Merge branch 'dev' of gitlab.inria.fr:vidjil/vidjil into...

Merge branch 'dev' of gitlab.inria.fr:vidjil/vidjil into feature-c/4014-clones-selectionnable-even-if-disable

.gitlab-ci.yml

@@ -51,12 +51,13 @@ test_germlines:
     - /^feature-.*g.*\/.*$/
     - schedules
 
-# Doc
+# Includes
 
 include:
-  - local: '/doc/.gitlab-ci.yml'
+  - local: '/doc/.gitlab-ci.yml' # Doc
   - local: 'algo/.gitlab-ci-compilers.yml' # Stage multiple_tests
   - local: 'algo/.gitlab-ci.yml' # Vidjil-algo pipelines
+  - template: Code-Quality.gitlab-ci.yml # Code quality
 
 # Algorithm
 
@@ -188,6 +189,7 @@ test_browser_unit:
   artifacts:
     paths:
     - browser/
+    when: always
   only:
     - /^feature-.*c.*\/.*$/
     - /^hotfix-.*c.*\/.*$/
@@ -207,7 +209,8 @@ test_browser_unit:
     - HEADLESS=1 make -C browser/test functional
   artifacts:
     paths:
-    - browser/
+    - browser/ 
+    when: always
     reports:
       junit: browser/test/test/TEST-*.xml
   only:
@@ -234,6 +237,7 @@ test_browser_unit:
   artifacts:
     paths:
     - browser/
+    when: always
     reports:
       junit: browser/test/test/TEST-*.xml
   only:
@@ -285,7 +289,14 @@ old-chrome-browser-functional-external-chrome:
   tags:
     - legacy
 
+# Code quality
+
 code_quality:
+  stage: test_quality
+  artifacts:
+    paths: [gl-code-quality-report.json]
+
+code_quality_custom:
   stage: test_quality
   script: make -C browser quality
   only:
@@ -412,6 +423,7 @@ deploy_review_server:
     - make -C browser icons
     - cp ./docker/vidjil-client/conf/conf.js ./browser/js/conf.js
     - sed -i -r "s/localhost/${CI_BUILD_REF_SLUG}.server.ci.vidjil.org/g" ./browser/js/conf.js
+    - 'sed -i "s/\"server_id\" : \"\"/\"server_id\" : \"${CI_BUILD_REF_SLUG}.server.ci.vidjil.org\"/" ./browser/js/conf.js'
     - sed -r 's/^.*FILE_SOURCE.*$/FILE_SOURCE="\/usr\/share\/vidjil\/demo"/' ./docker/vidjil-server/conf/defs.py > ./server/web2py/applications/vidjil/modules/defs.py
     - sed -i -e "/EMAIL_SUBJECT_START/c EMAIL_SUBJECT_START='[Vidjil/CI][$CI_COMMIT_REF_NAME]'" -e '/FROM_EMAIL/c FROM_EMAIL="server.ci@vidjil.org"' ./server/web2py/applications/vidjil/modules/defs.py
     - mv docker docker_${CI_BUILD_REF_SLUG}
@@ -423,7 +435,7 @@ deploy_review_server:
     - sed -i -r "s/WEB2PY_ADMIN_PASSWORD=/WEB2PY_ADMIN_PASSWORD=$REVIEW_SERVER_ADMIN_PASSWORD/" docker-compose.yml
     - cd ..
     - rsync -av --exclude .git . $REVIEW_SERVER:$REVIEW_SERVER_PATH_SERVER$CI_BUILD_REF_SLUG || $(case "$?" in 0|23) exit 0 ;; *) exit $?; esac)
-    - ssh $REVIEW_SERVER "cd $REVIEW_SERVER_PATH_SERVER; ./install_certs.sh ${CI_BUILD_REF_SLUG}; cd ${CI_BUILD_REF_SLUG}/docker_${CI_BUILD_REF_SLUG}; mkdir -p postfix/ssl; docker-compose up -d mysql fuse uwsgi nginx workers"
+    - ssh $REVIEW_SERVER "cd $REVIEW_SERVER_PATH_SERVER; ./install_certs.sh ${CI_BUILD_REF_SLUG}; cd ${CI_BUILD_REF_SLUG}/docker_${CI_BUILD_REF_SLUG}; mkdir -p postfix/ssl; docker-compose up -d mysql fuse uwsgi nginx workers; sleep 20s; docker-compose exec -T uwsgi bash -c 'cd /usr/share/vidjil/server/web2py/applications/vidjil/scripts; /usr/local/bin/gosu 1005 bash launch_python_script.sh load-sql.py -n /usr/share/vidjil/docker/ci/ci.sql'"
   environment:
     name: review_server/$CI_BUILD_REF_NAME
     url: http://$CI_BUILD_REF_SLUG.server.ci.vidjil.org/browser/

.gitlab/merge_request_templates/Release (vidjil-algo).md

@@ -32,14 +32,17 @@ Benchmarks
 * [ ] push: `git push origin master release-20XX-XX`
 * [ ] mirror to GH: `git push github master release-20XX.XX`
 * [ ] click `publish_release` (there may be changes to CD...)
+* [ ] deploy the doc
+
 
