mirror of
https://github.com/galaxyproject/galaxy.git
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Merge remote-tracking branch 'jmchilton/release_16.01' into release_16.01_merge_4
Conflicts: static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map
This commit is contained in:
John Chilton
@@ -497,16 +497,14 @@ var HistoryViewEdit = _super.extend(
|
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},
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/** */
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drop : function( ev ){
|
||||
//console.warn( 'dataTransfer:', ev.dataTransfer.getData( 'text' ) );
|
||||
//console.warn( 'dataTransfer:', ev.originalEvent.dataTransfer.getData( 'text' ) );
|
||||
ev.preventDefault();
|
||||
//ev.stopPropagation();
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ev.dataTransfer.dropEffect = 'move';
|
||||
|
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//console.debug( 'ev.dataTransfer:', ev.dataTransfer );
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var dataTransfer = ev.originalEvent.dataTransfer;
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dataTransfer.dropEffect = 'move';
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|
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var panel = this,
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data = ev.dataTransfer.getData( "text" );
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data = dataTransfer.getData( "text" );
|
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try {
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data = JSON.parse( data );
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|
||||
|
||||
@@ -1,96 +1,216 @@
|
||||
id: galaxy_ui
|
||||
name: Galaxy UI
|
||||
description: A gentle introduction to the Galaxy User Interface
|
||||
title_default: "Welcome to Galaxy"
|
||||
|
||||
# A tour is made of several steps, each of them beginning with a dash '-'
|
||||
steps:
|
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# 'title's will be displayed in the header of each step-container
|
||||
# If you don't specify any title, a default title is used, defined above.
|
||||
- title: "Welcome to Galaxy"
|
||||
content: "This short tour will walk you through Galaxy's user interface."
|
||||
# 'content' is the actual text that is shown to the user
|
||||
content: "This short tour will guide you through Galaxy's user interface.<br>
|
||||
You can navigate with your arrow keys and leave the tour at any time point with 'Escape' or the 'End tour' button."
|
||||
# backdrop is just one of many properties you can attach to one step-container,
|
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# a full reference can be found at http://bootstraptour.com/api/
|
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backdrop: true
|
||||
|
||||
- element: ".upload-button"
|
||||
intro: "Use this button to upload your data."
|
||||
# 'element' is the JQuery Selector (http://api.jquery.com/category/selectors/) of the element you want to describe
|
||||
# In this case we want to highlight the Upload button with the `.upload-button` selector
|
||||
- title: "Upload your data"
|
||||
element: ".upload-button"
|
||||
intro: "Galaxy supports many ways to get in your data.<br>
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Use this button to upload your data."
|
||||
# position of the text box relative to the selected element
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position: "right"
|
||||
# You can trigger click() events on arbitrary elements before (preclick) or after (postclick) the element is shown
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postclick:
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- ".upload-button"
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|
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- element: "button#btn-local"
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intro: "Upload data from your computer."
|
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- title: "Upload your data"
|
||||
element: "button#btn-local"
|
||||
intro: "You can upload data from your computer."
|
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position: "top"
|
||||
postclick:
|
||||
- "button#btn-new"
|
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- element: "button#btn-new"
|
||||
intro: "Copy and Paste data or include URLs."
|
||||
|
||||
- title: "Upload your data"
|
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element: "button#btn-new"
|
||||
intro: "Copy and paste data directly into Galaxy or include URLs that lead to your data"
|
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position: "top"
|
||||
preclick:
|
||||
- ".upload-button"
|
||||
|
||||
- element: "textarea#text-content"
|
||||
intro: "Insert data into Galaxy."
|
||||
- title: "Insert URLs"
|
||||
element: "textarea#text-content"
|
||||
intro: "URLs separated by a line break are automatically downloaded by Galaxy."
