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Changelog

v0.0.30 (in progress)

  • Update Seg Mask documentation

v0.0.29

  • Add CosMX directory schema
  • Update CosMX directory schema
  • Update Segmentation masks directory schema
  • Update Auto-fluorescence directory schema
  • Update CODEX directory schema
  • Update CODEX directory schema

v0.0.28

  • Update Xenium directory schema
  • Update GeoMx NGS directory schema
  • Add CosMX metadata schema

v0.0.27

  • Update Visium with probes directory schema pt 3
  • Update Segmentation masks directory schema
  • Updating tests based on new dir schema major versions and assayclassifier responses
  • Removing references to deprecated Search API endpoint 'assayname'
  • Update Phenocycler directory schema
  • Update GeoMx NGS directory schema
  • Update shared upload check
  • Release Xenium
  • Create Xenium directory schema
  • Error reporting changes, addition of summarized counts
  • Update Segmentation Mask link

v0.0.26

  • Update GeoMx NGS directory schema
  • Update MERFISH directory schema
  • Update LC-MS directory schema
  • Update Visium with probes directory schema
  • Update Visium with probes directory schema pt 2

v0.0.25

  • Update GeoMx NGS directory schema
  • Added EPIC dataset field derived_dataset_type to UNIQUE_FIELDS_MAP

v0.0.24

  • Release MERFISH
  • Add MERFISH directory schema
  • Fix documentation issue for MERFISH
  • Add CEDAR link for MERFISH
  • Update MERFISH directory schema
  • Update Phenocycler docs
  • Update MERFISH directory schema
  • Add next-gen Cell DIVE directory schema
  • Update MIBI directory schema
  • Update Visium no probes directory schema
  • Add Cell DIVE to index
  • Update Segmentation Masks directory schema
  • Update Visium with probes directory schema
  • Update Visium no probes directory schema
  • Update Visium with probes directory schema
  • Update Visium no probes directory schema
  • Change to EntityTypeInfo constraint format to support constraints endpoint

v0.0.23

  • Add token to validation_utils.get_assaytype_data, replace URL string concatenation with urllib

v0.0.22

  • Fix logging length issue in Upload.multi_parent
  • Minor change to Visium with probes directory schema
  • Minor change to Visium no probes directory schema
  • Update docs for Visium directories

v0.0.21

  • Fix the changelog to reflect the current version.
  • Fix row number mismatch between validation and spreadsheet validator response

v0.0.20

  • Fix row number mismatch between validation and spreadsheet validator response

v0.0.19

  • Directory validation changes for "shared" uploads
  • Update Phenocycler directory schema
  • Remove bad paths from LC-MS directory schema
  • Allow multiple comma-separated parent_sample_id values
  • Accommodate dir schema minor versions
  • Fix ORCID URL checking
  • Add MUSIC next-gen directory schema
  • Updating documentation
  • Change Upload error output to dataclass
  • Revert deprecation of field YAML files
  • Update MUSIC directory schema
  • Add semantic version to plugin test base class
  • Fix row number mismatch between validation and spreadsheet validator response
  • Adding entity constraints check
  • Adding ability to report names of successfully run plugins

v0.0.18

  • Update PhenoCycler directory schema
  • Update to prevent standalone child datasets in multi-assay upload
  • Update to prevent multiple dataset types in a non-multi-assay upload
  • Update MIBI directory schema
  • Update Visium (with probes) directory schema
  • Update Auto-fluorescence directory schema
  • Update Confocal directory schema
  • Update Enhanced SRS directory schema
  • Update Light Sheet directory schema
  • Update Second Harmonic Generation directory schema
  • Update Thick Section Multiphoton MxIF directory schema
  • Integrate SenNet app_context
  • Updating testing
  • Change to error messaging related to get_assaytype_data failures
  • Update Lightsheet directory schema
  • Update Histology to include description on OME-TIFFs
  • Update Histology with links
  • Update GeoMx NGS directory schema
  • Ported murine from SenNet
  • Update Histology directory schema
  • Bugfix stripping trailing slash in ingest api url
  • Converted upload _url_checks to use _get_method for SenNet compatibility
  • Add CEDAR template for murine-source
  • Add donor field descriptions back, remove murine-source descriptions
  • Temporarily exclude certain assays from the documentation

