Merge branch 'master' into release-1.1.2

CHANGELOG.md

@@ -16,12 +16,14 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
  - Shift - Click now Zoom in
 ### Changed
  - Refactored page definitions into blueprint module
+ - Removed entrypoint script
 ### Fixed
  - Navigation shortcuts does not trigger in text fields
  - Fixed crash when searching for only chromosome
  - Restored ability to search for transcripts by gene name
  - Fixed crash when Shift - Click in interactive canvas
  - Fixed checking of api return status in drawInteractiveContent
+ - Aligned highlight in interactive canvas
 
 ## [1.1.1]
 ### Fixed

Dockerfile

@@ -59,8 +59,7 @@ COPY --from=node-builder /usr/src/app/build/*/gens.min.* gens/blueprints/gens/st
 # Chown all the files to the app user
 COPY gens gens
 COPY utils utils
-COPY entrypoint.sh ./
-RUN chown -R app:app /home/app/app
+# make mountpoints and change ownership of app
+RUN mkdir -p /media /access /fs1 && chown -R app:app /home/app/app /media /access /fs1
 # Change the user to app
 USER app
-ENTRYPOINT ["./entrypoint.sh"]

RELEASE.md

@@ -0,0 +1,31 @@
+# Instructions to release a new version of Gens
+
+1. Create a release branch with the release name, e.g. `release-1.1.1` and checkout the branch
+
+    ```bash
+    git checkout -b release-1.1.1
+    ```
+
+2. Update version to, e.g. 1.1.1
+
+   - in `gens/__version__.py`
+   - in `package.json`
+
+3. Make sure `CHANGELOG.md`is up to date for the release
+
+
+4. Commit changes, push to github and create a pull request
+
+    ```bash
+    git add gens/__version__.py
+    git add package.json CHANGELOG.md
+    git commit -m "Release notes version 1.1.1"
+    git push -u origin release-1.1.1
+    ```
+
+5. On github click **create pull request**.
+
+6. After getting the pull request approved by a reviewer merge it to master.
+
+7. Draft a new release on GitHub, add some text - e.g. and abbreviated CHANGELOG - and release.
+This adds a version tag, builds docker image.

assets/css/gens.scss

@@ -280,9 +280,8 @@ html, body {
 }
 
 #region_field.error:disabled {
-    outline: 1px dotted red;
-    outline: 5px auto red;
-    background-color: $default-bg-color;
+    outline: 5px dotted red;
+    background-color: red;
 }
 
 #times {

assets/js/interactive.js

@@ -115,7 +115,7 @@ class InteractiveCanvas extends FrequencyTrack {
     // Initialize marker div
     this.markerElem = document.getElementById('interactive-marker');
     this.markerElem.style.height = `${this.plotHeight * 2}px`;
-    this.markerElem.style.top = `${this.y + 58}px`;
+    this.markerElem.style.top = `${this.y + 82}px`;
 
     // State values
     const input = inputField.value.split(/:|-/);
@@ -209,7 +209,13 @@ class InteractiveCanvas extends FrequencyTrack {
         // numerical sort
         const [start, end] = [this.start + Math.round((this.dragStart.x - this.x) / scale),
                               this.start + Math.round((this.dragEnd.x - this.x) / scale)].sort((a, b) => a - b);
-        this.loadChromosome(this.chromosome, start, end)
+        // if shift - click, zoom in a region 10
+        // fix for slowdown when shift clicking
+        if ( ( end - start ) < 10 ) {
+          this.zoomIn();
+        }
+        //
+        this.loadChromosome(this.chromosome, start, end + 1);
       }
       // reload window when stop draging
       if (this.drag) {
@@ -233,52 +239,55 @@ class InteractiveCanvas extends FrequencyTrack {
       const keystrokeDelay = 2000;
       document.addEventListener('keyevent', event => {
         const key = event.detail.key;
-        const excludeFileds = ['input', 'select', 'textarea'];
 
