Fix manual file upload and improve FLASHTnT parsing - #97
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Uploading result files in the "Manual Result Upload" tab crashed with
AttributeError: 'UploadedFile' object has no attribute 'suffix'
FileManager.store_file derived the stored file name from `file.suffix`,
which only exists on Path inputs - Streamlit's UploadedFile is a BytesIO
subclass that carries the original file name in `name`.
Two things kept the tab from working once past the crash:
- The dataset id was the part of the file name in front of the known
suffix. FLASHDeconv names its results `out_deconv.mzML` and
`anno_annotated.mzML`, so the two halves of one run were filed under the
datasets "out" and "anno" and never parsed together. Files with the
unchanged tool output names now go to a common dataset, renamed files
(`sample_deconv.mzML`) keep their experiment name as before.
- parseDeconv was called by its pre-refactor signature
(`parseDeconv(**results)`); it writes into the FileManager itself and
needs it plus the dataset id and a logger.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01RAyRJPFo13Xn4w8b4B8ju6
The FLASHTnT tab had the same three problems as the FLASHDeconv one: storing an UploadedFile crashed in FileManager.store_file (fixed in the previous commit), the dataset id was the part of the file name in front of the known suffix, and the parsers were called by a signature that no longer exists. FLASHDeconv and FLASHTnT name their results 'out_deconv.mzML', 'anno_annotated.mzML', 'tags.tsv' and 'protein.tsv', so the files of one run were filed under the datasets "out", "anno" and (for the tsv files) not at all - the tab only matched '*_tagged.tsv' and '*_protein.tsv', which FLASHTnT never writes. Files with the unchanged output names now go to a common dataset and 'tags.tsv' is accepted next to the previously expected '*_tagged.tsv'; renamed files keep their experiment name. parseTnT no longer returns dataframes, it writes into the FileManager and needs it plus the dataset id and a logger, and it reads the deconvolution tolerance - so, as in Workflow.execution(), parseDeconv runs first unless the dataset was deconvolved before. Incomplete uploads are reported instead of raising a KeyError. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01RAyRJPFo13Xn4w8b4B8ju6
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Summary
Fixes a critical bug in manual result upload that prevented Streamlit
UploadedFileobjects from being stored, and refactors the upload workflows to handle tool-generated file names correctly. Also improves FLASHTnT to parse deconvolution data before tag matching.Key Changes
FileManager fix (src/workflow/FileManager.py)
FileManager.store_file()now handles file-like objects (Streamlit'sUploadedFile) that lack asuffixattribute by falling back to extracting the extension from thenameattributeAttributeError: 'UploadedFile' object has no attribute 'suffix'FLASHDeconv upload workflow (content/FLASHDeconv/FLASHDeconvWorkflow.py)
process_uploaded_files()to use a declarativeUPLOAD_FILE_TYPEStuple mapping file suffixes to name tags and tool prefixesdefault_dataset(timestamped) to group files with tool-generated names (out_deconv.mzML,anno_annotated.mzML) that would otherwise split into separate datasetsFLASHTnT upload workflow (content/FLASHTnT/FLASHTnTWorkflow.py)
UPLOAD_FILE_TYPESanddefault_dataset_tagged.tsvfile name (maps totags_tsv)parseDeconv()beforeparseTnT()to ensure deconvolution data is available for tag matchingpartial=Truetoget_results()calls to allow processing with incomplete file setsdeconv_mzML,anno_annotated_mzML,tags_tsv,protein_tsv) before processingTest coverage (tests/test_manual_upload.py)
UploadedFileobjectsPathinputImplementation Details
UPLOAD_FILE_TYPEStuples are defined locally in each workflow page (cannot be imported without Streamlit runtime) and reproduced in tests as literalsexperiment = file.name[:-len(suffix)].rstrip('_')extracts the experiment name, then falls back todefault_datasetif the result is empty or matches the tool prefixdefault_datasetusestime.strftime('uploaded_%Y%m%d-%H%M%S')to create unique, human-readable dataset names for ungrouped uploadshttps://claude.ai/code/session_01RAyRJPFo13Xn4w8b4B8ju6