Data manager : HPA resources and "Get expression profiles" -> file not found

[yvandenb]

History shared with David

Get Expression profiles" tool  - selection of "HPA normal tissue 03/02/2020" version -> 
Error in read_file(args$ref_file, TRUE) : File not found !
Calls: main -> read_file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '/home/proteore/shed_tools/toolshed.g2.bx.psu.edu/repos/proteore/proteore_expression_levels_by_tissue/56c93d1fc8fd/proteore_expression_levels_by_tissue/tool-data/HPA_normal_tissue_03-02-2020.tsv': No such file or directory
Execution halted

As the file was not found, I updated this HPA file using the data manager, now OK - don't know why the previous release file is not found ? this one (i.e. 03/02/2020 version) should now be removed

[yvandenb]

another bug identified (by galaxy-p team); https://docs.google.com/document/d/1N_cgQAmrF5PobjWalr7Qz-aM8qr2p0WVZ-OeZXdk-m0/edit?usp=sharing using "Add expression data" tool and selecting "HPA full atlas 2020" as HPA source file version, the "gene description" is not returned in the output file even if selected ? of note, this is not the case when using the "HPA full Atlas 2018" source file

[davidchristiany]

This bug has already been fixed in the last version of "add expression data" tool: 2020.04.06 In the shared history (google doc) this is the previous version used: 2020.01.24 Maybe we should remove it from proteore.org

[yvandenb]

Maybe we should remove it from proteore.org

Yes for sure, yet this version is not visible anymore from my proteore.org interface, neither the latest ?? What's going on ?

[davidchristiany]

I don't know I'm on it, I didn't remove anything, just updated the list.

Edit: This is the same problem we talk about, it has been removed from the data table, I don't know how or why

[davidchristiany]

@yvandenb Can you tell me which source file is missing on Add expression data and get expression profile please ? I will put it back manually.

[yvandenb]

What about doing this myself by using the data manager ? btw the file name is "full protein Atlas", the version I updated should be in May (see my first post above)

[davidchristiany]

You can use the data manager, but try one by one and refresh the corresponding data table (admin) to see if something happen.

btw the file name is "full protein Atlas"

For add expression data ?

[yvandenb]

logged as admin; updating "Full Atlas" file using the data manager (via admin interface)...what I see in the "Add_expression_data" GUI

[yvandenb]

now logged as "yvdb" running again "Add expression data" with the new HPA file version (04/06/2020) => all features (fields)requested are there :-)