October 2024 release

client/src/components/Pages/Summary/Main/Summary.tsx

@@ -156,6 +156,8 @@ export const Summary: React.FC<Props> = ({ setVisibleTab }) => {
     setFormattedFusion(formattedFusion);
   }, [fusion]);
 
+  console.log(formattedFusion);
+
   return (
     <>
       {(!validationErrors || validationErrors.length === 0) &&

client/yarn.lock

@@ -2232,6 +2232,7 @@
     "@types/react-is" "^16.7.1 || ^17.0.0"
     prop-types "^15.8.1"
     react-is "^18.2.0"
+
 "@nicolo-ribaudo/[email protected]":
   version "5.1.1-v1"
   resolved "https://registry.yarnpkg.com/@nicolo-ribaudo/eslint-scope-5-internals/-/eslint-scope-5-internals-5.1.1-v1.tgz#dbf733a965ca47b1973177dc0bb6c889edcfb129"
@@ -11025,9 +11026,9 @@ webidl-conversions@^6.1.0:
   integrity sha512-qBIvFLGiBpLjfwmYAaHPXsn+ho5xZnGvyGvsarywGNc8VyQJUMHJ8OBKGGrPER0okBeMDaan4mNBlgBROxuI8w==
 
 webpack-dev-middleware@^5.3.1:
-  version "5.3.3"
-  resolved "https://registry.yarnpkg.com/webpack-dev-middleware/-/webpack-dev-middleware-5.3.3.tgz#efae67c2793908e7311f1d9b06f2a08dcc97e51f"
-  integrity sha512-hj5CYrY0bZLB+eTO+x/j67Pkrquiy7kWepMHmUMoPsmcUaeEnQJqFzHJOyxgWlq746/wUuA64p9ta34Kyb01pA==
+  version "5.3.4"
+  resolved "https://registry.yarnpkg.com/webpack-dev-middleware/-/webpack-dev-middleware-5.3.4.tgz#eb7b39281cbce10e104eb2b8bf2b63fce49a3517"
+  integrity sha512-BVdTqhhs+0IfoeAf7EoH5WE+exCmqGerHfDM0IL096Px60Tq2Mn9MAbnaGUe6HiMa41KMCYF19gyzZmBcq/o4Q==
   dependencies:
     colorette "^2.0.10"
     memfs "^3.4.3"

