Metadata inconsistency in field `thumbnail_file_abs_path`

[icaoberg]

There is a field named thumbnail_file_abs_path in the metadata model that is a child of ingest_metadata. This field used to be created during ingestion.

• Issue. The full path is incorrect. The path in entity.thumbnail_file_abs_path should be changed with the values in files. (See table below.)

• Solution. Replace the values in entity.thumbnail_file_abs_path with the values in files. (See table below.)

+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
|     | hubmap_id       | status    | is_protected   | data_type   | assay_category   | entity.thumbnail_file_abs_path                                                                    | files                                                                                         |
+=====+=================+===========+================+=============+==================+===================================================================================================+===============================================================================================+
|   2 | HBM882.DMQM.597 | Published | False          | AF          | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/5eb7d04d71566c53dfc9eb1c7346c68d/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/5eb7d04d71566c53dfc9eb1c7346c68d/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
|   3 | HBM298.JRGF.528 | Published | False          | AF          | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/f54b458ca42f7112d0e0751c9ba41492/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/f54b458ca42f7112d0e0751c9ba41492/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
|   5 | HBM535.QCJS.935 | Published | False          | AF          | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/57299edf509b218aa9b4c4a2e1d979bd/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/57299edf509b218aa9b4c4a2e1d979bd/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
|   6 | HBM969.JXDC.887 | Published | False          | AF          | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/6a037ddcb811f77f726b9f78e5d369a2/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/6a037ddcb811f77f726b9f78e5d369a2/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
|   9 | HBM475.ZQFV.863 | Published | False          | AF          | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/3f42c9ebe348f7aca2419ce95f40ab79/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/3f42c9ebe348f7aca2419ce95f40ab79/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
|  12 | HBM953.NRFF.685 | Published | False          | AF          | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/d3e05111d84be552b98f5fe2b18e3054/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/d3e05111d84be552b98f5fe2b18e3054/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
|  13 | HBM887.KLQQ.878 | Published | False          | AF          | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/b529b1c59c2b8aa232105d3f8fe31c35/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/b529b1c59c2b8aa232105d3f8fe31c35/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
|  16 | HBM447.NXPZ.263 | Published | False          | AF          | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/2bc6713576dda7c7e6378aec38df437d/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/2bc6713576dda7c7e6378aec38df437d/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
|  24 | HBM284.PMDZ.547 | Published | False          | AF          | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/4c04a73e87f0b5deb00d88d4cb20095d/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/4c04a73e87f0b5deb00d88d4cb20095d/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
|  25 | HBM287.DWFS.254 | Published | False          | AF          | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/7ede2efa49ae0dc50c9cb8afb276ebe4/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/7ede2efa49ae0dc50c9cb8afb276ebe4/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
|  27 | HBM372.RSXT.622 | Published | False          | AF          | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/1accbd367bac01690a733c77460371a7/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/1accbd367bac01690a733c77460371a7/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
|  28 | HBM644.MDVT.295 | Published | False          | AF          | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/7aa0816fc26641fb86fe9a2e89a22625/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/7aa0816fc26641fb86fe9a2e89a22625/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
|  31 | HBM974.JDVS.328 | Published | False          | AF          | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/379ec1e6f7f0633a62997136db2854a7/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/379ec1e6f7f0633a62997136db2854a7/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
|  32 | HBM632.MXJF.562 | Published | False          | AF          | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/38ba22b0a2bdace0d0dd7504cbe15aae/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/38ba22b0a2bdace0d0dd7504cbe15aae/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
| 373 | HBM325.RVSR.229 | Published | False          | PAS         | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/0d1f7b2917325a7778ffecacb7ddba6f/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/0d1f7b2917325a7778ffecacb7ddba6f/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
| 374 | HBM324.MKTZ.248 | Published | False          | PAS         | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/8da53b8ece9625d5a5c00f8555f67d31/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/8da53b8ece9625d5a5c00f8555f67d31/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
| 375 | HBM836.VTFP.364 | Published | False          | PAS         | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/664b8227e17ee2a35a504dd8c19c2531/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/664b8227e17ee2a35a504dd8c19c2531/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
| 381 | HBM484.RDZR.494 | Published | False          | PAS         | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/36c3a6eb7a731478caee82c14d2cbe2a/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/36c3a6eb7a731478caee82c14d2cbe2a/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
| 386 | HBM528.QSDN.323 | Published | False          | PAS         | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/4c810d998f5c336f0a848170ea58cbd9/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/4c810d998f5c336f0a848170ea58cbd9/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
| 387 | HBM635.BSPV.599 | Published | False          | PAS         | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/c1216834ff5b1e981998cf8aec809a44/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/c1216834ff5b1e981998cf8aec809a44/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
| 391 | HBM892.SQNT.843 | Published | False          | PAS         | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/dbe61e60497b81fd8e9f4c8ec0f0391d/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/dbe61e60497b81fd8e9f4c8ec0f0391d/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
| 393 | HBM655.VSLD.867 | Published | False          | PAS         | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/c8387452cb4f64896339eef69eef342b/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/c8387452cb4f64896339eef69eef342b/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
| 394 | HBM623.BNWW.574 | Published | False          | PAS         | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/3b32eb6790f1c60004119b84c86b2120/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/3b32eb6790f1c60004119b84c86b2120/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
| 395 | HBM872.HWNB.835 | Published | False          | PAS         | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/37d962aafc47832300d1c863c70608ec/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/37d962aafc47832300d1c863c70608ec/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
| 398 | HBM937.TDGJ.774 | Published | False          | PAS         | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/aa198c566a3ee9ad703d66685cf65a63/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/aa198c566a3ee9ad703d66685cf65a63/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
| 400 | HBM685.HZFG.838 | Published | False          | PAS         | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/d55e751748bd094ff5b0b55befb08d41/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/d55e751748bd094ff5b0b55befb08d41/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
| 406 | HBM428.QSKJ.486 | Published | False          | PAS         | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/2758f0523316876db1e63fc1d2c51d1b/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/2758f0523316876db1e63fc1d2c51d1b/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
| 407 | HBM969.MLWK.466 | Published | False          | PAS         | imaging          | /hive/hubmap/data/consortium/Vanderbilt TMC/07317dfade92994d6fbbe9faef1236f7/extras/thumbnail.jpg | [PosixPath('/hive/hubmap/data/public/07317dfade92994d6fbbe9faef1236f7/extras/thumbnail.jpg')] |
+-----+-----------------+-----------+----------------+-------------+------------------+---------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+

[icaoberg]

Other issues that need to be addressed

• This field is not present in every published dataset. Should it?
• Should a thumbnail file exist for every published imaging dataset? Is this something that we should generate?
• Is this file used in the portal? If not, what is used in the portal?

cc @pdblood