rbbt-rest 1.2.34 → 1.2.35
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- checksums.yaml +8 -8
- data/share/views/compass/help.sass +20 -0
- data/share/views/help.haml +47 -66
- data/share/views/help/UI.haml +250 -0
- data/share/views/help/workflow.haml +1 -1
- data/share/views/public/img/UI/action_control.png +0 -0
- data/share/views/public/img/UI/action_control_wire.png +0 -0
- data/share/views/public/img/UI/actions.png +0 -0
- data/share/views/public/img/UI/actions_wire.png +0 -0
- data/share/views/public/img/UI/cytoscape.png +0 -0
- data/share/views/public/img/UI/d3js.png +0 -0
- data/share/views/public/img/UI/favourites.png +0 -0
- data/share/views/public/img/UI/favourites_wire.png +0 -0
- data/share/views/public/img/UI/jmol.png +0 -0
- data/share/views/public/img/UI/report.png +0 -0
- data/share/views/public/img/UI/report_wire.png +0 -0
- data/share/views/public/img/UI/table.png +0 -0
- data/share/views/public/img/UI/topbar.png +0 -0
- data/share/views/public/img/UI/topbar_wire.png +0 -0
- metadata +17 -2
checksums.yaml
CHANGED
@@ -1,15 +1,15 @@
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---
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!binary "U0hBMQ==":
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metadata.gz: !binary |-
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ZTdlZWRiOGE3MmQyMjU0YTQxODM0ODM0NjZkNzE3ZmM5ZGI4MDMzZA==
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data.tar.gz: !binary |-
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MmNlODFmYTYwZTRlMWJjMTZmNzhkODUyOTkyZjNlYzIyNTBiMmQwNg==
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SHA512:
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metadata.gz: !binary |-
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NzM4NGU4MDc1OTJiYTM4NjI0Zjk3MDZjYzA1YWI0OWZhZGE4OTczOTgyM2Fj
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ODAyOWY5MTYzZTNiNGFlNTY1YzliMDMxOWM1ZmRmMTZkZWVjZWVmN2YzNjkz
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YzM1ZDBmZTg3YjczYThjMTIzMWJiMDgwZTFiYjBkZjljODgwOGU=
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data.tar.gz: !binary |-
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M2M5NjQ3MGYxNmZiYTBlNDdkMmE5MjViNjRkOTVkYWViNTg5ZDVkOGEwZjIw
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YzQ4NzY3NGRmMThmOThhODMwYWJjMTNmNWNmM2FiMjJiNmU4ZjQ0MjczZjEz
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YjdhZTJiNmYzNzI3NGFhYzkyOTRkYWRiZTVjOThmNGM5Zjg4MmI=
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a.help
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font-size: 1.2em
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display: block
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.UI
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dd
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.description, .images
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+grid-column(6, $float:left)
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& > dd
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+grid-row()
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& > .description, .images
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+grid-column(6, $float:left)
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& > .images > dl
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& > dt
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width: 40%
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& > dd > img
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display: block
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margin: auto
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data/share/views/help.haml
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:markdown
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Overview
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========
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##Overview
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This application is designed for integration of data and functionalities.
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It design is based on the idea of the `Entity`: any thing that can be
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unambiguously identified and be subject of investigation. Examples of
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entities are: genes, proteins, SNPs, samples, pathways, etc.
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Each entity has a report, which depends on the type of entity it is.
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### A word on performance
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Each entity has a report, which depends on the type of entity it is. All
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reports are computed on the fly and cached. In addition to the main reports,
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entities have `actions`, which are sub-reports that implement particular
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analysis. For instance, for gene entities, one of the actions is to display a
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summary of the relevance of that gene across the collection of studies that
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you have access to. In addition to entities, there are reports for lists of
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entities and for entity maps, which are tables that relate entities to values,
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such as genes to their average mutation frequency.
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process may require plenty of infrastructure: downloading of datasets,
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building databases, computing preliminary results, etc. A lot of this
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processing is reused system-wide. This means that the application starts slow
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but gets quicker. Unlike other applications with a more limited scope this
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system cannot foresee what the user will be interested in, so not all this
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infrastructure can be built before hand and must be built on demand. We pay
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a price for flexibility by sacrificing responsiveness. But the system has
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plenty of tricks to be as efficient as possible and to reuse as much as
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possible.
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### Entity annotations
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The `Entity` subsystem annotates identifiers for entities with additional information
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to help their complete and unambiguous identification.
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#### Organisms and builds
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When you identify a gene with the string `TP53` we might think that the gene
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is unambiguously identified, however, it is not. First of all, we need to
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know to which organism this gene belongs to, each TP53 gene from different
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organisms is a different gene. Not only that, but the TP53 gene changes
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slightly from build to build, in particular, its chromosomal position may
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shift. For that reason genes are not only characterized by the organism they
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belong to but also by the version of the build we are considering.