v0.0.17

  • Update atacseq cedar link
  • Add Phenocycler next-gen directory schema
  • Update Histology next-gen directory schema
  • Add LC-MS next-gen directory schema
  • Add GeoMx NGS next-gen directory schema
  • Update PhenoCycler and Histology to 2.2.0
  • Update CEDAR links for PhenoCycler & Histology
  • Refactor Upload to avoid validating the same contributors.tsv multiple times / running plugins over files multiple times
  • Add entry for segmentation-mask
  • Modify directory schema validation such that it takes empty directories into account
  • Add Publication next-gen directory schema
  • Update ATAC/RNA/10X documentation
  • Update Cell Dive documentation
  • Update to support passing list of data_paths to ingest-validation-tests plugins
  • Adding linting/formatting GitHub actions

v0.0.16

  • add support for Publication type
  • updated issue templates.
  • removed donor metadata spec (had not been in use)
  • Added examples for fields with pattern constraint
  • Replaced preparation_temperature with preparation_condition and updated associated enumerations in the sample-section, sample-block, and sample-suspension schemas
  • Replaced storage_temperature with storage_method and updated associated enumerations in the sample-section, sample-block, and sample-suspension schemas
  • Updated enum 'bulk RNA' assay type to be 'bulk-RNA' across tools
  • Adding organ v2 schema
  • Added publication docs
  • Removed double publication enum (P/p)
  • Updated publication directory schema 20230616
  • Changes for CEDAR docs
  • Tweaks for CEDAR release
  • Release new assays with links
  • Fix in place to avoid assay conflicts with new assays
  • Rework wording for CEDAR updates
  • Updated upload.py to integrate CEDAR validation, replaced walrus operators, removed unused import
  • Updated CEDAR validation routine based on changes to Spreadsheet Validator
  • Updated tests based on changes to error dict structure
  • Tested both CEDAR and local validation paths
  • Make changes to Histology based on feedback
  • Update documentation based on feedback
  • Addtional changes to Histology
  • Adding SenNet display changes
  • Add contributor TSV CEDAR checking
  • Add CEDAR examples
  • Update CEDAR links for set of assays
  • Split docs into current and deprecated
  • Update Visium CEDAR template link
  • Remove Visium draft attribute
  • Bugfix datetime constraint in library_creation_date.yaml
  • Update LCMS and add NanoSplits
  • Update descriptions for segmentation masks
  • Add description to codex doc page
  • Bail earlier in validation if there are errors in metadata/dir/refs
  • Update Antibodies
  • Remove NanoSplits
  • Update hifi, mibi, imc
  • Fix imc-2d docs
  • Fix imc-2d dir docs
  • Add link to OME-Tiff docs
  • Remove WGS, CE-MS, GC-MS, and RNAseq (GeoMx)
  • Update histology and segmentation mask directory schemas
  • Update hifi-slide to hifi-slides
  • Fix changelog error
  • Fix CI
  • Update MIBI and IMC2D directory schemas
  • Fix to support display of errors for CEDAR template metadata
  • Upate Auto-fluorescence, Confocal, and Light Sheet directory schemas
  • Additional updates to next-gen histology directory schema
  • Implemented soft assay types/assayclassifier endpoint for canonical assay names and dir structures
  • Added mock response test data for offline testing
  • Add more assays
  • Correct Auto-fluorescence lab_processed/annotations path description
  • Add Visium with probes next-gen directory schema
  • Update MALDI, SIMS, DESI, Visium no probes, and HiFi-Slide directory schemas
  • Fix paths in Histology, MIBI, IMC2D, AF, Confocal, Light Sheet, and Visium with probes directory schemas
  • Add CODEX, Thick section Multiphoton MxIF, Second Harmonic Generation, and Enhanced Stimulated Raman Spectroscopy (SRS) next-gen directory schemas
  • Move Thick section Multiphoton MxIF next-gen directory schema to placeholder file
  • Update file path in Visium no probes, Histology, AF, MxIF, SHG, SRS, Confocal, Light Sheet, MALDI, SIMS, DESI
  • Remove Organ CEDAR page
  • Draft next-gen directory schema for SNARE-seq2
  • Added multi-assay support
  • Delete GeoMX
  • Update soft typing to use hyphen, not underscore
  • Add SNARE-seq2 and RNAseq with probes next-gen directory schema
  • Remove the draft tag from SNARE-seq2
  • Regenerate docs for SNARE-seq2