requirements.txt

@@ -1,90 +1,156 @@
 agct==0.1.0.dev2
-aiofiles==24.1.0
-annotated-types==0.7.0
-anyio==4.4.0
-asttokens==2.4.1
-async-timeout==4.0.3
-asyncpg==0.29.0
-attrs==24.2.0
-biocommons.seqrepo==0.6.9
+aiofiles==23.1.0
+annotated-types==0.6.0
+anyio==3.7.1
+appdirs==1.4.4
+appnope==0.1.3
+asttokens==2.2.1
+async-lru==2.0.4
+asyncio-atexit==1.0.1
+asyncpg==0.28.0
+attrs==23.1.0
+backcall==0.2.0
+bcrypt==4.2.0
+beautifulsoup4==4.12.2
+biocommons.seqrepo==0.6.5
 bioutils==0.5.8.post1
-black==24.8.0
-boto3==1.35.3
-botocore==1.35.3
+black==23.10.1
+boto3==1.28.11
+botocore==1.31.11
+bs4==0.0.1
+bump-pydantic==0.7.0
 canonicaljson==2.0.0
-certifi==2024.7.4
+certifi==2023.7.22
+cffi==1.17.1
 cfgv==3.4.0
-charset-normalizer==3.3.2
-click==8.1.7
+charset-normalizer==3.2.0
+click==8.1.6
 coloredlogs==15.0.1
-configparser==7.1.0
+configparser==6.0.0
 cool_seq_tool==0.7.1
-coverage==7.6.1
+coverage==7.3.2
+cryptography==43.0.1
+cssselect==1.2.0
+Cython==3.0.0
 decorator==5.1.1
-distlib==0.3.8
-executing==2.0.1
-fastapi==0.112.1
-filelock==3.15.4
+Deprecated==1.2.14
+distlib==0.3.7
+docutils==0.20.1
+executing==1.2.0
+fake-useragent==1.1.3
+fastapi==0.100.0
+filelock==3.12.4
 fusor==0.4.4
 ga4gh.vrs==2.0.0a10
+ga4gh.vrsatile.pydantic==0.2.0
 gene-normalizer==0.4.0
+googleapis-common-protos==1.65.0
 h11==0.14.0
 hgvs==1.5.4
 httpcore==1.0.5
-httpx==0.27.0
+httpx==0.27.2
 humanfriendly==10.0
-identify==2.6.0
-idna==3.7
-importlib_metadata==8.4.0
+identify==2.5.30
+idna==3.4
+importlib-metadata==6.8.0
+inflection==0.5.1
 iniconfig==2.0.0
-ipython==8.26.0
-jedi==0.19.1
-Jinja2==3.1.4
+ipython==8.14.0
+jedi==0.18.2
+Jinja2==3.1.2
 jmespath==1.0.1
-MarkupSafe==2.1.5
-matplotlib-inline==0.1.7
+jsonschema==3.2.0
+libcst==1.1.0
+lxml==4.9.3
+Markdown==3.4.4
+markdown-it-py==3.0.0
+MarkupSafe==2.1.3
+matplotlib-inline==0.1.6
+mdurl==0.1.2
 mypy-extensions==1.0.0
-nodeenv==1.9.1
-packaging==24.1
+nest-asyncio==1.6.0
+nodeenv==1.8.0
+numpy==1.25.1
+opentelemetry-api==1.27.0
+opentelemetry-exporter-otlp-proto-common==1.27.0
+opentelemetry-exporter-otlp-proto-http==1.27.0
+opentelemetry-instrumentation==0.48b0
+opentelemetry-instrumentation-httpx==0.48b0
+opentelemetry-instrumentation-requests==0.48b0
+opentelemetry-instrumentation-threading==0.48b0
+opentelemetry-instrumentation-urllib==0.48b0
+opentelemetry-proto==1.27.0
+opentelemetry-sdk==1.27.0
+opentelemetry-semantic-conventions==0.48b0
+opentelemetry-util-http==0.48b0
+packaging==23.2
+pandas==2.0.3
+paramiko==3.5.0
+parse==1.19.1
 Parsley==1.3
-parso==0.8.4
-pathspec==0.12.1
-pexpect==4.9.0
-platformdirs==4.2.2
-pluggy==1.5.0
-polars==1.5.0
+parso==0.8.3
+pathspec==0.11.2
+pexpect==4.8.0
+pickleshare==0.7.5
+platformdirs==3.11.0
+pluggy==1.3.0
+polars==1.3.0
 pre-commit==3.8.0
-prompt_toolkit==3.0.47
-psycopg2==2.9.9
+prompt-toolkit==3.0.39
+protobuf==4.25.5
+psutil==5.9.8
+psycopg2==2.9.6
 psycopg2-binary==2.9.9
 ptyprocess==0.7.0
-pure_eval==0.2.3
+pure-eval==0.2.2
+pycparser==2.22
 pydantic==2.4.2
+pydantic-to-typescript==1.0.10
 pydantic-to-typescript2==1.0.4
 pydantic_core==2.10.1
-Pygments==2.18.0
-pysam==0.22.1
-pytest==8.3.2
-pytest-asyncio==0.24.0
-pytest-cov==5.0.0
-python-dateutil==2.9.0.post0
-PyYAML==6.0.2
-requests==2.32.3
+pyee==8.2.2
+Pygments==2.15.1
+pyliftover==0.4
+PyNaCl==1.5.0
+pyppeteer==1.0.2
+pyquery==2.0.0
+pyrsistent==0.19.3
+pysam==0.21.0
+pysftp==0.2.9
+pytest==7.4.2
+pytest-asyncio==0.21.1
+pytest-cov==4.1.0
+python-dateutil==2.8.2
+python-jsonschema-objects==0.4.2
+pytz==2023.3
+PyYAML==6.0.1
+requests==2.31.0
+requests-html==0.10.0
+rich==13.6.0
 ruff==0.5.0
-s3transfer==0.10.2
+s3transfer==0.6.1
 six==1.16.0
-sniffio==1.3.1
-sqlparse==0.5.1
-stack-data==0.6.3
-starlette==0.38.2
+sniffio==1.3.0
+soupsieve==2.4.1
+sqlparse==0.4.4
+stack-data==0.6.2
+starlette==0.27.0
+synapseclient==4.5.1
 tabulate==0.9.0
 tqdm==4.66.5
-traitlets==5.14.3
-typing_extensions==4.12.2
-urllib3==1.26.19
-uvicorn==0.30.6
-virtualenv==20.26.3
-wags_tails==0.1.4
-wcwidth==0.2.13
+traitlets==5.9.0
+typer==0.9.0
+typing-inspect==0.9.0
+typing_extensions==4.7.1
+tzdata==2023.3
+urllib3==1.26.20
+uta-tools==0.1.3
+uvicorn==0.23.1
+virtualenv==20.24.5
+w3lib==2.1.1
+wags_tails==0.1.3
+wcwidth==0.2.6
+websockets==10.4
+wrapt==1.16.0
 yoyo-migrations==8.2.0
-zipp==3.20.0
+zipp==3.16.2