|
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position: "top"
|
||||
textinsert: |
|
||||
https://raw.githubusercontent.com/arq5x/bedtools/master/test/merge/a.full.bed
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||||
https://raw.githubusercontent.com/arq5x/bedtools/master/test/merge/a.full.bed
|
||||
https://raw.githubusercontent.com/arq5x/bedtools/master/test/merge/a.full.bed
|
||||
https://raw.githubusercontent.com/bgruening/galaxytools/adf077b912ddebd97b07b947b855cdd2862ed8ef/tools/augustus/test-data/human_augustus.fa
|
||||
https://raw.githubusercontent.com/bgruening/galaxytools/adf077b912ddebd97b07b947b855cdd2862ed8ef/tools/sailfish/test-data/reads_2.fastq
|
||||
https://raw.githubusercontent.com/bgruening/galaxytools/adf077b912ddebd97b07b947b855cdd2862ed8ef/tools/statistics/test-data/anderson.tabular
|
||||
|
||||
- element: "button#btn-start"
|
||||
- title: "Start the upload"
|
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element: "button#btn-start"
|
||||
intro: "Upload the data into your Galaxy history."
|
||||
position: "bottom"
|
||||
position: "top"
|
||||
postclick:
|
||||
- "button#btn-start"
|
||||
|
||||
- element: "button#btn-close"
|
||||
intro: "Hit the close button in upload."
|
||||
position: "bottom"
|
||||
- title: "Close upload/download manager"
|
||||
element: "button#btn-close"
|
||||
intro: "Close the upload manager with this button or with a click outside of the manager window."
|
||||
position: "top"
|
||||
postclick:
|
||||
- "#btn-close"
|
||||
|
||||
- title: "Tools"
|
||||
element: "#left"
|
||||
intro: "This is your ToolBox. All tools available in your Galaxy instance you can find here."
|
||||
position: "right"
|
||||
|
||||
- element: 'a[href$="tool_runner?tool_id=Filter1"]'
|
||||
- title: "Tool search bar"
|
||||
element: '#tool-search-query'
|
||||
intro: "You can search for tools by keywords."
|
||||
position: "right"
|
||||
textinsert: 'filter'
|
||||
|
||||
- title: "Tool categories"
|
||||
element: '#title_filter > a'
|
||||
intro: "Tools are grouped into categories to make them easier to find."
|
||||
position: "right"
|
||||
preclick:
|
||||
- 'a[href$="tool_runner?tool_id=Filter1"]'
|
||||
postclick:
|
||||
- "#title_filter a"
|
||||
|
||||
- element: '#center-panel'
|
||||
intro: "This is your Filter tool."
|
||||
- title: "Select a tool"
|
||||
element: 'a[href$="tool_runner?tool_id=Filter1"]'
|
||||
intro: "Select and load a tool for your analysis by clicking the underlined link."
|
||||
position: "right"
|
||||
preclick:
|
||||
- '#center-panel'
|
||||
postclick:
|
||||
- 'a[href$="tool_runner?tool_id=Filter1"]'
|
||||
|
||||
- element: '#uid-0'
|
||||
intro: "Your tool parameters."
|
||||
- title: "Filter Tool"
|
||||
element: '#center-panel'
|
||||
intro: "Your tool is loaded into the main Galaxy page and ready for use."
|
||||
position: "right"
|
||||
#backdropContainer: 'background'
|
||||
#backdrop: true
|
||||
|
||||
- title: "Tool parameters"
|
||||
element: '#uid-0'
|
||||
intro: "Here you can choose your tool parameters. Select your input dataset from your history and specify parameters for your analysis."
|
||||
position: "right"
|
||||
|
||||
- element: 'div.toolHelp'
|
||||
intro: "Your tool parameters."
|
||||
- title: "Tool help"
|
||||
element: 'div.ui-form-help'
|
||||
intro: "Every Galaxy tool has a help section with detailed information about the tool and its parameters.
|
||||
Have a look and study your tool in depth by reading it."
|
||||
position: "top"
|
||||
|
||||
- title: "Run your tool"
|
||||
element: '#execute'
|
||||
intro: "Click on 'Execute' to run your tool and send it to the compute cluster.
|
||||
Don't be afraid to test different settings in parallel. Galaxy can handle multiple runs of the same tool."
