Branch out the milestone reporting functionality for individual studies

[jaybee84]

• facilitate milestone reporting for a funded study
• use cases
• which plots are most helpful
• timeline of milestone
• where should it be hosted
• automated email notification to Sage Curator for annotation check
• If annotation status >> 50%, automated email to studyLead with generated milestone report

[jaybee84]

This is high priority for V2.0 release. So I am adding more details to the issue to properly scope it.

Vision: Study-lead submitted a data sharing plan(DSP) at the beginning of their funding term outlining their milestone deliverables(number of files/samples of certain experiments) and the due dates. When the due dates approach, this module will help the users track the milestone.

The DSPs are tracked here: https://www.synapse.org/#!Synapse:syn23364404/tables/

An example script that has been used for milestone plotting: https://raw.githubusercontent.com/Sage-Bionetworks/nfResources/master/milestoneReports/R/milestoneTools.R

Expected Output: An added section to the Study Summary page named "Milestone Report" with the following :

1. Date of upcoming milestone
2. A plot with 2 bars == expected data, uploaded data (within last 2 months)
3. Annotation status of uploaded data for this milestone
4. A time series plot with expected data and uploaded data for each milestone date.

[jaybee84]

The vision for the plot:

In the Study Summary Page, a study is selected and the following "Milestone Report Box" (containing a bar plot) emerges in addition to the other plots:

1. Top level dropdown list to choose a certain milestone [This milestone number and the associated date of upload is pulled in from Incoming Data Table]
2. For a chosen milestone, use date_of_upload column to make a bar plot with:
   • 1st bar = fileFormats + min_upload_estimate from Incoming Data Table (data expected)
   • 2nd bar = use the date_of_upload as today's date and count files uploaded within "X number of Days (+/-)", bar of count of files for each fileFormat [fill = fileFormat, y-axis = count] (use "New Submissions Module logic to power this)
3. Include a field for user to state the "X number of days" desired for viewing