server/tests/integration/test_constructors.py

@@ -148,41 +148,31 @@ async def test_build_tx_segment_ec(
 
     # test handle invalid transcript
     await check_response(
-        "/api/construct/structural_element/tx_segment_ect?transcript=NM_0012529.3&exon_start=3",
+        "/api/construct/structural_element/tx_segment_ec?transcript=NM_0012529.3&exon_start=3",
         {"warnings": ["No exons found given NM_0012529.3"]},
         check_tx_element_response,
     )
 
 
 @pytest.mark.asyncio()
-async def test_build_segment_gct(
-    check_response, check_tx_element_response, tpm3_tx_t_element
+async def test_build_segment_gc(
+    check_response, check_tx_element_response, tpm3_tx_g_element, tpm3_tx_t_element
 ):
     """Test correct functioning of transcript segment element construction using
-    genomic coordinates and transcript.
+    genomic coordinates and gene name.
     """
     await check_response(
-        "/api/construct/structural_element/tx_segment_gct?transcript=NM_152263.4&chromosome=NC_000001.11&start=154171416&end=154171417",
-        {"element": tpm3_tx_t_element},
-        check_tx_element_response,
-    )
-    await check_response(
-        "/api/construct/structural_element/tx_segment_gct?transcript=refseq%3ANM_152263.4&chromosome=NC_000001.11&start=154171416&end=154171417",
-        {"element": tpm3_tx_t_element},
+        "/api/construct/structural_element/tx_segment_gc?gene=TPM3&chromosome=NC_000001.11&start=154171416&end=154171417",
+        {"element": tpm3_tx_g_element},
         check_tx_element_response,
     )
 
-
-@pytest.mark.asyncio()
-async def test_build_segment_gc(
-    check_response, check_tx_element_response, tpm3_tx_g_element
-):
     """Test correct functioning of transcript segment element construction using
-    genomic coordinates and gene name.
+    genomic coordinates and transcript.
     """
     await check_response(
-        "/api/construct/structural_element/tx_segment_gc?gene=TPM3&chromosome=NC_000001.11&start=154171416&end=154171417",
-        {"element": tpm3_tx_g_element},
+        "/api/construct/structural_element/tx_segment_gc?transcript=NM_152263.4&chromosome=NC_000001.11&start=154171416&end=154171417",
+        {"element": tpm3_tx_t_element},
         check_tx_element_response,
     )