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We annotate entities with their organism and build using the following
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convention. The organism is specified with a three letter code, the first is
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uppercase and is the first letter of the first term in the organism name ("H"
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for Homo) and the last two the first two letter of the second term ("sa" for
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sapiens); this is the convention followed by KeGG, it is succinct and
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collision free in our experience. The build is specified afterwards with a
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date code; "Hsa/may2009" represents the _Homo s._ organism as was known in
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May 2009 i.e. hg18 build; whereas "Hsa/jan2013" corresponds to a recent
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version of the hg19 build.
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#### Identifier formats
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Genes can be identified through a substantial number of identifier formats:
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Ensembl Gene ID, Entrez Gene ID, Associated Gene Name (gene symbol). We use
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the Ensembl BioMart to download an identifier translation resource. The name
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of the formats corresponds to the names used in the Ensembl BioMart and must
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be *followed to the letter including case*. The gene `Entity` is prepared to handle all the
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necessary translations between identifiers across different resources
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transparently. But the user *must* be aware of this fact or may run into
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trouble.
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:markdown
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##User interface
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The user interface offers a general structure for all reports that allows to
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enact workflows, explore the results and connect functionalities with one
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another. This web site is 'responsive', meaning that it adapts to the size
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of the device you are using: computer, tablet, or phone. On small devices many
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of the layout elements shift around or get hidden behind toggle buttons to
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acomodate themselves better to the screen size. The examples bellow are taken
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from a computer screen.
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%ul
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%li
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%a(href='/help/entity' class="help") Entity subsystem
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=partial_render('help/UI')
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:markdown
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##Workflows
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In addition to exploring entity reports, this site servers collections of
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core functionalities through the Workflow subsystem. This is the same
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interface that is used as a REST web server, so it serves to document it.
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%table
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%caption Available workflows on this site
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%thead
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%tr
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%th Workflow
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%th Description
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%tbody
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- Sinatra::RbbtRESTWorkflow::WORKFLOWS.each do |workflow|
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- next if workflow.asynchronous_exports.empty? and workflow.synchronous_exports.empty? and workflow.exec_exports.empty?
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%tr
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%th
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%a(href="#{'/' << workflow.to_s}")= Misc.humanize(workflow.to_s)
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%td
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- description = workflow.workflow_description || ""
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- case
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- when description.empty?
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No description
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- else
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= description.split("\n\n").first
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@@ -0,0 +1,250 @@
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%dl.tabs.UI.active
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%dt.next.active.show Report structure
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%dd.show
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.description
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:markdown
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This application presents reports for individual entities, lists of
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entities, and entity maps. Each type of entity (gene, study, pathway, etc.)
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has its own report template, and they are prepared on demand.
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All reports have the same overall structure; the images show a report
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for a genotyping study from the ICGC project. The top-bar is always
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there and provides a placeholder for several functionalities, most
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importantly the control of `favourites`.
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Bellow the top-bar comes the report itself. It consists of a title, a
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side-bar, a description, and an `action controller`. In general the
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side-bar is used to show general meta-data about the entity and the
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description to show a brief overview.
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The action controller offers access to `actions` which are like
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sub-reports. Each type of entity has its own actions. If the entity
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type in particular does not have any action defined the action
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controller will not be displayed. When an action is selected, it will
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be displayed below, in the area called action loader.
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Actions can also be opened in their own page, these pages are like reports
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but with no action controller or side-bar
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.images
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%dl.tabs.active.show
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%dt.next.show Snapshot
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%dd.show
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%img(src="/img/UI/report.png")
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%dt.next Explanation
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%dd
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%img(src="/img/UI/report_wire.png")
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%dt.next Top-bar
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%dd
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.description
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:markdown
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The top-bar provides access to several functionalities. Clicking on the
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title of the application will link to its front-page.
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Next to it is the reload-button, which is used to force the server to
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recalculate a report, otherwise the report will be taken from a cache.
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This is useful when a report has given an error or when when it was
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updated somehow. *Note:* After a reload of the report, the browser might
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still try to get the file from its own cache, so you might need to use
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the reload button in the browser as well. I'm planning to fix this.
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Next is the `favourites` controls, which we will discuss shortly. After
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that there might be a search box, if the server was started with that
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functionality. This search box can be configured to identify any type
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of entity, but generally it is only genes.
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The final component of the top-bar, which I label "Extra", has the user
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controls, which allows to login or logout, and the job bookmarks,
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where bookmarked actions are kept. Will discuss bookmarking actions
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latter.
