open SeqRepo directory /usr/local/share/seqrepo/2024-02-20
+  seqrepo-rest-service_1  | OSError: Unable to open SeqRepo directory /usr/local/share/seqrepo/2024-12-20
   vrs-python_seqrepo-rest-service_1 exited with code 1
   ```
 

docker-compose.yml

@@ -1,6 +1,6 @@
 services:
   seqrepo:
-    image: biocommons/seqrepo:2024-02-20
+    image: biocommons/seqrepo:2024-12-20
     volumes:
       - seqrepo_vol:/usr/local/share/seqrepo
 
@@ -11,16 +11,16 @@ services:
       - seqrepo_vol:/usr/local/share/seqrepo
     depends_on:
       - seqrepo
-    command: seqrepo-rest-service -w /usr/local/share/seqrepo/2024-02-20
+    command: seqrepo-rest-service -w /usr/local/share/seqrepo/2024-12-20
     network_mode: bridge
     ports:
       - 5000:5000
 
   uta:
     # Test:
-    # psql -XAt postgres://anonymous@localhost/uta -c 'select count(*) from uta_20210129b.transcript'
+    # psql -XAt postgres://anonymous@localhost/uta -c 'select count(*) from uta_20241220.transcript'
     # 314227
-    image: biocommons/uta:uta_20210129b
+    image: biocommons/uta:uta_20241220
     environment:
       - POSTGRES_PASSWORD=some-password-that-you-make-up
     volumes:

docs/extras/vcf_annotator.md

@@ -20,13 +20,13 @@ Like other VRS-Python tools, the VCF annotator requires access to [sequence and
 For example, to use a local set of SeqRepo data, you can use an absolute file path:
 
 ```commandline
-vrs-annotate vcf --dataproxy_uri="seqrepo+file:///usr/local/share/seqrepo/2024-02-20/" --vcf_out=out.vcf.gz input.vcf.gz
+vrs-annotate vcf --dataproxy_uri="seqrepo+file:///usr/local/share/seqrepo/2024-12-20/" --vcf_out=out.vcf.gz input.vcf.gz
 ```
 
 Alternative, a relative file path:
 
 ```commandline
-vrs-annotate vcf --dataproxy_uri="seqrepo+../seqrepo/2024-02-20/" --vcf_out=out.vcf.gz input.vcf.gz
+vrs-annotate vcf --dataproxy_uri="seqrepo+../seqrepo/2024-12-20/" --vcf_out=out.vcf.gz input.vcf.gz
 ```
 
 Or an alternate REST path:

docs/setup_help/uta_installation.md

@@ -17,17 +17,17 @@
 8. Exit postgres
    1. `\q`
 9. Download the UTA database and place it in the uta database object that you created before (**This step takes around 5 hours**).
-   1. `export UTA_VERSION=uta_20210129.pgd.gz\ncurl -O http://dl.biocommons.org/uta/$UTA_VERSION\ngzip -cdq ${UTA_VERSION} | psql -h localhost -U uta_admin --echo-errors --single-transaction -v ON_ERROR_STOP=1 -d uta -p 5432`
+   1. `export UTA_VERSION=uta_20241220.pgd.gz\ncurl -O http://dl.biocommons.org/uta/$UTA_VERSION\ngzip -cdq ${UTA_VERSION} | psql -h localhost -U uta_admin --echo-errors --single-transaction -v ON_ERROR_STOP=1 -d uta -p 5432`
 10. Set your UTA path
-    1. `export UTA_DB_URL=postgresql://uta_admin@localhost:5432/uta/uta_20210129`
+    1. `export UTA_DB_URL=postgresql://uta_admin@localhost:5432/uta/uta_20241220`
