scout-browser 4.98.0__py3-none-any.whl → 4.100.0__py3-none-any.whl

scout/utils/ensembl_biomart_clients.py

@@ -4,9 +4,10 @@ from typing import Dict, Iterator
 import requests
 
 LOG = logging.getLogger(__name__)
-SCHUG_BASE = "https://schug-stage.scilifelab.se"
+SCHUG_BASE = "https://schug.scilifelab.se"
 
 BUILDS: Dict[str, str] = {"37": "GRCh37", "38": "GRCh38"}
+CHROM_SEPARATOR = "[success]"
 
 SCHUG_RESOURCE_URL: Dict[str, str] = {
     "genes": "/genes/ensembl_genes/?build=",

scout/utils/ensembl_rest_clients.py

@@ -1,30 +1,27 @@
 """Code for talking to ensembl rest API"""
 
 import logging
+from typing import Optional
 from urllib.parse import urlencode
 
 import requests
+from flask import flash
 
 LOG = logging.getLogger(__name__)
 
 HEADERS = {"Content-type": "application/json"}
-RESTAPI_37 = "https://grch37.rest.ensembl.org"
-RESTAPI_38 = "https://rest.ensembl.org"
+RESTAPI_URL = "https://rest.ensembl.org"
 
 
 class EnsemblRestApiClient:
     """A class handling requests and responses to and from the Ensembl REST APIs.
-    Endpoints for human build 37: https://grch37.rest.ensembl.org
-    Endpoints for human build 38: http://rest.ensembl.org/
+    Endpoint: http://rest.ensembl.org/
     Documentation: https://github.com/Ensembl/ensembl-rest/wiki
     doi:10.1093/bioinformatics/btu613
     """
 
-    def __init__(self, build="37"):
-        if build == "38":
-            self.server = RESTAPI_38
-        else:
-            self.server = RESTAPI_37
+    def __init__(self):
+        self.server = RESTAPI_URL
 
     def build_url(self, endpoint, params=None):
         """Build an url to query ensembml"""
@@ -34,7 +31,7 @@ class EnsemblRestApiClient:
         return "".join([self.server, endpoint])
 
     @staticmethod
-    def send_request(url):
+    def send_request(url) -> Optional[dict]:
         """Sends the actual request to the server and returns the response
 
         Accepts:
@@ -43,33 +40,29 @@ class EnsemblRestApiClient:
         Returns:
             data(dict): dictionary from json response
         """
-        data = {}
+        error = None
+        data = None
         try:
             response = requests.get(url, headers=HEADERS)
-            if response.status_code == 404:
-                LOG.info("Request failed for url %s\n", url)
-                response.raise_for_status()
-            data = response.json()
-        except requests.exceptions.MissingSchema as err:
-            LOG.info("Request failed for url %s: Error: %s\n", url, err)
-            data = err
-        except requests.exceptions.HTTPError as err:
-            LOG.info("Request failed for url %s: Error: %s\n", url, err)
-            data = err
+            if response.status_code not in [404, 500]:
+
+                data = response.json()
+            else:
+                error = f"Ensembl request failed with code:{response.status_code} for url {url}"
+        except requests.exceptions.MissingSchema:
+            error = f"Ensembl request failed with MissingSchema error for url {url}"
+        except requests.exceptions.HTTPError:
+            error = f"Ensembl request failed with HTTPError error for url {url}"
+
+        if error:
+            flash(error)
         return data
 
-    def liftover(self, build, chrom, start, end=None):
+    def liftover(
+        self, build: str, chrom: str, start: int, end: Optional[int] = None
+    ) -> Optional[dict]:
         """Perform variant liftover using Ensembl REST API
-
-        Args:
-            build(str): genome build: "37" or "38"
-            chrom(str): 1-22,X,Y,MT,M
-            start(int): start coordinate
-            stop(int): stop coordinate or None
-
-        Returns:
-            mappings(list of dict): example:
-                example: https://rest.ensembl.org/map/human/GRCh37/X:1000000..1000100:1/GRCh38?content-type=application/json
+        example: https://rest.ensembl.org/map/human/GRCh37/X:1000000..1000100:1/GRCh38?content-type=application/json
         """
 
         build = "GRCh38" if "38" in str(build) else "GRCh37"

scout/utils/hgvs.py

@@ -6,7 +6,7 @@ LOG = logging.getLogger(__name__)
 VALIDATOR_URL = "https://rest.variantvalidator.org/VariantValidator/variantvalidator/{}/{}/select?content-type=application%2Fjson"
 
 
-def validate_hgvs(build, desc):
+def validate_hgvs(build: str, desc: str) -> bool:
     """Validates a simple hgvs descriptor using the VariantValidator API (https://rest.variantvalidator.org/)
 
     Args:

scout/utils/scout_requests.py

@@ -8,7 +8,6 @@ from urllib.error import HTTPError
 
 import requests
 from defusedxml import ElementTree
-from flask import flash
 
 from scout.constants import HPO_URL, HPOTERMS_URL, ORPHA_URLS
 
@@ -344,7 +343,7 @@ def fetch_constraint():
         return exac_lines
 
 
-def fetch_refseq_version(refseq_acc):
+def fetch_refseq_version(refseq_acc: str) -> str:
     """Fetch refseq version from entrez and return refseq version
 
     Args:
@@ -362,7 +361,6 @@ def fetch_refseq_version(refseq_acc):
     try:
         resp = get_request(base_url.format(refseq_acc))
         if resp is None:
-            flash(f"Error: could not retrieve HGVS version for {refseq_acc} from Entrez eutils!")
             return version
         tree = ElementTree.fromstring(resp.content)
         version = tree.find("IdList").find("Id").text or version

{scout_browser-4.98.0.dist-info → scout_browser-4.100.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scout-browser
-Version: 4.98.0
+Version: 4.100.0
 Summary: Clinical DNA variant visualizer and browser
 Project-URL: Repository, https://github.com/Clinical-Genomics/scout
 Project-URL: Changelog, https://github.com/Clinical-Genomics/scout/blob/main/CHANGELOG.md
@@ -124,29 +124,25 @@ Instructions on how to run a Scout image connected to your local database or a c
 
 ## Installation
 
-<!-- You can install the latest release of Scout using `pip`:
-
-```bash
-pip install scout-browser
-
-# ... to include optional coverage tools you would use:
-pip install scout-browser[coverage]
-```
-
-If you would like to install Scout for local development: -->
+Here is a quick start. Please see e.g. the [Installation instructions](docs/install.md) for more details.
 
 ```bash
 git clone https://github.com/Clinical-Genomics/scout
 cd scout
-pip install --editable .
 ```
 
-Scout is configured to use `uv` if you like; either run, install, install as a tool or
-```
+Scout is configured to use `uv`; either run, install, or install as a tool.
+
+```bash
 uv sync --frozen
 uv run scout
 ```
 
+You can also install using pip:
+
+```
+pip install --editable .
+```
 
 Scout PDF reports are created using [Flask-WeasyPrint](https://pythonhosted.org/Flask-WeasyPrint/). This library requires external dependencies which need be installed separately (namely Cairo and Pango). See platform-specific instructions for Linux, macOS and Windows available on the WeasyPrint installation [pages](https://doc.courtbouillon.org/weasyprint/stable/first_steps.html#installation).