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.images
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%dl.tabs.active.show
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%dt.next.show Snapshot
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%dd.show
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%img(src="/img/UI/topbar.png")
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%dt.next Explanation
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%dd
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%img(src="/img/UI/topbar_wire.png")
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%dt.next Favourites
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%dd
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.description
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:markdown
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As we said before, we have reports for entities, lists, and maps.
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Clicking the star on the favourites control makes a favourite out of
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what-ever we are viewing: an entity, like a study; a list of entities,
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such as the genes mutated in the study; or a map, which could for
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instance map genes to the ratio of mutations per amino-acid in the
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COSMIC database.
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Favourites are used not only to track our interests, but as a means to
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communicate between different functionalities or parts of the
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application. We could for instance make a list of genes a favourite and
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then go to a study report, open the "Gene list in study" action, select
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our list from all the favourites and see a report of how these genes
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are affected in the study
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The favourite controls have an option to create a new list of entities
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from scratch. This allows a user, for instance, to make a list with her
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genes of interest instead of having to browse the application to find
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it. *Note:* New lists are not made favourite be default, you still need to
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click on the star once the report is shown.
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.images
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%dl.tabs.active.show
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%dt.next.show Snapshot
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%dd.show
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%img(src="/img/UI/favourites.png")
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%dt.next Explanation
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%dd
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%img(src="/img/UI/favourites_wire.png")
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%dt.next Actions
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%dd
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.description
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:markdown
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Actions are the primary way to integrate data and functionalities.
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Some actions are defined globally, but most commonly they are defined
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inside workflows; when a report is produced, all workflows are
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interrogated to see if they provide actions for it. The great majority
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of the actions are defined in the `Genomics` workflow.
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When an action is selected, it loads bellow the action controller. An
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action report consists of the content of the action, and optionally,
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parameter controls and an action description. When the action is loaded
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inside a report the parameter controls and description are hidden, but
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they can be shown using the action control buttons in the top left.
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Actions can also be opened in their own report by right clicking on its
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button.
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As with all reports, they are executed the first time they are
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requested and the result is cached for further access. The action
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control buttons can be used to reload the action, just like the reload
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button in the top-bar does for the complete report. The actions will
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of-course be recomputed for each configuration of parameters. The
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parameters of the action can be favourites from the user, lists or
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maps. These are presented to the user using an input `select`, and are
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synchronized with the user current favourites.
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If an action is used often with a particular combination of parameters.
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For instance the "Enrichment" action of gene lists performs an
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over-representation based analysis of functional classes. The
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functional classes include several pathway databases, protein domains,
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gene ages, etc. If we where interesting in performing enrichment
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analysis using GO biological process terms, we can use the paperclip
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button to set that configuration of parameters as default so that it
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always uses it initially.
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Some actions may require a significant amount of time to compute. The
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action controller tries to reload the action periodically until it is
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completed. Instead of having to wait on that page for it to finish, the
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user can click on the bookmark button, which will place a link in the
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"jobs" tab on the "Extra" menu of the top-bar, and come back to it
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later.
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.images
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%dl.tabs.active.show
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%dt.next.show.active Action Snapshot
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%dd.show
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%img(src="/img/UI/actions.png")
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%dt.next Action Explanation
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%dd
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%img(src="/img/UI/actions_wire.png")
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%dt.next Controller Snapshot
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%dd
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%img(src="/img/UI/action_control.png")
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%dt.next Controller Explanation
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%dd
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%img(src="/img/UI/action_control_wire.png")
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+
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+
|
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%dt.next Tables
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+
%dd
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.description
|
183
|
+
:markdown
|
184
|
+
|
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|
+
Tables in this application come enhanced with several functionalities.
|
186
|
+
The rows can be sort by the values of any column.
|
187
|
+
|
188
|
+
The values of the columns can also be used to filter the rows of the
|
189
|
+
table through the `filter` button. The filters are defined per-column,
|
190
|
+
and can contain exact strings, regular expressions like
|
191
|
+
`/(COMPLETE|PARTIAL) RESPONSE/i`, statements such as `> \< ==` or `!=`.
|
192
|
+
And, for columns containing entities they can be prefixed with the term
|
193
|
+
`name:` to force the filtering to work over the human readible text of
|
194
|
+
the entities e.g. `name:/SF3B\d+/` for a column containing 'Ensembl
|
195
|
+
Gene ID'.