|
||||
position: "right"
|
||||
- element: '#execute'
|
||||
intro: "Send your tool to the Compute Cluster."
|
||||
position: "right"
|
||||
preclick:
|
||||
postclick:
|
||||
- '#execute'
|
||||
- element: "#right"
|
||||
intro: "This is your history! All anylysis steps will be recorded and can be redone at any time."
|
||||
|
||||
- title: "History"
|
||||
element: "#right"
|
||||
intro: "This is your Galaxy history! All analysis steps with results of the tools and their parameters will be recorded here and can be redone at any time.<br>
|
||||
A running tool is shown in yellow and if your calculation is done, it turns green. If your dataset is
|
||||
grey this means you are queued and need to wait until your tool can be started. If your dataset turns into red, an error has occurred. Please report the bug to the Galaxy team with the bug report button."
|
||||
position: "left"
|
||||
- element: "#masthead"
|
||||
intro: "Your top panel will give you access to a lot of useful things."
|
||||
|
||||
- title: "Rename history"
|
||||
element: "#current-history-panel > div.controls > div.title > div"
|
||||
intro: "Name your history here and press enter."
|
||||
position: "left"
|
||||
preclick:
|
||||
- "#current-history-panel > div.controls > div.title > div"
|
||||
|
||||
- title: "View dataset"
|
||||
element: ".fa-eye:eq(0)"
|
||||
intro: "View your dataset by clicking the eye button."
|
||||
position: "left"
|
||||
#preclick:
|
||||
# - ".fa-eye:eq(0)"
|
||||
|
||||
- title: "Rename dataset"
|
||||
element: ".fa-pencil:eq(0)"
|
||||
intro: "Rename your dataset by clicking the pencil button."
|
||||
position: "left"
|
||||
#preclick:
|
||||
# - ".fa-pencil:eq(0)"
|
||||
|
||||
- title: "Remove dataset"
|
||||
element: ".fa-times:eq(0)"
|
||||
intro: "Delete your dataset by clicking the x-button."
|
||||
position: "left"
|
||||
#postclick:
|
||||
# - ".fa-times:eq(0)"
|
||||
|
||||
- title: "Dataset information"
|
||||
element: "div.title-bar.clear:eq(0)"
|
||||
intro: "Clicking on your dataset provides you with more information regarding your dataset (e.g. filetype or size)."
|
||||
position: "left"
|
||||
preclick:
|
||||
- "div.title-bar.clear:eq(0)"
|
||||
|
||||
- title: "Re-run tool"
|
||||
element: ".fa-refresh:eq(1)"
|
||||
intro: "By clicking the reload button, you can re-run your tool again (e.g. with different parameters or on another dataset)."
|
||||
position: "left"
|
||||
preclick:
|
||||
- ".fa-refresh:eq(1)"
|
||||
|
||||
|
||||
- title: "Panel collaps"
|
||||
element: "#left > div.unified-panel-footer > div.panel-collapse.left"
|
||||
intro: "To extend the view for your main Galaxy page in the middle, you can collapse the tool panel on the left hand side. Clicking the panel arrow on the right hand side, collapses the history."
|
||||
position: "top"
|
||||
postclick:
|
||||
- "#left > div.unified-panel-footer > div.panel-collapse.left"
|
||||
|
||||
- title: 'Top panel'
|
||||
element: "#masthead"
|
||||
intro: "The top panel will give you access to a lot of useful things."
|
||||
position: "bottom"
|
||||
- element: "#analysis"
|
||||
intro: "Start your <b>analysis</b> from here."
|
||||
|
||||
- title: 'Analyze data'
|
||||
element: "#analysis"
|
||||
intro: "This is the current view. Start your <b>analysis</b> from here."
|
||||
position: "bottom"
|
||||
- element: "#workflow"
|
||||
intro: "Manage, Import, Export and Share your <b>Workflows</b>."
|
||||
|
||||
- title: 'Workflow'
|
||||
element: "#workflow"
|
||||
intro: "Create, manage, import, export and share your <b>Workflows</b>."
