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Sage-Bionetworks / projectLive_NF

Live view of projects of funding partners
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Resolve issue 34 #76

Closed andrewelamb closed 4 years ago

allaway commented 4 years ago

Hey Andrew,

I think your understanding is correct, but Jineta wants to first test the changes by modifying the rds file instead of the Portal fileview to avoid inadvertently breaking annotations on the portal.

On Wed, Sep 2, 2020 at 7:37 AM andrewelamb notifications@github.com wrote:

@andrewelamb commented on this pull request.

In R/mod_new_submissions.R https://github.com/jaybee84/projectLive/pull/76#discussion_r482120423:

  • "new_files_table"
  • )
  • minimum_date <-
  • lubridate::now() -
  • lubridate::ddays(input$new_files_day_choice)
  • files_table <- group_object() %>%
  • purrr::pluck("files_table") %>%
  • dplyr::filter(!!rlang::sym(param_list$filter_column) > minimum_date) %>%
  • dplyr::arrange(!!rlang::sym(param_list$filter_column))
  • studies_table <- group_object() %>%
  • purrr::pluck("studies_table")
  • data1 <- files_table %>%

@jaybee84 https://github.com/jaybee84 @allaway https://github.com/allaway

Once again I may not be grasping something about portals. In my opinion if you need to have fundingAgency in every synapse table, in cases where they are inconsistent(like the files that that are unannotated), wouldn't the solution be to fix those in the synapse table? Presumably if you are using them in the portal, they should be correct there right? Then when we create the rds files from the sunapse table it would be correct also.

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jaybee84 commented 4 years ago

I think all of us agree any script adding annotations to files upstream should update the source synapse table and should run before making the RDS files for this app.

So in the small commit added yesterday, the line added is meant to catch any files that fell through the cracks. There have been use cases before where the Sage team was not notified of additions of unannotated files and so we did not know where to find files to update annotations. The new_submissions module can help act as an internal tracker for Sage folks for any files of this kind.

I imagine once the upstream annotation script is in place and is running regularly, the line added yesterday would become obsolete. But until then this can help us track down unannotated files that are existing today.