|
196
|
+
|
197
|
+
When a column contains entities, these are usualy listed in the table using
|
198
|
+
some identifier like 'Ensembl Gene ID' for genes or 'GO Term IDs', etc. When
|
199
|
+
displaying the table, it automatically substitutes these identifiers with
|
200
|
+
links to their corresponding reports, and lists them by name. Additionally
|
201
|
+
the `column` button allows the user to report the list of entities of any column
|
202
|
+
or, if the first column is itselve an entity, it allows the user to report
|
203
|
+
the `map` between the entities in this column and the values of any other column.
|
204
|
+
Maps are generally used as inputs to actions and tools.
|
205
|
+
|
206
|
+
The content of the table can be downloaded in two forms, as TSV files,
|
207
|
+
which is the original source of the table, or as Excel files. When
|
208
|
+
downloding as Excel files, since are generally intended to be read by
|
209
|
+
people, all entities listed that can be translated to a more human
|
210
|
+
readible identifier are translated automatically. This includes change
|
211
|
+
genes identifiers from `Ensembl Gene ID` to `Associated Gene Name`, or
|
212
|
+
changing KEGG pathway ids to their descriptive name.
|
213
|
+
|
214
|
+
.images
|
215
|
+
%img(src="/img/UI/table.png")
|
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|
+
|
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|
+
|
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|
+
%dt.next Tools
|
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|
+
%dd
|
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|
+
.description
|
221
|
+
:markdown
|
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|
+
|
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|
+
Some workflows implement `tools`, which provide special interactive
|
224
|
+
visualization for different types of data. For instance: the `Graph`
|
225
|
+
workflow implements the `cytoscape` tool, which is used to display
|
226
|
+
different kinds of entities connected through databases or analitical
|
227
|
+
results; the `Structure` `jmol` tool displays mutations in the
|
228
|
+
secondary and tertiary structures and complexes; and the `D3Js`
|
229
|
+
workflow that implements a tool to display `d3js` interactive SVG
|
230
|
+
figures. Alternative R is used through a native interface in Rbbt to
|
231
|
+
display plots using `ggplot2`.
|
232
|
+
|
233
|
+
These tools are used by different reports and actions. The `Graph`
|
234
|
+
workflow for instance redefines the template for `Gene` lists to
|
235
|
+
include a cytoscape plot to the description section of the report.
|
236
|
+
|
237
|
+
|
238
|
+
.images
|
239
|
+
%dl.tabs.active.show
|
240
|
+
%dt.next.show Cytoscape
|
241
|
+
%dd.show
|
242
|
+
%img(src="/img/UI/cytoscape.png")
|
243
|
+
|
244
|
+
%dt.next Jmol
|
245
|
+
%dd
|
246
|
+
%img(src="/img/UI/jmol.png")
|
247
|
+
|
248
|
+
%dt.next D3Js
|
249
|
+
%dd
|
250
|
+
%img(src="/img/UI/d3js.png")
|
Binary file
|
Binary file
|
Binary file
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: rbbt-rest
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 1.2.
|
4
|
+
version: 1.2.35
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2013-12-
|
11
|
+
date: 2013-12-20 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rake
|
@@ -255,6 +255,7 @@ files:
|
|
255
255
|
- share/views/error.haml
|
256
256
|
- share/views/form.haml
|
257
257
|
- share/views/help.haml
|
258
|
+
- share/views/help/UI.haml
|
258
259
|
- share/views/help/entity.haml
|
259
260
|
- share/views/help/workflow.haml
|
260
261
|
- share/views/job_info.haml
|
@@ -284,6 +285,20 @@ files:
|
|
284
285
|
- share/views/partials/table/filters.haml
|
285
286
|
- share/views/partials/table/page.haml
|
286
287
|
- share/views/public/favicon.gif
|
288
|
+
- share/views/public/img/UI/action_control.png
|
289
|
+
- share/views/public/img/UI/action_control_wire.png
|
290
|
+
- share/views/public/img/UI/actions.png
|
291
|
+
- share/views/public/img/UI/actions_wire.png
|
292
|
+
- share/views/public/img/UI/cytoscape.png
|
293
|
+
- share/views/public/img/UI/d3js.png
|
294
|
+
- share/views/public/img/UI/favourites.png
|
295
|
+
- share/views/public/img/UI/favourites_wire.png
|
296
|
+
- share/views/public/img/UI/jmol.png
|
297
|
+
- share/views/public/img/UI/report.png
|
298
|
+
- share/views/public/img/UI/report_wire.png
|
299
|
+
- share/views/public/img/UI/table.png
|
300
|
+
- share/views/public/img/UI/topbar.png
|
301
|
+
- share/views/public/img/UI/topbar_wire.png
|
287
302
|
- share/views/public/js/_ajax_replace.js
|
288
303
|
- share/views/public/js/_ellipsis.js
|
289
304
|
- share/views/public/js/_md5.js
|