v0.0.15 - 2023-04-04

  • Versioned directory structure schema
  • Added MxIF directory structure schema.
  • Added Lightsheet version 1.
  • bump nokogiri -> 1.13.9 (dependabot)
  • Add front-matter to exclude HCA from toc
  • Updated CODEX version 0 and documentation.
  • Provide an iterator over plugin test classes
  • Updated CODEX version 0.
  • Added Bulk RNA-seq directory structure schema.
  • Added SeqFISH directory structure schema.
  • Add a reminder that TSV validation is not sufficient.
  • Clearer presentation of unit fields in generated docs.
  • Make contributors_path required for HCA.
  • Parallelize tests.
  • Use the assay service to describe how assays are represented in the Portal.
  • Adding Comma Separated File support for tissue_id.
  • Update assay type for Cell DIVE.
  • Updated suspension-fields.yaml and associated files in /docs/sample-suspension.
  • Created extra_parameter on upload for future dynamic adding.
  • Updated ErrorReport class to be backwards compatible with external calls.
  • Added geoMX directory structure schema.
  • Update preparation_maldi_matrix in imaging MS schema to from enum to open string field.
  • Expand file types for stained to not be vendor locked to Leica's .scn. Include vendor-neutral .tiff.
  • Replaced enum Multiplexed Ion Beam Imaging with MIBI in src
  • Added raw as a potential directory to look for segmentation.json file for CODEX.
  • Updated error messages to be less programmer centric.
  • Updated ims-v2 spec to include DESI as an acceptable enumeration for ms_source.
  • Upgraded CI python definition to 3.9.
  • Update Cell DIVE with CEDAR UUID
  • Add Histology directory schemas
  • Fix Histology schema
  • Modify validation routine to support multi-assay schemas
  • Update MALDI, SIMS, and CODEX
  • Update DESI and remove NanoDESI
  • Support for conditional directory validation