-        if ( key === 'Enter' ) {
-          // Enter was pressed, process previous key presses.
-          const recentKeys = this.keyLogger.recentKeys(keystrokeDelay);
-          recentKeys.pop();  // skip Enter key
-          const lastKey = recentKeys[recentKeys.length - 1];
-          const numKeys = parseInt((recentKeys
-                                    .slice(lastKey.length - 2)
-                                    .filter(val => parseInt(val.key))
-                                    .map(val => val.key)
-                                    .join('')))
-          // process keys
-          if ( lastKey.key == 'x' || lastKey.key == 'y' ) {
-            this.loadChromosome(lastKey.key);
-          } else if ( numKeys && 0 < numKeys < 23 ) {
-            this.loadChromosome(numKeys);
-          } else {
-            return;
+        // dont act on key presses in input fields
+        const excludeFileds = ['input', 'select', 'textarea'];
+        if ( !excludeFileds.includes(event.detail.target.toLowerCase()) ) {
+          if ( key === 'Enter' ) {
+            // Enter was pressed, process previous key presses.
+            const recentKeys = this.keyLogger.recentKeys(keystrokeDelay);
+            recentKeys.pop();  // skip Enter key
+            const lastKey = recentKeys[recentKeys.length - 1];
+            const numKeys = parseInt((recentKeys
+                                      .slice(lastKey.length - 2)
+                                      .filter(val => parseInt(val.key))
+                                      .map(val => val.key)
+                                      .join('')))
+            // process keys
+            if ( lastKey.key == 'x' || lastKey.key == 'y' ) {
+              this.loadChromosome(lastKey.key);
+            } else if ( numKeys && 0 < numKeys < 23 ) {
+              this.loadChromosome(numKeys);
+            } else {
+              return;
+            }
+          }
+          switch (key) {
+            case 'ArrowLeft':
+              this.nextChromosome()
+              break;
+            case 'ArrowRight':
+              this.previousChromosome()
+              break;
+            case 'a':
+              this.panTracksLeft();
+              break;
+            case 'd':
+              this.panTracksRight();
+              break;
+            case 'ArrowUp':
+            case 'w':
+            case '+':
+              this.zoomIn();
+              break;
+            case 'ArrowDown':
+            case 's':
+            case '-':
+              this.zoomOut();
+              break;
+            default:
+              return;
           }
-        }
-        switch (key) {
-          case 'ArrowLeft':
-            this.nextChromosome()
-            break;
-          case 'ArrowRight':
-            this.previousChromosome()
-            break;
-          case 'a':
-            this.panTracksLeft();
-            break;
-          case 'd':
-            this.panTracksRight();
-            break;
-          case 'ArrowUp':
-          case 'w':
-          case '+':
-            this.zoomIn();
-            break;
-          case 'ArrowDown':
-          case 's':
-          case '-':
-            this.zoomOut();
-            break;
-          default:
-            return;
         }
       });
     });
@@ -346,6 +355,9 @@ class InteractiveCanvas extends FrequencyTrack {
       reduce_data: 1,
     }).then( (result) => {
       console.timeEnd('getcoverage');
+      if ( result.status == "error" ) {
+        throw result;
+      }
       // Clear canvas
       this.contentCanvas.getContext('2d').clearRect(0, 0,
         this.contentCanvas.width, this.contentCanvas.height);

assets/js/track.js

@@ -60,14 +60,17 @@ class Track {
     const chromosomes = ['1', '2', '3', '4', '5', '6', '7', '8', '9', '10',
       '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21',
       '22', 'X', 'Y']
-    const chromosome = regionString.split(':')[0];
-    if ( !chromosomes.includes(chromosome) ) {
-      throw `${chromosome} is not a valid chromosome`;
+    if ( regionString.includes(':') ) {
+      const [chromosome, position] = regionString.split(':');
+      // verify chromosome
+      if ( !chromosomes.includes(chromosome) ) {
+        throw `${chromosome} is not a valid chromosome`;
+      }
+      let [start, end] = position.split('-');
+      start = parseInt(start);
+      end = parseInt(end);
+      return [chromosome, start, end];
     }
-    let [start, end] = regionString.split(':')[1].split('-');
-    start = parseInt(start);
-    end = parseInt(end);
-    return [chromosome, start, end];
   }
 
   tracksYPos(heightOrder) {

gens/__init__.py

@@ -1,2 +1,2 @@
-from .app import create_app
 from .__version__ import VERSION as version
+from .app import create_app

gens/api.py

@@ -7,47 +7,19 @@
 from typing import List
 
 import attr
-from flask import abort, current_app, jsonify, request
-
 import cattr
 import connexion
+from flask import abort, current_app, jsonify, request
+
 from gens.db import RecordType, VariantCategory, query_records_in_region, query_variants
 from gens.exceptions import RegionParserException
 from gens.graph import REQUEST, get_cov, overview_chrom_dimensions, parse_region_str
 
