[MISC] Add mini entity tables after filename templates#781
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tsalo wants to merge 4 commits intobids-standard:masterfrom
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[MISC] Add mini entity tables after filename templates#781tsalo wants to merge 4 commits intobids-standard:masterfrom
tsalo wants to merge 4 commits intobids-standard:masterfrom
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This also means pointing to the HTML, rather than MD, file.
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One small bug I'm noticing- there are weird rows in some tables (see below for an example) where the datatype is set, but the suffix list (contents of the parens) is empty:
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I've resolved the issue by just skipping parts of the filtered schema where no suffixes are found. This is a hack, but until we have a better schema structure and/or filtering function, I think it's a solid solution. |
sappelhoff
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Apr 27, 2021
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I think it looks nice and helps ... good overview and accessible links 👍
Remi-Gau
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Apr 27, 2021
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Pending any negative feedback or requests for substantive changes, I think we can merge this on Tuesday (May 4). |
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TBH I find it a bit cluttering, but I don't want to stand in the way if others disagree. |
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If you feel that way I suspect some others will too. As this is more a user experience than pure content should I ping the google group and/or neurostars just to get a couple more opinions on this? |
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In response to the ping: looking at HTML version (didn't check PDF) - even though I love the structure, it does look a bit cluttered indeed... It is useful but it seems that edit: extra feature it brings are convenient hyperlinks to each entity such as https://bids-specification--781.org.readthedocs.build/99-appendices/09-entities.html#inv for Also, I wondered, if in HTML version we could simply wrap it into so it would become expandable: Entities table... table HTML goes here |
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I am mostly "nays" on that one, so might be better to close it, no? |
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tsalo
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* [SCHEMA] Add metadata term files (#762) * Draft a handful of metadata term files. * Add example with specific possible values. * Match the validator schemas better. * Fix formatting. * Fix formatting again! * Draft semi-functional rendering functions. * Use unit abbreviations. * Add more fields. * Get macro working. * Add terms from first table. * Add AnatomicalLandmarkCoordinateSystem. * fMRI task information table. * More terms. * More terms. * More terms. * EchoTime and FlipAngle * Add tables. * More tables. * More terms. * More terms. * More terms. * Fix spacing. * Clean things up. * More terms. * More terms! * More terms. * Some iEEG terms. * More iEEG terms. * Add ASL labeling terms. * Next batch. * More terms. * More terms. * More terms. * Fix mistakes. * Last terms. * Reference yamls. * Fix mistakes. * Change format of coordinate system files. * Use degree in associated files. * Some of the missing terms. * A few more terms. * Fix typos. * More terms. * More terms. * More terms. * More terms. * More terms. * More terms. * Last terms. * Fix link. * Fix internal links. * Fix links for real. * Derivative terms. * Fix up code link. * Use backslashes for continued strings. * Replace $ref with file contents. Also support plural datatype strings and all manner of newlines in descriptions. * Fix genetics. * Describe the structure of metadata YAML files. * Make metadatatype function recursive. * Improve search function. * Start adding PET fields. * Add some fields. * More terms. * More terms. * More terms. * Fix mistakes. * More terms. * Replace InstitutionDepartmentName with existing InstitutionalDepartmentName. * More terms. * More terms. * More terms. * More terms. * More terms. * More terms. * More terms. * Last terms. * Add unit format for strings. Unused for now but could be useful later. * Add dataset_relative and participant_relative string formats. * Update READMEs. * Fix formats in README. * Support table-specific metadata description extensions. * Employ description extensions with IntendedFor. * Remove explicit defaults from YAML files. * Replace Minimum with minimum. * Replace inclusiveMaximum with maximum. * Replace implicit links with explicit ones. * Rename key_name to name. * Rename "Unit" to "Units" * Improve make_metadata_table docstring. * Start addressing inconsistencies between rendered and hardcoded tables. * Fix typos in PET metadata From #786. * Add metadata fields from qMRI appendix. * Fix. * Address duplicate datatypes. Should address the "string or string or string or string" issue. * Wrap example strings in code. * Use enum for n/a instead of pattern. It's easier to identify as a special case. * Replace "string" with "n/a" when appropriate. * Address some inconsistencies. * Take a crack as SpatialReference. The type is complicated, but I _think_ I've got it figured out. * Apply suggestions from code review Thanks @effigies! Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu> * Update tools/schemacode/schema.py * search_structure --> dereference_yaml * Use faster loading approach. * Fix deprecation link. * Apply suggestions from code review Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu> * Update 01-magnetic-resonance-imaging-data.md * Add B0FieldIdentifier and B0FieldSource. * Revert type changes and add TODOs to check them. * Update tools/schemacode/schema.py * Replace remaining relative links. * Apply suggestions from code review Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu> * Add new coordinate systems from #775. * Grab hack from #781 (which wasn't merged). * Create HED.yaml * boldify table headers * add device info metadata * fix table fences * fix cell padding * fix cell padding this is getting old VERY quickly * Fix up DICOM tags in metadata. * Leverage "name" field for section-specific metadata definitions. * composite instances --> measurements Changes from #813. * Fix name of HED field. * Fix string formatting in coordinate system fields. * Move "preferably same as" to section-specific text. For #774 (comment) * Standardize DICOM Tag format. Still need to move the references out of the generic definitions. * Move mentions of DICOM Tags out of definitions. Only for fields that *also* appear in modalities that *don't* use DICOM. * Apply suggestions from code review Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org> * Generalize SoftwareFilters example. * Distinguish AnatomicalLandmarkCoordinates definitions. * Rename fmapEchoTime to match new format. * Apply suggestions from code review Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org> * Apply suggestions from code review Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org> * Address review. * Fix example manufacturer names. * TEMPORARY: fix osipi URL (revert when osipi.org is back) * Fix regex for identifying macros. * Partially address review. * Do not assume minItems is 1 for array terms. * composite instances --> measurements (again) * Update src/schema/metadata/MagneticFieldStrength.yaml Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org> * Update description to PharmaceuticalDoseTime #774 (comment) * Update 09-positron-emission-tomography.md * fix table pipe alignment * add pharmaceuticaldosetime fix to schema includes a bugfix to convert "should" (not casing, this was not intended as a SHOULD) to a MUST. * fix str examples * Apply suggestions from code review Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org> * Update src/schema/metadata/RepetitionTimeExcitation.yaml Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org> * Add DoseCalibrationFactor. * Update ScanDate definition and deprecate it. * Remove hardcoded tables. * Remove unused links. * Update tools/schemacode/schema.py Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu> Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu> Co-authored-by: Remi Gau <remi_gau@hotmail.com> Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org> Co-authored-by: mnoergaard <martin.noergaard@nru.dk>
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This implements a proposal of @Remi-Gau's to make it easier for readers to link to relevant entity definitions.
Changes proposed:
MACROS___make_entity_tableafter each call ofMACROS___make_filename_templateto generate a limited entity table for the suffixes/data types in the filename template.