v0.0.14 - 2022-06-23

  • bump tzingo -> 1.2.10 (dependabot)
  • Turn validation of enums back on.
  • Mods to plugin validator to fix import problems.
  • Return directory schema version and refactor.
  • Add new data_collection_mode values for MS assays.
  • Add "CODEX2" assay type.
  • Deprecate older LCMS schemas.
  • Updated LC-MS directory structure schema.
  • Remove HTML reporting options.
  • Updated IMS directory structure schema.
  • Add Clinical Imaging schemas.
  • Test under both Python 3.6 and Python 3.10
  • Cosmetic updates to the Slide-seq directory structure schema.
  • Fix rendering bug on CODEX page by adding linebreaks.
  • Add type hints.
  • Implement versioning for directory schemas.
  • After failure, explain how to continue testing from last error.
  • Add pathology_distance_unit in place.
  • Pin transitive dependencies.
  • New sample metadata schemas
  • Darker shade of blue, to be consistent with portal.
  • Dependabot upgrade to Nokogiri.
  • Remove reference to old Travis envvar, so post-merge CI run will pass.
  • Explain the distinction between the 10X kit versions.
  • Updated CODEX directory structure schema.
  • Added MIBI directory structure schema.
  • add snRNAseq-10xGenomics-v3
  • Make backward incompatible changes to ims-v2 in place, without a new version.
  • Preserve the key order in generated YAML, for readability.
  • Add 'Multiplex Ion Beam Imaging' assay name
  • Permanently remove snRNA and scATACseq assay names
  • add snRNAseq-10xGenomics-v2 to the scrnaseq assays
  • Move "Unique to this type" below the acquisition instrument fields.
  • Add CLI option to allow the use of deprecated schemas.
  • Allowing trailing slashes on dataset directories in metadata TSV.
  • Add acquisition instrument fields to MIBI that were left out by mistake.
  • Just use pytest to run doctests
  • Headers are no longer properties of fields.
  • Remove mention of extras/thumbnail.jpg.
  • Add release date to schema.
  • Add UMI fields to scrnaseq schema.
  • Add Excel sheet describing which fields show up in which schemas.
  • Add field descriptions to spreadsheet.
  • Temporarily disable checking the assay names in schemas against the global list. Entries in the global list are now commented out, and Joel will progressively uncomment them.
  • Moved dataset.json to raw or src_* directory for CODEX datasets.
  • Modify IMC docs

v0.0.13 - 2022-01-07

  • Make more fields explicitly numeric
  • Add more donor field descriptions.
  • Deprecate contributors-v0.
  • Add MIBI schema.
  • Add fields for LCMS v3.
  • Consistent rendering of code blocks in github pages and github preview.
  • Warn about trailing slashes in paths.
  • Optionally, dump validation report at the top of the upload.
  • In the report notes, record the version of the checkout.
  • Improve testing of generate_field_yaml.py.
  • Provides map in docs/ from fields to the entities and assays they are used in.
  • Give schema and version in success message.
  • Generate field-types.yaml.
  • Update assay list.
  • Added WGS directory structure schema.
  • Fixed regex on directory structure schema.
  • Check that assay terms match approved list. (Right now, they don't.)
  • Level 1 description of assay_category: Updated "3" assay categories to "4". Added imaging mass spec.
  • work around mypy importlib type hinting problem
  • Cleaned up LC-MS directory structure schema.
  • Added links to examples in the portal for 5 assays.
  • Make LC fields optional.
  • Present directory path examples in same column.
  • Updated LC-MS directory structure schema.
  • Work around mypy importlib type hinting problem.
  • Longer assay description for LCMS, and supporting machinery.
  • In CI, pin to older Ubuntu version to avoid SSL problems with Uniprot.
  • Level 1 description of assay_category: Updated "3" assay categories to "4".
  • Added imaging mass spec.
  • Work around mypy importlib type hinting problem.
  • Antibodies validation is broken; Move test out the way.
  • Make email validation effective.
  • Add a test to confirm that backslashes aren't ignored during validation.
  • Explain allowed values for booleans.
  • Update the lcms schema field "lc_temp_value" optional
  • Switch to Github CI.
  • cell_barcode_read description: comma-delimitted.
  • Update the lcms schema field "lc_temp_value" optional.
  • Hit a different URL for ORCID, that will not give us soft 404s.
  • In bash scripts, make python3 explicit.
  • Update the flowchart to reflect the roles of Bill and PK.
  • Add pipeline info.
  • Hotfix on CellDive directory to reflect changes to dataset.
  • Updated CellDive directory structure.
  • Updated CODEX directory structure.
  • Non-assay schema docs were not be update. Fix that.
  • Sample was being skipped in doc generation. Fix that.
  • Add to enums for perfusion_solutions and ms_source.
  • Upgrade from dependabot.

