Merge branch 'master' into zoomY

CHANGELOG.md

@@ -6,48 +6,63 @@ 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.
 ### Changed
 - Prettier for code formatting
 ### Fixed
-- Pan able to exit chromosome when using genome build 37 
-- `--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
-- Document track processing and loading
-- OAuth authentication
+ - Document track processing and loading
+ - OAuth authentication
 ### Changed
-- Use sample id instead of display name for variant retrieval
-- Hide balanced variants
-- Keyboard pan speed increased
-- Don't shrink pan window when attemting to pan over start
+ - Use sample id instead of display name for variant retrieval
+ - Hide balanced variants
+ - Keyboard pan speed increased
+ - Don't shrink pan window when attemting to pan over start
 
-## [2.1.1]
+## [2.1.1b]
 ### Added
 ### Changed
  - 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 bug that prevented updating annotation tracks
 
 ## [2.1.1]
 ### Added

Dockerfile

@@ -62,7 +62,7 @@ COPY --from=node-builder /usr/src/app/build/css/home.min.css /usr/src/app/build/
 COPY --from=node-builder /usr/src/app/build/*/gens.min.* gens/blueprints/gens/static/
 
 # make mountpoints and change ownership of app
-RUN mkdir -p /access /fs1/results && chown -R app:app /home/app/app /access /fs1
+RUN mkdir -p /access /fs1/results /fs1/results_dev && chown -R app:app /home/app/app /access /fs1 /fs1/results_dev
 # Change the user to app
 USER app
 

gens/api.py

@@ -193,7 +193,7 @@ def search_annotation(query: str, genome_build, annotation_type):
         response_code = 404
     else:
         start_elem = elements[0]
-        end_elem = max(elements[1:], key=lambda elem: elem.get("end"))
+        end_elem = max(elements[0:], key=lambda elem: elem.get("end"))
         data = {
             "chromosome": start_elem.get("chrom"),
             "start_pos": start_elem.get("start"),

gens/blueprints/gens/views.py

@@ -23,7 +23,6 @@
 
 
 @gens_bp.route("/<path:sample_name>", methods=["GET"])
-@cache.cached(timeout=60)
 def display_case(sample_name):
     """
     Renders the Gens template

gens/cache.py

@@ -1,4 +1,6 @@
 """Initiate cachig for app."""
 from flask_caching import Cache
+import tempfile
 
-cache = Cache(config={"CACHE_TYPE": "simple"})
+tmp_dir = tempfile.TemporaryDirectory(prefix="gens_cache_")
+cache = Cache(config={"CACHE_TYPE": "FileSystemCache", "CACHE_DIR": tmp_dir.name})

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()})