 After these steps, we merge back the release in `dev`:
 * [ ] merge this MR to dev
 
 ## After the release: deploy
 
-Sometimes, the deploy stages can occur several days after the release.
-Open a new internal issue with the "Deploy" template.
+* [ ] Click `deploy_release_prod` in the `deploy_prod` stage, deploying the release on `vidjil-algo-next` on the public server
+* [ ] Open a new internal issue with the `Deploy (vidjil-algo)` template : vdj#XXXXX
+
 
 /label ~cpp
 

algo/vidjil.cpp

@@ -291,16 +291,16 @@ int main (int argc, char **argv)
 
 
   // ----------------------------------------------------------------------------------------------------------------------
-  group = "Germline presets (at least one -g or -V/(-D)/-J option must be given)";
+  group = "Germline/recombination selection (at least one -g or -V/(-D)/-J option must be given)";
 
   vector <string> multi_germlines ;
   app.add_option("--germline,-g", multi_germlines, R"Z(
-         -g <.g FILE>(:FILTER)
-                    multiple locus/germlines, with tuned parameters.
+         -g <.g FILE>(:FOCUS) ...
+                    germline preset(s) (.g file(s)), detecting multiple recombinations, with tuned parameters.
                     Common values are '-g germline/homo-sapiens.g' or '-g germline/mus-musculus.g'
-                    The list of locus/recombinations can be restricted, such as in '-g germline/homo-sapiens.g:IGH,IGK,IGL'
+                    One can focus on some recombinations, such as in '-g germline/homo-sapiens.g:IGH,IGK,IGL'
          -g PATH
-                    multiple locus/germlines, shortcut for '-g PATH/)Z" DEFAULT_MULTI_GERMLINE_FILE R"Z(',
+                    human germline preset, shortcut for '-g PATH/)Z" DEFAULT_MULTI_GERMLINE_FILE R"Z(',
                     processes human TRA, TRB, TRG, TRD, IGH, IGK and IGL locus, possibly with incomplete/unusal recombinations)Z")
     -> group(group) -> type_name("GERMLINES");
 
@@ -314,7 +314,7 @@ int main (int argc, char **argv)
 
 
   app.add_option("-D", v_reps_D,
-                 "custom D germline multi-fasta file(s), analyze into V(D)J components")
+                 "custom D germline multi-fasta file(s) for V(D)J designation")
     -> group(group) -> type_name("FILE");
 