v0.0.12 - 2021-07-23

  • Catch unrecognized keys in dir schema.
  • Ammend LCMS docs.
  • Fix CI: point to right branch.
  • Document Donor and Sample Metadata process.
  • Make the network cache file JSON, for portability.
  • Dependabot update.
  • Fix typo.
  • Explain acronyms.
  • Add kwarg to pass-through to tests.
  • Update validate_upload.py docs.
  • Add new LCMS version, and clean up reused fields.
  • Make barcode fields optional.
  • User donor as a test-bed for ontology-enums.
  • Add a warning on pages where every version has been deprecated.
  • Add gcms.
  • Make some scatacseq fields optional.
  • Create CE-MS.
  • New version of IMS.
  • Add a warning on pages where every version has been deprecated.
  • Doc test for deprecated schemas.
  • Add 10X multiome to scatacseq.
  • Deprecated flag can now be added to schema.
  • CLEANUP rnaseq_assay_method.
  • cleanup resolution_z_unit.
  • Network problems in report, instead of quitting with stack trace.
  • New lightsheet schema, with description of changes.
  • Introduced Lightsheet directory schema.
  • Ensure that version numbers match the constraint inside the file.
  • maldiims to ims: Only touches URLs; doesn't affect validation.
  • Add script to validate any TSV.
  • Factor out exit status codes.
  • Pull out sc_isolation_tissue_dissociation.
  • sequencing_read_format is optional for HCA.
  • Disallow N/A values.
  • Pull out the fields that have only one variant.
  • Cleanup code for reference validations.
  • Better section headers.
  • Tighter validation of shared fields in assay schemas.
  • Another optional field in HCA scrnaseq.
  • Cleanup whitespace in yaml.
  • Tools to resolve duplicated field definitions.
  • Rearrange YAML so static processing works.

v0.0.11 - 2021-05-18

  • Updated AF and stained microscopy structure schema.
  • Updated CODEX directory structure schema.
  • No Donor and Tissue ID validation needed for HCA.
  • Longer description for Q30.
  • Setup GH Pages.
  • Fix bug with loading non-HCA schemas that have an HCA variant.
  • Fix bug in the maldiims schema to use correct file name extension
  • Update description of the .ibd and .imzML files in the maldiims schema
  • Added example maldiims folder structure
  • Updated README.md to reflect the examples/... folder structure
  • Use assay names to make titles.
  • Add formalin as a Sample perfusion_solution.
  • Style the GH Pages like the portal.
  • Catch metadata TSVs with non-ASCII characters.
  • More general ignore forurl-status-cache.
  • Support Windows environments by converting back-slashes for forward slashes.
  • Improve navigation and styling of new GH Pages.
  • In cleanup_whitespace.py, avoid printing extra newlines on windows.
  • Field templates for sequencing fields.
  • Missing data_path will no longer cause spurious errors when submission is interpretted as dataset.
  • README for examples/ directory.
  • Distinct error codes for different situations.
  • Field templates for library fields.
  • More doctests.
  • Loosen sequential items check, and improve error message.
  • Replace "submission" with "upload".

v0.0.10 - 2021-04-21

  • Remove inappropriate syntax highlighting from CLI docs.
  • Fix bug in report generation.
  • Remove contributors_path from HCA.
  • Make the codeowners more granular.
  • Distinguish v2 and v3 10x.
  • Add expected_cell_count.
  • Remove the sequence_limit where not appropriate.
  • Chuck missed source_project in scrnaseq-hca: Added now.
  • Distinguish v2 and v3 10x, and add to HCA as well.
  • Add 'Belzer MPS/KPS' as an option.
  • Remove links to YAML from MD.
  • Cleaned up description on 3D IMC directory schema.
  • Updated a description on 3D IMC directory schema.
  • Updated regular expression on CODEX directory schema.
  • Fix the generated TOC for antibodies.
  • Apply "units_for": Units only required is value is given.
  • Check for auto-incremented fields.
  • If it errors, add a note about cleanup_whitespace.py.
  • Apply missing constraints to scrnaseq.
  • Consistent pattern constraint for sequencing_read_format.
  • Diagram of overall repo structure; Explain doc build process.
  • Remove vestigial "Level 3".
  • Fixed typo in CODEX directory schema.
  • Make more fields optional in HCA scrnaseq.
  • Make it work with Python 3.6.
  • Create subdirectories for examples and tests to clean up the top level.
  • Add v1 for all schemas.
  • Introduce scrnaseq-hca.
  • Look for a source_project field to distinguish schemas.
  • Move script docs into subdirectory, and improve coverage.
  • Put TOC in blockquote: semantics are't right, but it indents.
  • Simplify sample ID regex.
  • Cache network responses to disk.
  • Add the generated YAML to the output directory.
  • Generate a report about the metadata values used in Elasticsearch.

