Repo mode #1546
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jkmarx
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Dec 6, 2016
scottx611x
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Jul 11, 2017
* Update the list graph and load D3.js version 4 (required for the latest version of the list graph). * Since D3 does not create a new object but overwrites the existing `window.d3` we have to load D3 v4 first. I added a special vendor block that can be removed once all scripts run on D3 v4. * Add missing annotation. * Integrate Intro.js. * Fix paths. * Initial overview intro about SATORI. Needs further refinements. * Use minified version. * Update version of Angular Intro.js. * Don't copy the source version and instead use the source map. * Make method names less ambiguous to be able to distinguish between multiple guides. * Remove unused launchPad controller. * Add default options for Intro.js to avoid code duplication. * Outsource Intro.js code as it is used across multiple controllers / directives. Add a second intro guide for the data set view. * Fix line break and add a little but of margin to the right of the headline. * Point to original repo as all changes have been borrowed from my fork. * Rename file and extend with two factory functions for handling special step directives. * Only use before change events for before and after executives. * Have context dependent intros. * Updates with new enhancer functions to simplify code. * Unfortunately intro.js guides have to be defined in the directive they describe. Making overview guides over multiple directives a but harder. * Rename for clarity. * Fix unit test by removing the additional div wrapper. * Remove comment and empty lines. * Limit blinking effect of the help button to 3 times. Otherwise it is too distracting. Also removed vendor code which is added by Grunt automatically. * Fix CSS for the new version of the list graph. * Split intros into different files. Renaming. * Rename for clarity. * Fix #1312 * IntroJS starter service. This service can be used to start other guides from within a guide. * Update IDs and names of the intro js methods. * Add very apparent button to go back to the exploration view when opening a preview in between. * Do not show separator when the "back to exploration" button is not shown. * Adjust styling of lists on an intro js tooltip. * Check if the intro js name is actually associated with a start function before calling it. * Refactor and create intro-js guides for an overview of SATORI, the data set view, the list graph, and the treemap. The actual steps of the guides need to be worked out but technically everything works. * Skeleton for the data set summary intro. * Avoid dots in the folder structure of JS scripts because Grunt relies on "*.js" to find JS files. * Avoid dots in the folder structure of JS scripts because Grunt relies on "*.js" to find JS files. * Don't copy over test (`.spec.js`) files as they don't need to be annotated, minified, etc. * Optimize all minified JS files for fast initial load time. * Add an _easteregg_ popup containing a usage scenario video of SATORI. * Add content to the data set summary tour. * Remove console.logs. * Fix minor visual bug. * Fix #1404. * Fix template. * Add custom _tour_ button to the list graph for starting the intro-js tour. * Rename button label. * Adjust coloring given the new visual node locking of the list-graph. * Helper method to trigger an SVG event. This allows to programmatically trigger events that get picked up by D3js. * Softify text a bit. * Advance list graph tour. * Increase timeout. * Fix coloring. * Fix minor styling issue. * Fix interconnected node locking. Refactor code for this. * Remove unnecessary check for clone IDs as this has been solved in the newest version of the list graph. * Make sure that the list graph initializes with the correct visible depth. * Add support for event based querying. * Adjust intro steps. Add two images for a visual explanation of precision and recall. * Enable dynamic SVG element highlighting to some extend. * Add puppet class to fetch and install neo4j ontologies * Include ontology install by default * Update `neo4j-ontologies` * Test very latest list graph * Fix import bug * Fix production build. * Close #1546. Close #1547. * Check if adapters are available before reloading. Caused in issue in the repo mode. * Avoid double incrementing to ensure 5 tries. * Add a new class for site related settings. Add a text field to customize the home page when running Refinery in the repository mode. * Add function to return the user ID of the logged-in user. Refactor service. * Load custom html on the repo page if available. * Helper command to update the investigation of MetaboLights data sets. * Remove title tooltip for now due to #1540. * Make with fixer for the repo mode more robust * Extend and rename management command * Use plural for clarity and update help text * Simplify * Add management command for update the data set instances * Update dataset name as well * Fix missing whitespace * Show accession if available * Fix dataset name updating * Forbid truncating of the highlighted title field * Add an option to overwrite existing data sets for cli-based isatab imports * Update list graph to v1 * Actually log error * Add a service to make a promise timeoutable. This is handy for network request that might got stuck. * Make