chore: update seqrepo and uta versions to 2024-12-20 (#514)

close #513

* Also re-ran test cassettes

Author: korikuzma

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\""
    ]
   },
   {

tests/cassettes/test_data_proxies[rest_dataproxy].yaml

@@ -27,9 +27,9 @@ interactions:
       Content-Type:
       - application/json
       Date:
-      - Wed, 26 Jun 2024 11:58:54 GMT
+      - Mon, 10 Mar 2025 16:23:25 GMT
       Server:
-      - Werkzeug/2.2.2 Python/3.10.4
+      - Werkzeug/2.2.3 Python/3.10.12
     status:
       code: 200
       message: OK
@@ -69,9 +69,9 @@ interactions:
       Content-Type:
       - application/json
       Date:
-      - Wed, 26 Jun 2024 11:58:54 GMT
+      - Mon, 10 Mar 2025 16:23:25 GMT
       Server:
-      - Werkzeug/2.2.2 Python/3.10.4
+      - Werkzeug/2.2.3 Python/3.10.12
     status:
       code: 200
       message: OK
@@ -99,9 +99,9 @@ interactions:
       Content-Type:
       - text/plain; charset=utf-8
       Date:
-      - Wed, 26 Jun 2024 11:58:54 GMT
+      - Mon, 10 Mar 2025 16:23:25 GMT
       Server:
-      - Werkzeug/2.2.2 Python/3.10.4
+      - Werkzeug/2.2.3 Python/3.10.12
     status:
       code: 200
       message: OK
@@ -129,9 +129,9 @@ interactions:
       Content-Type:
       - text/plain; charset=utf-8
       Date:
-      - Wed, 26 Jun 2024 11:58:54 GMT
+      - Mon, 10 Mar 2025 16:23:25 GMT
       Server:
-      - Werkzeug/2.2.2 Python/3.10.4
+      - Werkzeug/2.2.3 Python/3.10.12
     status:
       code: 200
       message: OK