   app.add_option("-J", v_reps_J,

browser/css/dark.css

@@ -4,9 +4,15 @@
 /* default tag color */
 /* #dcffed also available */
 #vmi-menu {
-  position: unset;
-  bottom: unset;
+  top: 32px;
+  right: 0;
   width: unset;
+  background-color: #000000;
+  margin: 6px 0 0 0;
+}
+#vmi-menu div {
+  padding: 5px;
+  border: 1px solid;
 }
 html {
   height: 100%;
@@ -52,14 +58,15 @@ ul {
 }
 #visu-container {
   position: relative;
+  display: flex;
   flex: 1 1 auto;
+  flex-flow: column;
   -khtml-user-select: none;
   -webkit-user-select: none;
   -moz-user-select: -moz-none;
   -ms-user-select: none;
   user-select: none;
-  height: 100%;
-  margin: auto;
+  width: 100%;
   overflow: hidden;
   background: #000000;
 }
@@ -107,28 +114,38 @@ ul {
   user-select: none;
   overflow: hidden;
 }
-#mid-container {
+#vidjil-panels {
   position: fixed;
-  display: flex;
-  flex: 1 1 auto;
   top: 32px;
+  left: 0;
   bottom: 125px ;
-  width: calc(100% - 6px + 6px);
-  overflow: hidden;
   background: #000000;
   margin: 6px;
+  display: flex;
+  flex: auto;
+  overflow: hidden;
+}
+.vidjil-panels-left {
+  width: calc(100% - 6px - 70px);
+}
+.vidjil-panels-full {
+  width: calc(100% - 6px);
+}
+#mid-container {
+  display: flex;
+  flex: auto;
+  overflow: hidden;
 }
 #right-container {
-  -khtml-user-select: none;
-  -webkit-user-select: none;
-  -moz-user-select: -moz-none;
-  -ms-user-select: none;
-  user-select: none;
+  display: flex;
+  flex: 1 0 auto;
+  flex-flow: column;
   float: right;
-  width: 0px;
+  width: 475px;
 }
 #left-container {
   display: flex;
+  flex: 1 0 auto;
   flex-flow: column;
   position: relative;
   width: 475px;
@@ -142,11 +159,16 @@ ul {
 #visu,
 #visu2 {
   height: 50%;
+  display: flex;
+  flex: auto;
   width: 100%;
 }
 #visu2 {
   max-height: calc(100% - 6px);
 }
+#visu3 {
+  height: 100%;
+}
 line {
   stroke: #586e75;
   stroke-width: 0.5;
@@ -414,6 +436,7 @@ line {
 #list {
   flex: 1 1 auto;
   height: 0px;
+  min-height: 20%;
   max-height: 100%;
   display: flex;
   flex-direction: column;
@@ -445,12 +468,9 @@ line {
   padding-right: 30px;
 }
 .list {
-  width: 445px;
-  display: block;
   padding: 2px;
 }
 .listElem {
-  width: 445px;
   font-size: 13px;
   cursor: pointer;
   -webkit-transition: color 0.2s;
@@ -459,19 +479,20 @@ line {
   transition: color 0.2s;
   padding: 1px 4px 4px 1px;
   height: 14px;
+  display: flex;
 }
 .selected {
   color: #fdf6e3;
 }
 .nameBox {
-  width: 300px;
   margin-right: 10px;
   overflow: hidden;
   display: inline-block;
   height: 16px;
   position: relative;
-  float: left;
   white-space: nowrap;
+  display: flex;
+  flex: 1 1 auto;
 }
 .seq-fixed .nameBox {
   width: 250px;
@@ -479,7 +500,6 @@ line {
 .list .axisBox,
 .axisBox span {
   max-width: 52px;
-  float: right;
   overflow: hidden;
   display: inline-block;
   max-height: 16px;
@@ -500,9 +520,8 @@ line {
 }
 .starBox {
   width: 16px;
-  float: right;
   height: 16px;
-  display: inline-block;
+  display: inline-flex;
   user-select: none;
   overflow: hidden;
 }
@@ -517,9 +536,8 @@ line {
 .infoBox {
   font-size: 90%;
   width: 16px;
-  float: right;
   height: 15px;
-  display: inline-block;
+  display: inline-flex;
   user-select: none;
   text-align: center;
   border: solid;
@@ -588,8 +606,6 @@ line {
 }
 /*style segmenter element*/
 .list_select {
-  width: 445px;
-  display: block;
   border: solid;
   border-width: 2px;
   padding: 0px;
@@ -606,7 +622,7 @@ line {
 }
 .seq-fixed {
   position: relative;
-  display: inline-block;
+  display: inline-flex;
   width: auto;
   margin: -2px;
   padding: 2px;
@@ -974,6 +990,10 @@ div.button {
   padding-left: 10px;
   padding-right: 10px;
 }
+.clipboard-button {
+  margin-left: -5px;
+  padding: 3px;
+}
 .smallbutton {
   cursor: pointer;
   font-size: 13px;
@@ -1063,9 +1083,8 @@ span.logo {
 }
 #bot-container {
   position: fixed;
-  left: 0;
   bottom: 0;
-  width: 100%;
+  left: 6px;
   border-top: solid;
   border-width: 6px;
   min-height: 125px;
@@ -1339,11 +1358,9 @@ span.warningReads {
 .axis_select select[selected=selected] {
   color: #fdf6e3;
 }
-#visu-separator {
+.visu-separator {
   position: relative;
   height: 6px;
-  cursor: move;
-  cursor: -webkit-grab;
   background: #333333;
 }
 #bot-separator {
@@ -1354,15 +1371,17 @@ span.warningReads {
   position: relative;
   top: -6px;
 }
-#vertical-separator {
+#vertical-separator,
+#vertical-separator-right {
   position: relative;
   float: left;
-  height: 100%;
   width: 6px;
-  line-height: calc(100% - 1px);
   background: #333333;
   cursor: pointer;
 }
+#vertical-separator-right {
+  float: right;
+}
 #visu-separator:hover,
 #vertical-separator:hover,
 #bot-separator:hover {
@@ -1906,11 +1925,12 @@ table.log textarea {
   border: 1px solid #333333;
   overflow-wrap: break-word;
   overflow-y: hidden;
-  max-width: 457px;
   min-height: 32px;
   max-height: 32px;
-  width: 100%;
+  width: 99%;
   background-color: #000000;
+  margin-left: auto;
+  margin-right: auto;
 }
 .patient_info_text {
   margin-bottom: 5px;
@@ -2284,3 +2304,30 @@ form .form_label {
 .list_lock_on {
   color: #839496;
 }
+.set_group {
+  display: inline-flex;
+  flex-wrap: wrap;
+  flex-direction: row;
+  margin-bottom: 25px;
+  margin-right: 15px;
+  flex-flow: column;
+  width: 48%;
+}
+.set_group_header {
+  width: 100%;
+}
+.set_cell {
+  word-break: break-all;
+}
+.set_data {
+  width: 100%;
+}
+.analysis_button {
+  display: inline-flex;
+}
+.margined-top {
+  margin-top: 10px;
+}
+.margined-bottom {
+  margin-bottom: 10px;
+}

browser/css/icons/Makefile

@@ -11,7 +11,7 @@ retrieve:
 
 ### Don't edit below ###
 
-FONTELLO_HOST ?= http://fontello.com
+FONTELLO_HOST ?= https://fontello.com
 
 fontopen:
 	@if test ! `which curl` ; then \

browser/css/light.css

@@ -4,9 +4,15 @@
 /* default tag color */
 /* #dcffed also available */
 #vmi-menu {
-  position: unset;
-  bottom: unset;
+  top: 32px;
+  right: 0;
   width: unset;
+  background-color: #ffffff;
+  margin: 6px 0 0 0;
+}