Normalise malformed / non-canonical SDRF column headers

[BioGeek]

SDRF column names are space- and case-sensitive (per the spec: "The SDRF is sensitive to spaces in column names (sourcename ≠ source name)… must NOT have a space before the bracket"). A header that deviates from the canonical name is therefore a different, unrecognised column. parse_sdrf validate-sdrf and downstream parsers silently skip it, so the data in that column is dropped even though the file still "validates" (all affected files here pass validation today, before and after the fix, the defect is invisible to the validator).

This PR fixes four header defects across 18 files. The first three are header-row-only renames (no data cells changed); the fourth drops a redundant duplicate column from one file.

Fixes

1. Trailing space inside the bracket in comment[modification parameters ]

datasets/PXD017710/PXD017710-silac.sdrf.tsv has three columns named comment[modification parameters ] (note the space before ]) alongside one correct comment[modification parameters]. Fixed to four clean comment[modification parameters] columns (repeated modification-parameters columns are valid SDRF, one per SILAC mod).

2. Pandas de-duplication suffix: comment[modification parameters].1

datasets/PXD071075/PXD071075.sdrf.tsv has comment[modification parameters].1 (the .1 is a pandas artifact from reading a file with duplicate column names and writing it back). Fixed to comment[modification parameters] (→ two valid repeated columns).

3. Non-canonical synonym: comment[ms2 analyzer type] → comment[ms2 mass analyzer]

15 files use comment[ms2 analyzer type] (one as comment[MS2 analyzer type]) for the concept the spec/sdrf-pipelines template calls comment[ms2 mass analyzer] (description: "Mass analyzer used for MS2 acquisition"). The values are identical in kind (NT=Orbitrap;AC=MS:1000484, NT=linear ion trap;AC=MS:1000291), so these rows are simply invisible under a name no tool looks for. Renamed to the canonical column. (No file contained both columns, so there are no collisions.)

4. Duplicate typo'd column dropped: comment[technical replcate]

datasets/PXD018241/PXD018241.sdrf.tsv carried both comment[technical replcate] (typo) and the correct comment[technical replicate]. Their values are identical (all 1 across the 20 rows), so the typo'd column is a redundant duplicate so I dropped it (31 → 30 columns). This is the one file where data rows change (a whole column is removed). It re-validates cleanly.

18 files changed

# comment[modification parameters ] / .1  -> comment[modification parameters]
datasets/PXD017710/PXD017710-silac.sdrf.tsv
datasets/PXD071075/PXD071075.sdrf.tsv

# comment[technical replcate] duplicate column dropped
datasets/PXD018241/PXD018241.sdrf.tsv

# comment[ms2 analyzer type] (or MS2) -> comment[ms2 mass analyzer]
datasets/PXD000534/PXD000534.sdrf.tsv
datasets/PXD000895/PXD000895.sdrf.tsv
datasets/PXD000999/PXD000999.sdrf.tsv
datasets/PXD001061/PXD001061.sdrf.tsv
datasets/PXD002171/PXD002171.sdrf.tsv
datasets/PXD004613/PXD004613.sdrf.tsv
datasets/PXD005507/PXD005507.sdrf.tsv
datasets/PXD011175/PXD011175.sdrf.tsv
datasets/PXD012593/PXD012593-srm.sdrf.tsv
datasets/PXD014565/PXD014565.sdrf.tsv
datasets/PXD015744/PXD015744.sdrf.tsv
datasets/PXD017035/PXD017035.sdrf.tsv
datasets/PXD018970/PXD018970.sdrf.tsv
datasets/PXD019123/PXD019123.sdrf.tsv
datasets/PXD023650/PXD023650.sdrf.tsv

Verification

• The 17 header renames are confined to the header row (git diff --numstat → 1 / 1 per file; no data row touched); PXD018241 (the dropped column) changes every row by design.
• All 18 files re-validate with parse_sdrf validate-sdrf --sdrf_file <f> --use_ols_cache_only: no new errors (same as before the change).

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Important

Review skipped

Review was skipped due to path filters

⛔ Files ignored due to path filters (18)

• datasets/PXD000534/PXD000534.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD000895/PXD000895.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD000999/PXD000999.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD001061/PXD001061.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD002171/PXD002171.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD004613/PXD004613.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD005507/PXD005507.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD011175/PXD011175.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD012593/PXD012593-srm.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD014565/PXD014565.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD015744/PXD015744.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD017035/PXD017035.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD017710/PXD017710-silac.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD018241/PXD018241.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD018970/PXD018970.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD019123/PXD019123.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD023650/PXD023650.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD071075/PXD071075.sdrf.tsv is excluded by !**/*.tsv

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[nithujohn]

Thank you for fixing it :)