+from .constants import CHROMOSOMES, HG_TYPE
 from .io import get_overview_json_path, get_tabix_files
 
 LOG = logging.getLogger(__name__)
 
-CHROMOSOMES = [
-    "1",
-    "2",
-    "3",
-    "4",
-    "5",
-    "6",
-    "7",
-    "8",
-    "9",
-    "10",
-    "11",
-    "12",
-    "13",
-    "14",
-    "15",
-    "16",
-    "17",
-    "18",
-    "19",
-    "20",
-    "21",
-    "22",
-    "X",
-    "Y",
-]
-
-HG_TYPE = (38, 19)
-
 
 @attr.s(auto_attribs=True, frozen=True)
 class ChromosomePosition:
@@ -173,9 +145,6 @@ def get_transcript_data(region, hg_type, collapsed):
         LOG.error("Could not find transcript in database")
         return abort(404)
 
-    with current_app.app_context():
-        collection = current_app.config["GENS_DB"][f"transcripts{hg_type}"]
-
     # Get transcripts within span [start_pos, end_pos] or transcripts that go over the span
     transcripts = list(
         query_records_in_region(
@@ -201,6 +170,36 @@ def get_transcript_data(region, hg_type, collapsed):
     )
 
 
+def search_annotation(query: str, hg_type, annotation_type):
+    """Search for anntations of genes and return their position."""
+    # Lookup queried element
+    collection = current_app.config["GENS_DB"][annotation_type]
+    db_query = {"gene_name": re.compile("^" + re.escape(query) + "$", re.IGNORECASE)}
+
+    if hg_type and int(hg_type) in HG_TYPE:
+        db_query['hg_type'] = hg_type
+
+    elements = collection.find(db_query, sort=[("start", 1), ("chrom", 1)])
+    # if no results was found
+    if elements.count() == 0:
+        msg = f"Did not find gene name: {query}"
+        LOG.warning(msg)
+        data = {'message': msg}
+        response_code = 404
+    else:
+        start_elem = elements.next()
+        end_elem = max(elements, key=lambda elem: elem.get('end'))
+        data = {
+            'chromosome': start_elem.get('chrom'),
+            'start_pos': start_elem.get('start'),
+            'end_pos': end_elem.get('end'),
+            'hg_type': start_elem.get('hg_type'),
+        }
+        response_code = 200
+
+    return jsonify({**data, 'status': response_code})
+
+
 def get_variant_data(sample_id, variant_category, **optional_kwargs):
     """Search Scout database for variants associated with a case and return info in JSON format."""
     default_height_order = 0

gens/app.py

@@ -6,20 +6,19 @@
 from datetime import date
 from logging.config import dictConfig
 
+import connexion
 from flask import abort, render_template, request
 from flask_compress import Compress
 from flask_debugtoolbar import DebugToolbarExtension
 
-import connexion
-
 from .__version__ import VERSION as version
-from .blueprints import gens_bp, about_bp
+from .blueprints import about_bp, gens_bp
 from .cache import cache
 from .db import init_database
+from .errors import generic_error, sample_not_found
 from .graph import parse_region_str
 from .io import BAF_SUFFIX, COV_SUFFIX, _get_filepath
 from .utils import get_hg_type
-from .errors import generic_error, sample_not_found
 
 toolbar = DebugToolbarExtension()
 dictConfig(

gens/blueprints/__init__.py

@@ -1,2 +1,2 @@
-from .gens.views import gens_bp
 from .about.views import about_bp
+from .gens.views import gens_bp

gens/blueprints/about/views.py

@@ -6,7 +6,6 @@
 
 import gens
 
-
 LOG = logging.getLogger(__name__)
 
 about_bp = Blueprint("about", __name__, template_folder="templates")