v0.0.9 - 2021-03-16

  • Fix typo in CellDIVE.
  • Update CLI usage to highlight sample validation.
  • Update lightsheet docs.
  • Update IMC docs.
  • Add concentration to antibodies.
  • Factor out Frictionless to give us more control over table validation.
  • Check for CSV instead of TSV.
  • Better error message for missing and mis-ordered fields.
  • No longer require contributor middle names.
  • Make network checks a part of the schema; Skip None values.
  • Check for values which Excel has "helpfully" auto-incremented.
  • Add 4C as a preservation temperature.
  • Add units_for, so unused units aren't needed in the spreadsheet.
  • Ivan is primary contact for directory work.
  • Make network checks a part of the schema.
  • Get rid of special-purpose logic for level-1
  • Fix typo in nano enum.
  • Clearer error when it can't find matching assay name.
  • Downgrade dependency for compatibility with HuBMAP commons.
  • Directory structure for scatacseq.
  • Add 3D IMC table and directory schemas.
  • Link to the yaml for both directory and metadata schemas.
  • Directory structure for scatacseq and scrnaseq: They share a symlink.
  • Add help document.
  • Factor out the checks, make OO, and make error messages configurable.
  • Slightly better errors when a directory is found when a TSV is expected.
  • Make as_text_list the default output format.
  • Script to generate CSV for fields and enums.
  • Add version number to schemas.
  • Clarify guidelines for direction schemas.

v0.0.8 - 2021-02-10

  • Update CODEX directory structure
  • Allow "X" as final character of ORCID.
  • Ping the respective services to confirm the ORCIDs, RR IDs, and Uniprot IDs are actually good.
  • Add encoding as CLI param.
  • Add --offline option, and use it internally.
  • Fix the CLI parameter parsing: Either --local_directory or --tsv_paths must be provided.
  • Allow examples of path rexes to be provided, and fix bug.
  • Use the SciCrunch resolver for RR IDs.
  • More helpful message if decoding error.
  • State stability policy.
  • Show the URL that produced the 404, and unify the code.
  • Warning if missing "assay_type".
  • Add lightsheet.
  • Add a slot for a free-text note.
  • Friendlier error if trying to validate Antibodies or Contributors as metadata.
  • Update directory description docs.
  • Upgrade to latest version of Frictionless. The content of error messages has changed.
  • Clarify description of CODEX channelnames_report.csv.
  • Add flowchart documenting the consensus submission process.
  • cleanup-whitespace.py
  • Issue templates to operationalize new process for handling post-release changes.
  • Support versioning of metadata schemas.
  • Add channel_id description to CellDIVE

v0.0.7 - 2021-01-13

  • Improved error messages in Excel.
  • Define donor terms.
  • Update MALDI terms.
  • Demonstrate that validation of one-line-tsv-in-directory will work.
  • Add an include mechanism to reduce duplication in the configs, and use it.
  • Add Celldive.
  • Add an include mechanism to reduce duplication in the configs.
  • New organs will be coming in. Loosen regex.
  • Give test.sh an optional argument, to pick-up the test run in the middle.
  • Remove wildcards from dir schemas which have not been delivered.
  • Update Celldive and CODEX directory schemas.
  • Sort file errors for stability.
  • Check protocols io DOIs.
  • Remove option to validate against directory structure in Globus.
  • Loosen ID regex to allow lymph nodes. (Chuck's mistake!)

