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Include schemas in the cidc_schemas package #95

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merged 11 commits into from Jul 10, 2019

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commented Jul 10, 2019

This PR is rebased off of #94 and should only be merged after that PR is merged.

This change moves the schemas/ directory into the cidc_schemas package, so that anyone who installs the package will have access to the most recent version of the data model schemas.

Making this move also makes default schema path resolution simple, enabling anyone who's installed to package to run, e.g.:

from cidc_schemas.json_validation import load_and_validate_schema
aliquot_schema = load_and_validate_schema('aliquot.json')
pbmc_template_schema = load_validate_schema('templates/pbmc_template.json')

without providing a path to a schemas directory.

@jim-bo jim-bo self-assigned this Jul 10, 2019

@jim-bo jim-bo self-requested a review Jul 10, 2019

@jim-bo

jim-bo approved these changes Jul 10, 2019

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no comments, will start to us this in the prism branch

@jim-bo jim-bo merged commit ea22b9f into master Jul 10, 2019

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jacoblurye added a commit that referenced this pull request Jul 10, 2019

Release changes on master (#96)
* Add installation from GitHub and release branch status (#93)

* Last bigone (#94)

* modified schema to embed assay into aliquot

* fixed typo

* renamed property in aliquot assays to assay to reflect usage

* Include schemas in the cidc_schemas package (#95)

* modified schema to embed assay into aliquot

* fixed typo

* renamed property in aliquot assays to assay to reflect usage

* Move schemas inside cidc_schemas

* Include schemas in distribution

* Update schema path logic to handle new location

* Update CLI commands in README

* Move schemas into cidc_schemas

* rename SCHEMA_ROOT to SCHEMA_DIR

* Add command to list all schemas from CLI

jacoblurye added a commit that referenced this pull request Jul 11, 2019

Release changes from master (#98)
* Add installation from GitHub and release branch status (#93)

* Last bigone (#94)

* modified schema to embed assay into aliquot

* fixed typo

* renamed property in aliquot assays to assay to reflect usage

* Include schemas in the cidc_schemas package (#95)

* modified schema to embed assay into aliquot

* fixed typo

* renamed property in aliquot assays to assay to reflect usage

* Move schemas inside cidc_schemas

* Include schemas in distribution

* Update schema path logic to handle new location

* Update CLI commands in README

* Move schemas into cidc_schemas

* rename SCHEMA_ROOT to SCHEMA_DIR

* Add command to list all schemas from CLI

* API updates (#97)

* Add SCHEMA_LIST as a constant

* Add option to get validation errors as a list of strings

* Convert assertions to validation errors

jacoblurye added a commit that referenced this pull request Jul 14, 2019

Release changes on master (#102)
* Add installation from GitHub and release branch status (#93)

* Last bigone (#94)

* modified schema to embed assay into aliquot

* fixed typo

* renamed property in aliquot assays to assay to reflect usage

* Include schemas in the cidc_schemas package (#95)

* modified schema to embed assay into aliquot

* fixed typo

* renamed property in aliquot assays to assay to reflect usage

* Move schemas inside cidc_schemas

* Include schemas in distribution

* Update schema path logic to handle new location

* Update CLI commands in README

* Move schemas into cidc_schemas

* rename SCHEMA_ROOT to SCHEMA_DIR

* Add command to list all schemas from CLI

* API updates (#97)

* Add SCHEMA_LIST as a constant

* Add option to get validation errors as a list of strings

* Convert assertions to validation errors

* Update type hints to reflect openpyxl loader interface (#100)

* Remove unused or unnecessary requirements (#101)

jacoblurye added a commit that referenced this pull request Jul 16, 2019

Release first pass at prism (#105)
* Add installation from GitHub and release branch status (#93)

* Last bigone (#94)

* modified schema to embed assay into aliquot

* fixed typo

* renamed property in aliquot assays to assay to reflect usage

* Include schemas in the cidc_schemas package (#95)

* modified schema to embed assay into aliquot

* fixed typo

* renamed property in aliquot assays to assay to reflect usage

* Move schemas inside cidc_schemas

* Include schemas in distribution

* Update schema path logic to handle new location

* Update CLI commands in README

* Move schemas into cidc_schemas

* rename SCHEMA_ROOT to SCHEMA_DIR

* Add command to list all schemas from CLI

* API updates (#97)

* Add SCHEMA_LIST as a constant

* Add option to get validation errors as a list of strings

* Convert assertions to validation errors

* Update type hints to reflect openpyxl loader interface (#100)

* Remove unused or unnecessary requirements (#101)

* Prism (#99)

* initial work on prism

* minor updates to support more complex loading of data

* first working commit of xlsx parser for whole blood shipping

* added partial working code for wes support, need to rebase to get working

* prism now works for wes

* forgot to add new requirements

* style updates to prism to address comments in #99

* updated test to address confusion on merge

* fixed broken type hint by changing function and updating code. remove extra library function

* simplified ref resolution for type coercion checking

jacoblurye added a commit that referenced this pull request Jul 18, 2019

Release file-generation (#108)
* Add installation from GitHub and release branch status (#93)

* Last bigone (#94)

* modified schema to embed assay into aliquot

* fixed typo

* renamed property in aliquot assays to assay to reflect usage

* Include schemas in the cidc_schemas package (#95)

* modified schema to embed assay into aliquot

* fixed typo

* renamed property in aliquot assays to assay to reflect usage

* Move schemas inside cidc_schemas

* Include schemas in distribution

* Update schema path logic to handle new location

* Update CLI commands in README

* Move schemas into cidc_schemas

* rename SCHEMA_ROOT to SCHEMA_DIR

* Add command to list all schemas from CLI

* API updates (#97)

* Add SCHEMA_LIST as a constant

* Add option to get validation errors as a list of strings

* Convert assertions to validation errors

* Update type hints to reflect openpyxl loader interface (#100)

* Remove unused or unnecessary requirements (#101)

* Prism (#99)

* initial work on prism

* minor updates to support more complex loading of data

* first working commit of xlsx parser for whole blood shipping

* added partial working code for wes support, need to rebase to get working

* prism now works for wes

* forgot to add new requirements

* style updates to prism to address comments in #99

* updated test to address confusion on merge

* fixed broken type hint by changing function and updating code. remove extra library function

* simplified ref resolution for type coercion checking

* added first prototype of filegen_wes (#107)
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