|
||||
position: "bottom"
|
||||
- element: "#shared"
|
||||
intro: "Get access to all <b>Workflows, <b>Histories</b>, <b>Pages</b>, <b>Visualizations</b> and you <b>Data Library</b> that are shared with you."
|
||||
|
||||
- title: 'Shared data'
|
||||
element: "#shared"
|
||||
intro: "Get access to all <b>Workflows</b>, <b>Histories</b>, <b>Pages</b>, <b>Visualizations</b> and your <b>Data Library</b> that are shared with you."
|
||||
position: "bottom"
|
||||
- element: "#visualization"
|
||||
intro: "Want to start visualize your data in Trackster? Start here!"
|
||||
|
||||
- title: 'Visualization'
|
||||
element: "#visualization"
|
||||
intro: "Do you want to start to visualize your data in Trackster? Start here!<br>Galaxy offers a lot more visualizations!"
|
||||
position: "bottom"
|
||||
- element: "#help"
|
||||
intro: "Here you get more help from the Galaxy <b>Community</b> with Videos and a QA board."
|
||||
|
||||
- title: 'Help'
|
||||
element: "#help"
|
||||
intro: "Here you get more help from the Galaxy <b>Community</b> with Videos, a QA board and more tours."
|
||||
position: "bottom"
|
||||
- element: "#user"
|
||||
|
||||
- title: 'User Preferences'
|
||||
element: "#user"
|
||||
intro: "Login and start your analysis!"
|
||||
position: "bottom"
|
||||
|
||||
- title: 'Scratchbook'
|
||||
element: "#enable-scratchbook"
|
||||
intro: "Scratchbook offers you multiple visualizations next to each other. Have a look at our Scratchbook tour to learn more about it."
|
||||
position: "bottom"
|
||||
|
||||
- title: "Enjoy Galaxy"
|
||||
intro: "Thanks for taking this tour! Happy research with Galaxy!"
|
||||
|
||||
@@ -1,90 +1,95 @@
|
||||
name: History Introduction
|
||||
description: A detailed introduction to the <b>Galaxy History</b>
|
||||
description: A detailed introduction to the Galaxy History
|
||||
title_default: "Galaxy History Introduction"
|
||||
steps:
|
||||
- content: "This short tour will walk you through <b>Galaxy's History</b> and datasets."
|
||||
- content: "This short tour will guide you through <b>Galaxy's History</b> and datasets."
|
||||
|
||||
- element: ".upload-button"
|
||||
- title: "Upload data"
|
||||
element: ".upload-button"
|
||||
intro: |
|
||||
At first we get some data into your Galaxy and into your History.<br>
|
||||
Use this button to upload your data.
|
||||
"At first we upload some data into your Galaxy history.<br>
|
||||
Use this button to upload your data."
|
||||
position: "right"
|
||||
postclick:
|
||||
- ".upload-button"
|
||||
|
||||
- element: "button#btn-local"
|
||||
intro: "Upload data from your computer."
|
||||
- title: "Upload your data"
|
||||
element: "button#btn-local"
|
||||
intro: "You can upload data from your computer."
|
||||
position: "top"
|
||||
postclick:
|
||||
- "button#btn-new"
|
||||
|
||||
- element: "button#btn-new"
|
||||
intro: "Copy and Paste data or include URLs to data which will be fetched automatically by Galaxy."
|
||||
- title: "Upload your data"
|
||||
element: "button#btn-new"
|
||||
intro: "Copy and paste data directly into Galaxy or include URLs that lead to your data."
|
||||
position: "top"
|
||||
|
||||
- element: "textarea#text-content"
|
||||
intro: "We insert some URLs to get example data in Galaxy."
|
||||
- title: "Insert URLs"
|
||||
element: "textarea#text-content"
|
||||
intro: "URLs separated by a line break are automatically downloaded by Galaxy."