 ###Optional installation step
 11. If you wanted to wait for the 5 hour update till later please follow these steps instead:
 12. Download the UTA database and place it in the uta database object that you created before.
-    1. `export UTA_VERSION=uta_20210129.pgd.gz
+    1. `export UTA_VERSION=uta_20241220.pgd.gz
 curl -O http://dl.biocommons.org/uta/$UTA_VERSION
 gzip -cdq ${UTA_VERSION} | grep -v "^REFRESH MATERIALIZED VIEW" | psql -h localhost -U uta_admin --echo-errors --single-transaction -v ON_ERROR_STOP=1 -d uta -p 5432`
 13. Run the refresh materialized view commands
-    1. `REFRESH MATERIALIZED VIEW uta_20210129.exon_set_exons_fp_mv;`
-    2. `REFRESH MATERIALIZED VIEW uta_20210129.tx_exon_set_summary_mv;`
-    3. `REFRESH MATERIALIZED VIEW uta_20210129.tx_def_summary_mv;`
-    4. `REFRESH MATERIALIZED VIEW uta_20210129.tx_similarity_mv;` #**This step will take 5 or more hours**
+    1. `REFRESH MATERIALIZED VIEW uta_20241220.exon_set_exons_fp_mv;`
+    2. `REFRESH MATERIALIZED VIEW uta_20241220.tx_exon_set_summary_mv;`
+    3. `REFRESH MATERIALIZED VIEW uta_20241220.tx_def_summary_mv;`
+    4. `REFRESH MATERIALIZED VIEW uta_20241220.tx_similarity_mv;` #**This step will take 5 or more hours**

notebooks/getting_started/1_Quick_Start.ipynb

@@ -92,7 +92,7 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "os.environ[\"UTA_DB_URL\"] = \"postgresql://anonymous:anonymous@uta.biocommons.org:5432/uta/uta_20210129b\""
+    "os.environ[\"UTA_DB_URL\"] = \"postgresql://anonymous:anonymous@uta.biocommons.org:5432/uta/uta_20241220\""
    ]
   },
   {

notebooks/getting_started/4_Exploring_the_AlleleTranslator.ipynb

@@ -112,7 +112,7 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "os.environ[\"UTA_DB_URL\"] = \"postgresql://anonymous:anonymous@uta.biocommons.org:5432/uta/uta_20210129b\""
+    "os.environ[\"UTA_DB_URL\"] = \"postgresql://anonymous:anonymous@uta.biocommons.org:5432/uta/uta_20241220\""
    ]
   },
   {

notebooks/getting_started/5_Exploring_the_CnvTranslator.ipynb

@@ -122,7 +122,7 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "os.environ[\"UTA_DB_URL\"] = \"postgresql://anonymous:anonymous@uta.biocommons.org:5432/uta/uta_20210129b\""
+    "os.environ[\"UTA_DB_URL\"] = \"postgresql://anonymous:anonymous@uta.biocommons.org:5432/uta/uta_20241220\""
    ]
   },
   {

notebooks/getting_started/6_Upcoming_features.ipynb

@@ -112,7 +112,7 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "os.environ[\"UTA_DB_URL\"] = \"postgresql://anonymous:anonymous@uta.biocommons.org:5432/uta/uta_20210129b\""
+    "os.environ[\"UTA_DB_URL\"] = \"postgresql://anonymous:anonymous@uta.biocommons.org:5432/uta/uta_20241220\""
    ]
   },
   {

src/ga4gh/core/models.py

@@ -146,13 +146,17 @@ class Coding(Element, BaseModelForbidExtra):
     )
     system: str = Field(
         ...,
-        description="The terminology/code system that defined the code. May be reported as a free-text name (e.g. 'Sequence Ontology'), but it is preferable to provide a uri/url for the system. When the 'code' is reported as a CURIE, the 'system' should be reported as the uri that the CURIE's prefix expands to (e.g. 'http://purl.obofoundry.org/so.owl/' for the Sequence Ontology).",
+        description="The terminology/code system that defined the code. May be reported as a free-text name (e.g. 'Sequence Ontology'), but it is preferable to provide a uri/url for the system.",
     )
     systemVersion: Optional[str] = Field(  # noqa: N815
         None,
         description="Version of the terminology or code system that provided the code.",
     )
     code: code  # Cannot use Field due to PydanticUserError: field name and type annotation must not clash.
+    iris: Optional[list[iriReference]] = Field(
+        None,
+        description="A list of IRIs that are associated with the coding. This can be used to provide additional context or to link to additional information about the concept.",
+    )
 
 
 class ConceptMapping(Element, BaseModelForbidExtra):
@@ -193,40 +197,30 @@ class Extension(Element, BaseModelForbidExtra):
 
 
 class MappableConcept(Element, BaseModelForbidExtra):
-    """A concept name that may be mapped to one or more `Codings`."""
+    """A concept based on a primaryCoding and/or name that may be mapped to one or more other `Codings`."""
 
     conceptType: Optional[str] = Field(  # noqa: N815
         None,
         description="A term indicating the type of concept being represented by the MappableConcept.",
     )
     name: Optional[str] = Field(None, description="A primary name for the concept.")
-    primaryCode: Optional[code] = Field(  # noqa: N815
+    primaryCoding: Optional[Coding] = Field(  # noqa: N815
         None,
-        description="A primary code for the concept that is used to identify the concept in a terminology or code system. If there is a public code system for the primaryCode then it should also be specified in the mappings array with a relation of 'exactMatch'. This attribute is provided to both allow a more technical code to be used when a public Coding with a system is not available as well as when it is available but should be identified as the primary code.",
+        description="A primary coding for the concept.",
     )
     mappings: Optional[list[ConceptMapping]] = Field(
         None,
         description="A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.",
     )
 
-    class ga4gh:  # noqa: N801
-        """Contain properties used for computing digests"""
-
-        inherent: tuple[str] = ("primaryCode",)
-
     @model_validator(mode="after")
-    def require_name_or_primary_code(cls, v):  # noqa: ANN001 N805 ANN201
-        """Ensure that ``name`` or ``primaryCode`` is provided"""
-        if v.primaryCode is None and v.name is None:
-            err_msg = "`One of name` or `primaryCode` must be provided."
+    def require_name_or_primary_coding(cls, v):  # noqa: ANN001 N805 ANN201
+        """Ensure that ``name`` or ``primaryCoding`` is provided"""
+        if v.primaryCoding is None and v.name is None:
+            err_msg = "One of `name` or `primaryCoding` must be provided."
             raise ValueError(err_msg)
         return v
 
-    def ga4gh_serialize(self) -> Optional[str]:  # noqa: D102
-        if self.primaryCode:
-            return self.primaryCode.root
-        return None
-
 
 Element.model_rebuild()
 Entity.model_rebuild()