Changes in version 1.1.10                        

Changes made from 1.1.0 to 1.1.10

2020.11.24

Workflow module R session

  - Now workflow module R session uses a background child R process,
    which runs independently to the parent R session which runs shiny.
  - So the shiny will be not blocked while code is running in the
    background (you can still click other buttons when the child session
    is busy) -- synchronous and non-blocking. A child indicator is also
    placed in the UI, updates every second.
  - The UI design of R session is similar to Rstudio. Four panels,
    source code, console, log (specific to SPR), and plots.
  - Standard out/error and plots are captured in the workflow folder.
    Users can download them in the bundle on step 5 Workflow Run.
  - Plots will be displayed on the plots panel. Now supports plots that
    opens R device (base and ggplot), html widget plots are not
    supported as this moment.

General UI

  - A new shiny disconnection popup for SPS. Besides the gray layer on
    shiny disconnection, a panel will be displayed to users to indicate
    the problem. Similar to what shows on a shiny server, but more
    informative and also works locally.

RNAseq module

  - redesigned the UI and server logic. Plots for DEG analysis and
    Canvas connections will be added soon.

2020.10.30

General UI

  - Added a "Go Top" button on the right bottom corner, clicking on this
    button will automatically scroll to the top of the page. This button
    only shows up when client has > 50px scroll height.

2020.10.30

Workflow module CWL tab

  - Now the CWL file and CWL input file can be be edited. The edits will
    be imported to CWL parser every one second. Now this is a very
    useful place to test or write new CWL scripts.

2020.10.27

Workflow module CWL tab

  - Now this tab has a dynamically rendered dropdown panel which allows
    users to choose which column for the targets table to map to the
    variables in CWL input file.

2020.10.27

Workflow module fully functioning

  - Now you can run a full example workflow in SPS by choosing the
    "Example" option on workflow setup step.

  - Other systemPipeR preconfiged workflows will cause problems because
    formatting issues that will cause errors in systemPipeR::runWF
    function, not introduced by SPS. Please wait the updates on
    systemPipeR to fix this. You can still use SPS to prepare files for
    all workflows. That means, step 1-4 will work, step 5 will give you
    errors if you choose a workflow which is not "Example".

2020.10.22

Rework on the workflow part

  - All 3 tabs merged into the main tab

  - changed config tab to CWL tab

  - added support for the running wf as a sub tab

  - Now the main tab has 5 subtabs, they are all connected.

  - Better guidelines for users, step-like usage, can't reach other
    steps if a previous step is not completed.

  - Original snapshot management drop down page changed to running
    workflow session. This session will lock users to a unique page,
    they can't interactive other app parts on the page(working directory
    changed), to prevent app crash due to wd change.

Other changes

  - A new UI component spsTimeline : horizontal timeline UI unit, has
    status, can be updated on server by updateSpsTimeline.

  - A new UI bsHoverPopover: enhanced high level function of
    bsPlus::HoverPopover, additional JS used to make the popover work on
    buttons as well.

  - Fixed some link problems in renderDesc. Better links in renderDesc,
    enlarged and spacing animation for links.

  - Change on about page
    
      - The news is now rendered on about tab in the app
    
      - reduced developer content on about page.
    
      - changed developer emails to github links.

2020.10.09

Change on visualization

  - RNAseq part is now only in one tab as big module: users upload the
    targets file and a raw count table, and make different plots in
    subtabs.
    
      - This introduced a lot of dependencies, will decide later if we
        keep as it is or separate it to spsBio.