|
||||
position: "bottom"
|
||||
textinsert: |
|
||||
file://home/bag/Bilder/Python-Programming-in-Galaxy.png
|
||||
file://home/bag/Downloads/a.tab
|
||||
https://wiki.galaxyproject.org/Images/GalaxyLogo?action=AttachFile&do=get&target=galaxy_project_logo.jpg
|
||||
https://raw.githubusercontent.com/bgruening/galaxytools/adf077b912ddebd97b07b947b855cdd2862ed8ef/tools/statistics/test-data/anderson.tabular
|
||||
|
||||
- element: "button#btn-start"
|
||||
- title: "Upload your data"
|
||||
element: "button#btn-start"
|
||||
intro: "Upload the data into your Galaxy <b>History</b>."
|
||||
position: "bottom"
|
||||
position: "top"
|
||||
postclick:
|
||||
- "button#btn-start"
|
||||
- "button#btn-close"
|
||||
|
||||
- element: "#right"
|
||||
intro: "This is your history! All anylysis steps will be recorded and can be redone at any time."
|
||||
- title: "History"
|
||||
element: "#right"
|
||||
intro: "This is your history! All analysis steps will be recorded and can be redone at any time."
|
||||
position: "left"
|
||||
|
||||
- element: "#dataset-2d9035b3fc152403"
|
||||
- title: "Dataset information"
|
||||
element: "div.title-bar.clear:eq(0)"
|
||||
intro: "This is one of your uploaded datasets. You can get more informations and options like different visualizations by clicking on it."
|
||||
position: "left"
|
||||
postclick:
|
||||
- "#dataset-2d9035b3fc152403 > div.title-bar.clear > div > span.name"
|
||||
- "div.title-bar.clear:eq(0)"
|
||||
|
||||
- element: "#dataset-2d9035b3fc152403 > div.details > div.summary > div.datatype > label"
|
||||
title: "Metadata"
|
||||
intro: "Galaxy has assigned a datatype too your dataset during upload, which you can see here."
|
||||
- title: "Metadata"
|
||||
element: "#current-history-panel > div.list-items > div:nth-child(1) > div.details > div.summary > div.datatype > label"
|
||||
intro: "Galaxy has assigned a datatype to your dataset during upload, which you can see here."
|
||||
position: "left"
|
||||
|
||||
- element: "#dataset-2d9035b3fc152403 > div.details > div.actions.clear > div.left > a.download-btn.icon-btn"
|
||||
- element: "#current-history-panel > div.list-items > div:nth-child(1) > div.details > div.actions.clear > div.left > a.download-btn.icon-btn"
|
||||
title: "Download your dataset"
|
||||
intro: "You can download every dataset by using the floppy disc symbol."
|
||||
position: "left"
|
||||
|
||||
- element: "#dataset-2d9035b3fc152403 > div.details > div.actions.clear > div.left > a.icon-btn.params-btn"
|
||||
- element: "#current-history-panel > div.list-items > div:nth-child(1) > div.details > div.actions.clear > div.left > a.icon-btn.params-btn"
|
||||
title: "Even more information"
|
||||
intro: "Get an overview of all metadata associated with your dataset by using the Information symbol."
|
||||
position: "left"
|
||||
preclick:
|
||||
- "#dataset-2d9035b3fc152403 > div.details > div.actions.clear > div.left > a.icon-btn.params-btn"
|
||||
- "#current-history-panel > div.list-items > div:nth-child(1) > div.details > div.actions.clear > div.left > a.icon-btn.params-btn"
|
||||
|
||||
|
||||
|
||||
- element: "#dataset-2d9035b3fc152403 > div.primary-actions > a.icon-btn.display-btn"
|
||||
- element: "#current-history-panel > div.list-items > div:nth-child(1) > div.primary-actions > a.icon-btn.display-btn"
|
||||
title: "Inspect your data"
|
||||
intro: "The eye symbol can be used to look at your data."
