Commit 6b667dd6 authored by Vidjil Team's avatar Vidjil Team

Merge remote-tracking branch 'origin/dev' into feature-sc/1469-get-reads

parents fd657600 6c8d2a62
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -w 20 -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG $VIDJIL_DATA/test-random-consensus.fa.gz > consensus-default.log
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -w 20 -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG --consensus-on-random-sample $VIDJIL_DATA/test-random-consensus.fa.gz > consensus-random.log
!NO_LAUNCHER:
!LAUNCH: diff consensus-default.log consensus-random.log
!EXIT_CODE: 1
......
......@@ -406,18 +406,17 @@ line {
flex: 1 1 auto;
height: 0px;
max-height: 100%;
display: flex;
flex-direction: column;
}
#data {
flex: 0 1 auto;
border: none;
}
#list_clones {
flex: 1 1 auto;
flex: 0 1 auto;
overflow-y: scroll;
overflow-x: hidden;
height: calc(100% - 30px);
/*100% - list_menu height */
max-height: 100%;
width: 100%;
padding: 2px;
}
......
......@@ -406,18 +406,17 @@ line {
flex: 1 1 auto;
height: 0px;
max-height: 100%;
display: flex;
flex-direction: column;
}
#data {
flex: 0 1 auto;
border: none;
}
#list_clones {
flex: 1 1 auto;
flex: 0 1 auto;
overflow-y: scroll;
overflow-x: hidden;
height: calc(100% - 30px);
/*100% - list_menu height */
max-height: 100%;
width: 100%;
padding: 2px;
}
......
......@@ -406,18 +406,17 @@ line {
flex: 1 1 auto;
height: 0px;
max-height: 100%;
display: flex;
flex-direction: column;
}
#data {
flex: 0 1 auto;
border: none;
}
#list_clones {
flex: 1 1 auto;
flex: 0 1 auto;
overflow-y: scroll;
overflow-x: hidden;
height: calc(100% - 30px);
/*100% - list_menu height */
max-height: 100%;
width: 100%;
padding: 2px;
}
......
......@@ -405,17 +405,16 @@ line {
flex: 1 1 auto;
height: 0px;
max-height: 100%;
display: flex;
flex-direction: column;
}
#data {
flex: 0 1 auto;
}
#list_clones {
flex: 1 1 auto;
flex: 0 1 auto;
overflow-y: scroll;
overflow-x: hidden;
height: calc(100% - 30px);
/*100% - list_menu height */
max-height: 100%;
width: 100%;
padding: 2px;
}
......
......@@ -406,18 +406,17 @@ line {
flex: 1 1 auto;
height: 0px;
max-height: 100%;
display: flex;
flex-direction: column;
}
#data {
flex: 0 1 auto;
border: none;
}
#list_clones {
flex: 1 1 auto;
flex: 0 1 auto;
overflow-y: scroll;
overflow-x: hidden;
height: calc(100% - 30px);
/*100% - list_menu height */
max-height: 100%;
width: 100%;
padding: 2px;
}
......
......@@ -522,6 +522,8 @@ line {
flex: 1 1 auto;
height: 0px; // set scrollbar flex will override height
max-height: 100%;
display: flex;
flex-direction: column;
}
#data{
......@@ -530,11 +532,9 @@ line {
}
#list_clones{
flex: 1 1 auto;
flex: 0 1 auto;
overflow-y : scroll;
overflow-x : hidden;
height : calc(~"100% - 30px"); /*100% - list_menu height */
max-height: 100%;
width: 100%;
padding:2px;
}
......
......@@ -253,6 +253,7 @@ function imgtPostForSegmenter(species, data, system, segmenter, override_imgt_op
var input = document.createElement('input');
input.type = 'checkbox';
input.id = 'imgt_cdr3_input_check';
input.checked = false;
$(input).on("click", function() {
if(this.checked) {
segmenter.highlight[1].field = "CDR3-IMGT";
......@@ -264,7 +265,6 @@ function imgtPostForSegmenter(species, data, system, segmenter, override_imgt_op
segmenter.update();
});
input.click();
var label = document.createElement('label');
label.setAttribute("for", 'imgt_cdr3_input_check');
label.innerHTML = 'CDR3-IMGT';
......@@ -278,6 +278,7 @@ function imgtPostForSegmenter(species, data, system, segmenter, override_imgt_op
input = document.createElement('input');
input.type = 'checkbox';
input.id = 'imgt_vdj_input_check';
input.checked = false;
$(input).on("click", function() {
if(this.checked) {
segmenter.highlight[2].field = "V-REGION";
......@@ -295,7 +296,6 @@ function imgtPostForSegmenter(species, data, system, segmenter, override_imgt_op
segmenter.update();
});
input.click();
label = document.createElement('label');
label.setAttribute("for", 'imgt_vdj_input_check');
label.innerHTML = "V/D/J-IMGT";
......
......@@ -53,7 +53,7 @@ class ExternalTest < BrowserTest
begin
$b.clone_in_scatterplot('25').click
$b.span(:id => "toIMGTSeg" ).click
$b.segmenter_checkbox_imgt_vdj.wait_until(&:present?)
$b.until { $b.segmenter_checkbox_imgt_vdj.present? }
clone_info = $b.clone_info_segmenter('25')
productive_title = clone_info[:axis].element(:class => 'productivity-IMGT').title
......
......@@ -219,7 +219,7 @@ class TestMultilocus < BrowserTest
def test_14_export_sample_report
if ENV['WATIR_CHROME']
if $b.driver.capabilities.browser_name == 'chrome'
skip "Issue #3699 must be solved first"
end
......
......@@ -10,7 +10,7 @@ class VidjilBrowser < Watir::Browser
Selenium::WebDriver::Chrome.path = ENV['WATIR_BROWSER_PATH']
end
# :chrome or :safari
if ENV['WATIR_CHROME']
if ENV['WATIR_CHROME'] or ENV['WATIR_BROWSER_PATH'].include? "chrom"
super :chrome
elsif ENV['WATIR_MARIONETTE']
super :firefox
......
firefox/v32/firefox
firefox/v45/firefox
chrome/default/chrome
This changelog concerns vijil-algo, the algorithmic part (C++) of the Vidjil platform.
2019-03-XX The Vidjil Team
2019-03-14 The Vidjil Team
* New --consensus-on-random-sample experimental option (core/representative.cpp) #3764
* Aho-Corasick automaton used by default (vidjil.cpp) #2566, will bring speed-ups in a future release
* Refactored command and option names, deprecate some short options names (vidjil.cpp) #3295 #3772
......
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