citation loading time out after 10s and display a more useful error message * Add missing query parameter * Add missing doc-string * Fix method and add doc-string * Add extra html fields for title and description and update / initialize them properly to avoid stale title and description highlighting. Close #1583 * Fix loading bug related to AngularJS. See here angular/angular.js#13590 * Unify intro-js tours but keep exit on ESC * Allow reset without changing the URL * Adjust intro guides * Ensure a consistent start and exit of the intro js tutorial * Enhance tutorials and make sure that they correctly start and exit * Make sure that `afterExecution` is triggered properly when going backwards as well * Add introjs button and a maximizer button to the treemap's top-bar * Unify look of intro-js starter buttons * Finish content of the treemap intro-js * Reset visible depth to 1 and not 0. Remove unnecessary $rootScope.$apply(). Make sure the introjs guide is properly initialized and exited. * Replace floatbox with flexbox for more flexibility. Add 2 more buttons to show the state if the window size. Style active button. * Add angular local storage helper service * Add a skeleton vis window size service that stores the size in local storage for persistency * Fix logic * Implement minimizing and maximizing of the treemap and list-graph * Add rerendering to treemap when the window size is maximized etc. * Fix annoying double pixel border * Make the list graph resizable as well. * Custom icons for maximizing, minimizing, and equalizing * Move exploration help into the main panel header * List exploration terms (visual only at the moment) * Remove console logs * Re-render the list-graph and treemap on window resize events * Visible depth must be >=1 * Ignore OWL:Thing as a query. Treemap does not notify on initial loading * Transmit complete treemap init data * Fix typo. Add prop setter to avoid undefined errors. Add placeholder method for toggling query term modes * Fix broken API calls and set queryTerms in init * Fix broken calls * Implement query mode toggling and notification * Distinguish between all and selected dataSets to fix _not_ queries * Fix typo and simplify code * Apply patch to fix bar updates * Make query mode more readible * Mention the query terms * Add unique ID to the query term list. Make sure no term is duplicated * Return the root status and label * Simplify and update root status * Include a demonstration of how to query by a term and how the query term list looks like * Hide prev button for the last two steps as going back breaks things * Update to the latest version * Fix typo * Simplify * Properly unroot with the query term list * Fix annotation set import * Extend entry point classes with MetaboLights related ontologies * Fix issue with custom root terms being children of other root terms. Excluded two broad root terms. * Add setting for satori demo * Disable file browser when satori demo is active * Add auto logins for SATORI demo * Avoid OWL:Thing as a parent for non-root terms * Add doc string * Automatically load the screenshot layout for the satori demo * Indicate state by changing the tense * Adjust button and border style for the screenshot design * Set screenshot via Django to avoid flickering * Remove unused variable * Do not explicitly set _cellular component_ as root node * Hide border * Disable link to file browser in SATORI demo mode * Update text * Fix toggle issue of SATORI vis in repo mode * Disable sauce * Fix a very rare and hard to track down bug * Fix direction of tool tip * Remove call of undefined object * Update custom entry points. Add comment. * Add `data item` to the root nodes * Fix bug when node to be highlighted as not been drawn * Adjust explore button when in SATORI demo mode * Update d3-list-graph * Add entry point term for MS * Add entry points. * Add MI and NCBITaxon entry terms. * Update list graph * Add method for normalizing URIs (NCBITaxon for now) * Update printing, add URI normalization, add third case when accession is a URI * Remove inconsistent NCBITaxon URIs and do not use BFO umbrella terms. * Fix bug when resizing the treemap. Do not re-add eventListeners on re-rendering. * Enable zooming into a terminal node * Node nonsense subtree * Fix a resize bug caused by recalculating a set layout. * Update list graph * Fix layout recalculating when rerendering * Remove logging * Reset visible depth when manually zooming in to avoid confusion (i.e., to zoom into what was seen before) * Init cache only once * Fix a bug when adding all retrieved data sets of a query selection to the data cart. Pull all data when data sets have no ID * Refactor normalizing ont URIs and apply it to the annotations API * Fix bug * Use $window * Without the resolution `fab vm update` fails * Update migration number * Use provider as module is not available. Remove pointer to nonexistent controller. * Generify auto login * Attempt to fix stupidity of Fritz * Remove unused code * Use static method * Use `that` instead of `self` * Update to `self.stdout.write` * Delete accidentally added files * Make sure original annotations are not modified * Simplify settings for auto login * Remove utility commands for Metabolight ISA-Tabs * Remove optimize js... * Update ID to fix launchpad intro-js tutorial * Output files at compile location
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