|
||||
position: "left"
|
||||
preclick:
|
||||
- "#dataset-2d9035b3fc152403 > div.primary-actions > a.icon-btn.display-btn"
|
||||
- "#current-history-panel > div.list-items > div:nth-child(1) > div.primary-actions > a.icon-btn.display-btn"
|
||||
|
||||
- element: "#dataset-2d9035b3fc152403 > div.primary-actions > a.icon-btn.edit-btn"
|
||||
- element: "#current-history-panel > div.list-items > div:nth-child(1) > div.primary-actions > a.icon-btn.edit-btn"
|
||||
title: "Edit metadata"
|
||||
intro: "With the pencil button you can edit metadata attributes of your dataset, like the associated filetype or the dataset name."
|
||||
position: "left"
|
||||
preclick:
|
||||
- "#dataset-2d9035b3fc152403 > div.primary-actions > a.icon-btn.edit-btn"
|
||||
- "#current-history-panel > div.list-items > div:nth-child(1) > div.primary-actions > a.icon-btn.edit-btn"
|
||||
|
||||
- element: "#dataset-2d9035b3fc152403 > div.primary-actions > a.icon-btn.delete-btn"
|
||||
- element: "#current-history-panel > div.list-items > div:nth-child(1) > div.primary-actions > a.icon-btn.delete-btn"
|
||||
title: "Remove datasets"
|
||||
intro: "You can remove a dataset from the history with the cross symbol."
|
||||
position: "left"
|
||||
postclick:
|
||||
- "#dataset-2d9035b3fc152403 > div.primary-actions > a.icon-btn.delete-btn"
|
||||
- "#current-history-panel > div.list-items > div:nth-child(1) > div.primary-actions > a.icon-btn.delete-btn"
|
||||
|
||||
- element: "#current-history-panel > div.controls > div.subtitle > a"
|
||||
title: "Include all deleted datasets"
|
||||
@@ -93,14 +98,14 @@ steps:
|
||||
postclick:
|
||||
- "#current-history-panel > div.controls > div.subtitle > a"
|
||||
|
||||
- element: "#dataset-2d9035b3fc152403 > div.warnings > div > a"
|
||||
- element: "#current-history-panel > div.list-items > div:nth-child(1) > div.warnings > div > a"
|
||||
title: "Undeleting a dataset"
|
||||
intro: |
|
||||
"Galaxy datasets are only marked as deleled and can be recovered by exeecuting this link.
|
||||
Please note that datasets marked as deleted can be purged by your administrator at any time. :beer: "
|
||||
Galaxy datasets are only marked as deleled and can be recovered by clicking this link.
|
||||
Please note that datasets marked as deleted can be purged by your administrator at any time.
|
||||
position: "bottom"
|
||||
postclick:
|
||||
- "#dataset-2d9035b3fc152403 > div.warnings > div > a"
|
||||
- "#current-history-panel > div.list-items > div:nth-child(1) > div.warnings > div > a"
|
||||
|
||||
- element: "#current-history-panel > div.controls > div.subtitle > a"
|
||||
title: "Hiding all deleted datasets"
|
||||
@@ -111,7 +116,7 @@ steps:
|
||||
|
||||
- element: "#current-history-panel > div.controls > div.title > div"
|
||||
title: "Change your History name"
|
||||
intro: "You can change the history name clicking on the title"
|
||||
intro: "You can change the history name clicking on the title."
|
||||
position: "bottom"
|
||||
preclick:
|
||||
- "#current-history-panel > div.controls > div.title > div"
|
||||
@@ -122,11 +127,11 @@ steps:
|
||||
position: "left"
|
||||
textinsert: "WWFSMD"
|
||||
preclick:
|
||||
- "#current-history-panel > div.controls > div.search > div > input"
|
||||
- "#current-history-panel > div.controls > div.search > div > input"
|
||||
|
||||
- element: "#history-options-button"
|
||||
title: "History Options"
|
||||
intro: "In the History menue you will find a lot more usful History options."
|
||||
intro: "In the History menu you will find a lot more useful History options."
|
||||
position: "left"
|
||||
postclick:
|
||||
- "#history-options-button"
|
||||
|
||||
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Reference in New Issue
Block a user