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ucsdlib / damsmanager

DAMS Manager
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Remove 6 components from CCR2 object #319

Closed hjsyoo closed 5 years ago

hjsyoo commented 5 years ago

Descriptive summary

The following components (metadata and files) should be removed from https://library.ucsd.edu/dc/object/bb3963059d.

  1. Jupyter notebook for identifying and extracting the apo clusters (component 10)
  2. Jupyter notebook for identifying and extracting the holo clusters (component 11)
  3. Jupyter notebook for SASA calculations, distances analyses, and chi angle calculations (component 15)
  4. Jupyter notebook for RMSF analysis (component 16)
  5. Jupyter notebook for water analysis (component 17)
  6. Jupyter notebook for sodium analysis (component 18)

Related work

Link to related tickets or prior related work here.

gamontoya commented 5 years ago

@lsitu Do you have the bandwidth to do this?

lsitu commented 5 years ago

@gamontoya Sure. I'll work on it.

lsitu commented 5 years ago

@gamontoya / @hjsyoo I think we may have to restructure the component orders and re-ingest the files with component index larger that 12. Where can I find the source files for the object? Thanks.

hjsyoo commented 5 years ago

@lsitu They're here: Metadata file location: //rdcp-staging/rdcp-0141-ccr2-landscape/Final_Metadata/ Content files location: //rdcp-staging/rdcp-0141-ccr2-landscape/Final_Files/ Final_Files still contains the component files that should be removed from prod. Let me know if any of it is unclear. Thanks!

lsitu commented 5 years ago

@hjsyoo It looks like there are some files in //rdcp-staging/rdcp-0141-ccr2-landscape/file_replace, which were ingested for the object. Should I use those files as well?

lsitu commented 5 years ago

Also, I can't find file ccr2_apo_123_aligned_nopopc.dcd and ccr2_holo_234_aligned_nopopc.dcd in both locations.

lsitu commented 5 years ago

Never mind, I found both file ccr2_apo_123_aligned_nopopc.dcd and ccr2_holo_234_aligned_nopopc.dcd in sub-directory.

hjsyoo commented 5 years ago

@lsitu I’ve already moved the two files needed from file_replace into Final_Files, so please don’t use that folder. The remaining files in file replace are old versions.

lsitu commented 5 years ago

It looks like files placeholder_text_conda_environment.yml and placeholder_text_pip_environment.txt that we need are still in the file_replace folder.

hjsyoo commented 5 years ago

No, those were placeholders that we put in temporarily, until the researcher confirmed that the originals were correct. So the files we should use are the ones indicated in the OLR. The OLR is correct with respect to filenames, except for the 6 components that should be removed.

Sorry @lsitu, just realized that this ticket I created today (but am still spec'ing for DOMM) would help clear up the issue I just described. https://github.com/ucsdlib/dams-metadata/issues/120. If you use the correct files in \Final_Files, I won't really need that other ticket.

lsitu commented 5 years ago

@hjsyoo Okay, I'll use those two files in ucsdlib/dams-metadata#120. Yes, you don't need ticketucsdlib/dams-metadata#120 since I have to re-ingest those two files.

lsitu commented 5 years ago

@gamontoya / @hjsyoo I've deleted all components and files above and restructure those components with index larger than 12. Those files attached to the components restructured are also re-ingested. I think the restructured object https://library.ucsd.edu/dc/object/bb3963059d is ready for review now.

hjsyoo commented 5 years ago

@lsitu Thank you! Looks great.