Upload Errors:
TSV Errors:
examples/dataset-examples/bad-tsv-formats/upload/codex-metadata.tsv, column 'contributors_path', value 'contributors.tsv':
- 'File has no data rows: examples/dataset-examples/bad-tsv-formats/upload/contributors.tsv.'
examples/dataset-examples/bad-tsv-formats/upload/codex-metadata.tsv, column 'antibodies_path', value 'antibodies.tsv':
- 'File does not exist: examples/dataset-examples/bad-tsv-formats/upload/antibodies.tsv.'
Directory Errors:
examples/dataset-examples/bad-tsv-formats/upload/codex-metadata.tsv, column 'data_path', value 'dataset-1/':
examples/dataset-examples/bad-tsv-formats/upload/dataset-1 (as codex-v1-with-dataset-json):
Not allowed:
- channelnames.txt.
- cyc002_reg001_200216_112537/1_00001_Z001_CH1.tif.
- experiment.json.
- exposure_times.txt.
- segmentation.json.
Required but missing:
- (processed|drv_[^/]*)/.*.
- (raw|src_.*)/.*.
- (raw|src_.*)/[cC]yc.*_reg.*/.*_Z.*_CH.*\.tif.
- (raw|src_[^/]*)/dataset\.json.
- extras/dir-schema-v1-with-dataset-json.
Metadata TSV Validation Errors:
Local Validation Errors:
examples/dataset-examples/bad-tsv-formats/upload/codex-metadata.tsv (as codex-v0):
- 'On row 2, column "donor_id", value "not-uuid" fails because it does not match
the expected pattern. Example: ABC123'
- 'On row 2, column "tissue_id", value "not-uuid" fails because it does not match
the expected pattern. Example: ABC123-BL-1-2-3_456'
- On row 2, column "execution_datetime", value "not-time" fails because it is
not in the format YYYY-MM-DD Hour:Minute.
- On row 2, column "protocols_io_doi", value "10\.17504/protocols.io.menc3de"
fails because it does not match the expected pattern.
- 'On row 2, column "analyte_class", value "analyte_class" fails because it is
not one of these: "protein".'
- On row 2, column "is_targeted", value "is_targeted" fails because it is neither
true nor false.
- 'On row 2, column "acquisition_instrument_vendor", value "acquisition_instrument_vendor"
fails because it is not one of these: "Keyence", "Zeiss".'
- 'On row 2, column "acquisition_instrument_model", value "acquisition_instrument_model"
fails because it is not one of these: "BZ-X800", "BZ-X710", "Axio Observer Z1".'
- On row 2, column "resolution_x_value", value "forty-two" fails because it is
not in numerical form.
- 'On row 2, column "resolution_x_unit", value "inches" fails because it is not
one of these: "mm", "um", "nm".'
- On row 2, column "resolution_y_value", value "forty-two" fails because it is
not in numerical form.
- 'On row 2, column "resolution_y_unit", value "inches" fails because it is not
one of these: "mm", "um", "nm".'
- On row 2, column "resolution_z_value", value "forty-two" fails because it is
not in numerical form.
- 'On row 2, column "resolution_z_unit", value "inches" fails because it is not
one of these: "mm", "um", "nm".'
- 'On row 2, column "preparation_instrument_vendor", value "preparation_instrument_vendor"
fails because it is not one of these: "CODEX".'
- 'On row 2, column "preparation_instrument_model", value "preparation_instrument_model"
fails because it is not one of these: "version 1 robot", "prototype robot -
Stanford/Nolan Lab".'
- On row 2, column "number_of_antibodies", value "0.5" fails because it is not
an integer.
- On row 2, column "number_of_channels", value "0.5" fails because it is not an
integer.
- On row 2, column "number_of_cycles", value "0.5" fails because it is not an
integer.
- On row 2, column "section_prep_protocols_io_doi", value "not-doi" fails because
it does not match the expected pattern.
- On row 2, column "reagent_prep_protocols_io_doi", value "not-doi" fails because
it does not match the expected pattern.
Hint: 'If validation fails because of extra whitespace in the TSV, try:
src/cleanup_whitespace.py --tsv_in original.tsv --tsv_out clean.tsv.'