spreadsheets with missing project/dataset values lead to uninformative errors #24

erickmartins · 2023-09-29T15:35:53Z

the code is just a little redundant. The load_md_from_file() function contains this block of code that drops any rows with an empty filename/project/dataset entry before it even gets to the code in validate_import_md() that would give the verbose error about missing dataset values

if any but not all datasets are missing, it deletes the rows that are missing datasets, and then it wouldn't error because validate_import_md() would get a truncated dataframe and just import the rows with dataset entries and not warn about the ones without

* req updates, generating filelist and running prepare * stub for xml edition * stubs for xml edition functions * checking json columns * adding projects and datasets * adding screens, started work on annotations * sorted out annotation dictionary * annotations added * annotations done (for images) * stubs for plate xml edition * plates annotated and in the right screens * updating dependencies * moving transfer.xml as well * minimal unpack usage * completed unpack command * commenting out import_targets * bumping cli-transfer to 0.7.1 for relative filepaths * using full omero path * bumped cli-transfer * updated readme * using production group * fixing typo * added debug print * debug prints * more debug prints * removing debug prints * debug echo * another debug echo * removing temp files, checking if json exists before using it * removing debug echo * testing if xml exists, new version cli-transfer * making `moved_files.txt` removable * removing dataset duplicates * added echo for deleting temp files * allowing temp files to be deleted * successes should be logged now * lil cleanup * debug print, fixed wrong template issue * using chmod correctly * chmodding to 774 instead * oopsie * removing temp files in the right place * wrong indent * using exists correctly * time to debug plates * debugging the heck out of it * debug debug debug * cleaner debug * one more debug print * debugs * found the culprit * ah, * different error! * still debugging * debugus * ah, again * using new ome-types parameters * flake8 pass * adds helpful messages to solve #24 * removing debug print and adding notes about legacy code * bumping library versions * pinning upper versions of dependencies * checking for datasets in columns as well * removing ambiguous variables in loops

erickmartins added a commit that referenced this issue Oct 10, 2023

adds helpful messages to solve #24

620fd54

erickmartins mentioned this issue Oct 10, 2023

Use cli transfer #25

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spreadsheets with missing project/dataset values lead to uninformative errors #24

spreadsheets with missing project/dataset values lead to uninformative errors #24

erickmartins commented Sep 29, 2023 •

edited

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spreadsheets with missing project/dataset values lead to uninformative errors #24

spreadsheets with missing project/dataset values lead to uninformative errors #24

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erickmartins commented Sep 29, 2023 • edited Loading

erickmartins commented Sep 29, 2023 •

edited

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