NEWS.md

In systemPipeShiny: systemPipeShiny: An Interactive Framework for Workflow Management and Visualization

systemPipeShiny 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.

systemPipeShiny documentation built on March 16, 2021, 6:01 p.m.