v0.0.6 - 2020-12-07

  • Add thumbnail to directory schema.
  • Add machinery to include regex examples in docs.
  • Run mypy, but only on the one file that has type annotations.
  • Consolidate TSV reading to avoid inconsistencies in character encoding.
  • Remove option for directory schema "subtypes".
  • Read type from first line of TSV, instead of from filename.
  • Remove vestigial line from flake8 config.
  • Instructions for working groups providing descriptions.
  • Remove extraneous parts from Sample doc.
  • Document contributors.tsv
  • Warn if two TSVs are for the same assay type.
  • Give example of single TSV validation.
  • Add SLIDEseq.
  • Add antibodies.tsv.
  • Generate Excel files.
  • Fix a commandline hint when tests fail.
  • Escape RE in directory schema.
  • Unify generation of assay and other docs.
  • Supply XLSX for non-assays.
  • Fix links.
  • Unconstrain channel_id and uniprot.
  • SLIDEseq dir schema.
  • Test validation of antibodies.tsv

v0.0.5 - 2020-11-09

  • Change "mixif" to "mxif".
  • Expose sample field descriptions for use in portal.
  • Add missing assay type to enum.
  • ng/ul to nM.
  • Change to flat directory schema structure.
  • Dir Schema for MALDI-IMS.
  • AF dir schema.
  • Update README, and diagram.
  • Add extras directory.
  • Prettier HTML output.
  • Add donor.yaml, where we can explain donor metadata fields, and hook it into field-descriptions.yaml.
  • Add ingest-validation-tests submodule.
  • nanodesi/pots table schema.
  • Add as_text_list option.
  • plugin_validator started.
  • Add donor.yaml, where we can explain donor metadata fields.
  • Fix the build.
  • Now that we have agreed on extras/, expose in docs.
  • Contributors table schema.
  • Add extra validation hooks.
  • Add nano docs.
  • Run plugin tests only from command line argument
  • Add stained imagery directory schema.
  • Update CODEX directory schema: Require PDF.
  • Get rid of unified.yaml.
  • Point at docs on portal.
  • Remove missing example.
  • Add is_qa_qc to dir schema table.
  • Add passing contributors.tsv

v0.0.4 - 2020-06-26

Added

  • Add Sample field descriptions.
  • Change to "validate_samples".
  • Get enums in sync, and doctest the logic.
  • Add liquid nitrogen
  • Revise sample metadata.
  • Fix Regexes in MD.
  • Sample metadata validation
  • ... and fill in draft details.
  • ... and fill in headers and add unit columns.
  • Fill in TODOs.
  • Generate unified description list.
  • Links to background docs.
  • Pre-fill enums in TSVs
  • Generator will stub the Level-1 overrides.
  • Units on IMC.
  • Submission structure diagram.
  • Autogenerate "Leave blank if not applicable".
  • Add bulkrnaseq and bulkatacseq.
  • Add WGS and IMC.
  • Dump unified yaml for each type. (This will be pulled on the portal side.)
  • Add enum constraints to unit fields, and replace TODOs.
  • Check that directory schemas exist.

