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Clinical-Genomics-Lund · Nov 19, 2024 · 3301c19 · 3301c19
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,28 +6,34 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 
 ## [Unreleased]
 ### Added
-- `--force` flag to `gens loads sample` for overwriting any existing sample in case of key conflict.
-- `--force` flag prints a warning to stderr when overwriting an existing sample.
-- `gens delete sample` command
-- Height ordering for variants track.
+ - `--force` flag to `gens loads sample` for overwriting any existing sample in case of key conflict.
+ - `--force` flag prints a warning to stderr when overwriting an existing sample.
+ - `gens delete sample` command
+ - Height ordering for variants track.
 ### Fixed
-- Pan able to exit chrosome when using genome build 17 
-- `--force` flag `update_one` call not being called properly
-- Incorrect total sample count on home page.
-- Some typos and documentation.
-- Labels often not being visible on larger variants.
+ - Pan able to exit chrosome when using genome build 17 
+ - `--force` flag `update_one` call not being called properly
+ - Incorrect total sample count on home page.
+ - Some typos and documentation.
+ - Labels often not being visible on larger variants.
+### Merged for Solna from Lund 2.1.2
+#### Changed
+ - Changed cached method from simple to file system as it would be thread safe
+#### Fixed
+ - Fixed cache issue that could result in chromosome information not being updated
+ - Fixed max arg error when searching for some genes
+ - Fixed bug that prevented updating annotation tracks
 
 ## [2.3]
 ### Added
-- Link out to Scout: introduce config variable for base URL
-- Link out to Scout: case links on home sample list
-- Link out to Scout: click variant to open Scout page
-
+ - Link out to Scout: introduce config variable for base URL
+ - Link out to Scout: case links on home sample list
+ - Link out to Scout: click variant to open Scout page
 ### Changed
-- Archive prod docker image with release tag name. Update action versions.
+ - Archive prod docker image with release tag name. Update action versions.
 ### Fixed
-- Error image background static path
-- GitHub action DockerHub push on release
+ - Error image background static path
+ - GitHub action DockerHub push on release
 
 ## [2.2]
 ### Added
@@ -36,19 +42,24 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 ### Changed
  - Use sample id instead of display name for variant retrieval
  - Hide balanced variants
- - Fixed bug that prevented updating annotation tracks
+ - Keyboard pan speed increased
  - Don't shrink pan window when attemting to pan over start
 
-## [2.1.1]
+## [2.1.1b]
 ### Added
 ### Changed
- - Changed cached method from simple to file system as it would be thread safe
  - Changes the main view's page title to be `sample_name` and adds `sample_name` and `case_id` to the header title
  - Updated external images used in GitHub actions, including tj-actions/branch-names to v7 (fixes a security issue)
  - Updated Python and MongoDB version used in tests workflow to 3.8 and 7 respectively
+
+## [2.1.2 Lund only - Solna version in Unreleased/2.4]
+### Added
+### Changed
+ - Changed cached method from simple to file system as it would be thread safe
 ### Fixed
  - Fixed cache issue that could result in chromosome information not being updated
- - Fixed max arg error when searching for some genes
+ - Fixed max arg error when searching for some genes 
+ - Fixed bug that prevented updating annotation tracks
 
 ## [2.1.1]
 ### Added

diff --git a/gens/blueprints/gens/templates/gens.html b/gens/blueprints/gens/templates/gens.html
@@ -8,7 +8,6 @@
             <canvas id='{{ track_name }}-content' class='info-canvas'></canvas>
             <canvas id='{{ track_name }}-draw' class='info-canvas offscreen'></canvas>
             <div id='{{ track_name }}-titles' class='info-titles'></div>
-            <button id='{{ track_name }}-expand-button' class='info-expand-button'>Expand</button>
         </div>
     </div>
 {% endmacro %}

diff --git a/gens/blueprints/home/templates/home.html b/gens/blueprints/home/templates/home.html
@@ -36,7 +36,7 @@ <h1>Samples</h1>
         <td>Sample id</td>
         <td>Case id</td>
         <td>Genome build</td>
-        <td>Overivew file</td>
+        <td>Overview file</td>
         <td>BAM/BAF found</td>
         <td>Import date</td>
       </tr>

diff --git a/gens/commands/base.py b/gens/commands/base.py
@@ -9,6 +9,7 @@
 from .index import index as index_command
 from .load import load as load_command
 from .view import view as view_command
+from .delete import delete as delete_command
 
 
 @click.group(
@@ -26,3 +27,4 @@ def cli(*args, **kwargs):
 cli.add_command(index_command)
 cli.add_command(load_command)
 cli.add_command(view_command)
+cli.add_command(delete_command)
diff --git a/gens/db/__init__.py b/gens/db/__init__.py
@@ -9,4 +9,4 @@
 from .index import create_index, create_indexes, get_indexes, update_indexes
 from .samples import COLLECTION as SAMPLES_COLLECTION
 from .samples import (SampleNotFoundError, get_samples, query_sample,
-                      store_sample)
+                      store_sample, delete_sample)
diff --git a/gens/db/annotation.py b/gens/db/annotation.py
@@ -22,7 +22,7 @@ def register_data_update(track_type, name=None):
     db = app.config["GENS_DB"][UPDATES]
     LOG.debug(f"Creating timestamp for {track_type}")
     track = {"track": track_type, "name": name}
-    db.delete_one(track)  # remove old track
+    db.delete_many(track)  # remove old track
     db.insert_one({**track, "timestamp": datetime.datetime.now()})
 
 

diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -11,6 +11,10 @@
   "scripts": {
     "build": "gulp build",
     "lint": "eslint assets",
+    "lint:fix": "npm run lint -- --fix",
+    "prettier": "npx prettier assets  --check",
+    "prettier:fix": "npm run prettier -- --write",
+    "format": "npm run prettier:fix && npm run lint:fix",
     "watch": "gulp watch",
     "test": "jest"
   },
@@ -47,6 +51,7 @@
     "@babel/preset-env": "^7.13.10",
     "css-loader": "^5.2.7",
     "eslint": "^7.22.0",
+    "eslint-config-prettier": "^9.1.0",
     "eslint-config-standard": "^16.0.2",
     "eslint-plugin-import": "^2.22.1",
     "eslint-plugin-node": "^11.1.0",
@@ -58,6 +63,7 @@
     "gulp-sourcemaps": "^3.0.0",
     "identity-obj-proxy": "^3.0.0",
     "jest": "^26.6.3",
+    "prettier": "3.3.3",
     "process": "^0.11.10",
     "regenerator-runtime": "^0.13.7",
     "sass": "^1.32.8",

diff --git a/setup.py b/setup.py
@@ -25,14 +25,9 @@
     packages=find_packages(),
     zip_safe=False,
     install_requires=[
-        "Click>=7.0",
-        "Flask>=1.1.2, <2.3",
-        "flask-debugtoolbar>=0.11.0",
-        "flask-caching>=1.9.0",
-        "itsdangerous>=1.1.0",
-        "Jinja2>=2.11.1",
-        "MarkupSafe>=1.1.1",
-        "Werkzeug>=1.0.0",
+        "Click",
+        "Flask",
+        "flask-caching",
         "pymongo>=3.9.0",
         "gtfparse>=1.2.0",
         "pysam>=0.15.4",