Changed

  • Simplified directory validation.
  • mass -> mz.
  • bulkrnaseq QA is just RIN.
  • Add bytes to IMC.
  • LCMS capitals.
  • Update wgs enum
  • More accurate sample ID regex.
  • Reorder LCMS fields.
  • atacseq to scatacseq.
  • Make sc_isolation_enrichment in scrnaseq optional.
  • Free-form cell_barcode_read.
  • Add bulkrnaseq, bulkatacseq, and wgs fields.
  • mass/charge is unitless in MS: Remove field.
  • TSV parsing conforms to excel-tsv: No longer ignoring backslashes.
  • More explicit label for patterns in MD.
  • TSV filenames match what will be required downstream.
  • IMS -> MALDI-IMS

Removed

  • avg_insert_size from bulkatacseq.

v0.0.3 - 2020-05-04

Added

  • Additional scrnaseq types and columns.
  • Add a number of Assay types for Vanderbilt.
  • Friendlier error if data_path is missing.
  • Add polysaccharides as analyte_class.
  • Ignore glob patterns and not just fixed files. If other patterns are given, dot-files must be explicitly ignored.

Changed

  • Remove parenthesis from assay type.
  • Assume Latin-1 encoding for TSVs rather than UTF-8.
  • Update LC-MS fields.
  • Separate level-2 schemas in source.
  • Separate type and TSV path with space instead of ":" in CLI.
  • Make analyte_class optional for some assays.
  • Tweak LCMS fields.

v0.0.2 - 2020-04-25

Added

  • Mirror Globus directory to local cache.
  • Fix --type_metadata so it still works without a submission directory.
  • Add --optional_fields to temporarily ignore the given fields.
  • Add --ignore_files to ignore particular top-level files.
  • Ignore dot-files. No command-line option to enable stricter validation, for now.
  • Add scrnaseq.
  • Open error report in browser.

Changed

  • Make the ATACseq validation more flexible.
  • Less confusing representation of enums in docs.
  • Allow lower level schemas to override aspects of the Level 1 schema.
  • Make DOIs required again: Fields to consider optional can be set on commandline.
  • Add more options to atacseq enum.
  • Update CODEX directory schema to match what is actually delivered.

v0.0.1 - 2020-04-13

Added

  • Validate structure of Akoya CODEX submissions.
  • Generate submission template.
  • Check that fixture-based tests actually ran.
  • Check types early, rather than waiting for file-not-found.
  • Generate JSON Schema from simpler Table Schema.
  • Use schema to check that submission headers are correct, and reference by letter if not.
  • Filling in details for CODEX Schema.
  • Stanford directory schema.
  • Convert column numbers to spreadsheet-style letters.
  • Table of contents in generated doc.
  • Added number_of_channels
  • Added constraints to generated docs.
  • Support timezone offset (rather than abbreviation).
  • Add ATAC-seq and revise schema; fixed caps; Added descriptions.
  • Validate DOIs for protocols.io.
  • Added "Paths" section to both.
  • Make periods in blank lines optional.
  • Make fields required.
  • Validate donor and sample IDs.
  • Check that CLI docs are up to date.
  • Validate the data_path.
  • Allow multiple metadata.tsvs.
  • Validate against Globus.
  • Support multiple TSVs.
  • Use
    in ToC.
  • Link to Google doc spec.
  • Allow Globus File Browser URL to be used directly.
  • Gratuitous Emojis!
  • seqfish
  • Deeply structured YAML error reports.
  • Check for multiply referenced, or unreferenced paths.

Changed

  • CSV -> TSV
  • Make the schema validation errors more readable
  • Doctests are scanned from directory, rather than read from single file.
  • Change the modeling of replicate groups.
  • parent_id to tissue_id
  • Link to raw TSV.
  • No more UUIDs.
  • Ignore blank lines in TSV.
  • Tighter numeric constraints on ATAC-seq.
  • Generate all docs at once.
  • Add more enums.
  • Unify Level 1 metadata definitions.
  • Revert DOI format.
  • No longer checking consistency of donor and sample.
  • Remove generic schema.
  • python3 in hash-bang.
  • Reorganize fixtures.
  • Stop generating JSON Schema, for now.
  • Define path fields only in one place.
  • Remove timezone offset.
  • Autogenerate parts of table schema.
  • New note to clarify git is required.