From 5fb2ca0b13c5a6ae53c57264e79e89be3619eb21 Mon Sep 17 00:00:00 2001 From: aydawka Date: Fri, 29 Aug 2025 21:16:41 -0700 Subject: [PATCH 1/4] fix: update validate docs --- docs/modules/validate.md | 28 +++++++++---------- .../schemas/participants.schema.json | 2 +- 2 files changed, 15 insertions(+), 15 deletions(-) diff --git a/docs/modules/validate.md b/docs/modules/validate.md index 9639d09..987e95d 100644 --- a/docs/modules/validate.md +++ b/docs/modules/validate.md @@ -30,9 +30,9 @@ Provide the data required for your `dataset_description` file in this paramater. | ------ | ------------- | -------- | ------------------------------------------ | | Object | {} | yes | Data object following the required schemas | -More information about the required data can be found in the [dataset_description](https://github.com/AI-READI/high-level-dataset-structure/blob/specifications/main/v1.0.0/schemas/dataset_description.schema.json) schema. +More information about the required data can be found in the [dataset_description](https://github.com/AI-READI/cds-specification/tree/main/docs/schemas/dataset_description.schema.json) schema. -You can the hosted validator [here](https://www.jsonschemavalidator.net/s/makBzCFq) if you want a better understanding or visualization of the schema for the input. +You can the hosted validator [here](https://www.jsonschemavalidator.net/s/Uaohwh1p) if you want a better understanding or visualization of the schema for the input. #### Returns @@ -46,9 +46,9 @@ You can the hosted validator [here](https://www.jsonschemavalidator.net/s/makBzC from pyfairdatatools import validate data = { - "Title": "My Dataset", - "Identifier": "10.5281/zenodo.1234567", - "IdentifierType": "DOI" + "title": "My Dataset", + "identifier": "10.5281/zenodo.1234567", + "identifierType": "DOI" } output = validate.validate_dataset_description(data = data) @@ -70,9 +70,9 @@ Provide the data required for your `study_description` file in this paramater. | ------ | ------------- | -------- | ------------------------------------------ | | Object | {} | yes | Data object following the required schemas | -More information about the required data can be found in the [study_description](https://github.com/AI-READI/high-level-dataset-structure/blob/specifications/main/v1.0.0/schemas/dataset_description.schema.json) schema. +More information about the required data can be found in the [study_description](https://github.com/AI-READI/cds-specification/tree/main/docs/schemas/study_description.schema.json) schema. -You can the hosted validator [here](https://www.jsonschemavalidator.net/s/cmkkqm9P) if you want a better understanding or visualization of the schema for the input. +You can host the validator [here](https://www.jsonschemavalidator.net/s/pfpR4Klf) if you want a better understanding or visualization of the schema for the input. #### Returns @@ -110,9 +110,9 @@ Provide the data required for your `README` file in this paramater. | ------ | ------------- | -------- | ------------------------------------------ | | Object | {} | yes | Data object following the required schemas | -More information about the required data can be found in the [README](../schemas/README.md) schema. +More information about the required data can be found in the [README](https://github.com/AI-READI/pyfairdatatools/blob/main/pyfairdatatools/schemas/readme.schema.json) schema. -You can the hosted validator [here](https://www.jsonschemavalidator.net/s/aNSmlcv1) if you want a better understanding or visualization of the schema for the input. +You can host the validator [here](https://www.jsonschemavalidator.net/s/qGe6d1wH) if you want a better understanding or visualization of the schema for the input. #### Returns @@ -126,9 +126,9 @@ You can the hosted validator [here](https://www.jsonschemavalidator.net/s/aNSmlc from pyfairdatatools import validate data = { - "Title": "My Dataset", - "Identifier": "10.5281/zenodo.1234567", - "Version": "1.0.0", + "title": "My Dataset", + "identifier": "10.5281/zenodo.1234567", + "version": "1.0.0", } output = validate.validate_readme(data = data) @@ -184,9 +184,9 @@ Provide the data required for your `participants.tsv` file in this paramater. | ------ | ------------- | -------- | ------------------------------------------ | | Object | {} | yes | Data object following the required schemas | -More information about the required data can be found in the [participants](../schemas/participants.md) schema. +More information about the required data can be found in the [participants](https://github.com/AI-READI/pyfairdatatools/blob/main/pyfairdatatools/schemas/participants.schema.json) schema. -You can the hosted validator [here](https://www.jsonschemavalidator.net/s/aNSmlcv1) if you want a better understanding or visualization of the schema for the input. +You can host the validator [here](https://www.jsonschemavalidator.net/s/AGbykeCI) if you want a better understanding or visualization of the schema for the input. #### Returns diff --git a/pyfairdatatools/schemas/participants.schema.json b/pyfairdatatools/schemas/participants.schema.json index 5bea664..4ffaff1 100644 --- a/pyfairdatatools/schemas/participants.schema.json +++ b/pyfairdatatools/schemas/participants.schema.json @@ -1,7 +1,7 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://schema.aireadi.org/files/participants.json", - "title": "README", + "title": "Participants", "description": "Additional text here", "type": "array", "items": { From 1853b004d7fff506d228462b368a5b21f18648c0 Mon Sep 17 00:00:00 2001 From: aydawka Date: Fri, 29 Aug 2025 21:58:05 -0700 Subject: [PATCH 2/4] fix: update generate docs --- docs/modules/generate.md | 6 +++--- docs/modules/validate.md | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/modules/generate.md b/docs/modules/generate.md index de1cac1..9950b10 100644 --- a/docs/modules/generate.md +++ b/docs/modules/generate.md @@ -30,7 +30,7 @@ Provide the data required for your `dataset_description` file in this paramater. | ------ | ------------- | -------- | ------------------------------------------ | | Object | {} | yes | Data object following the required schemas | -More information about the required data can be found in the [dataset_description](../schemas/dataset_description.md) schema. +More information about the required data can be found in the [dataset_description](https://github.com/AI-READI/pyfairdatatools/blob/main/pyfairdatatools/schemas/dataset_description.schema.json) schema. ##### file_path @@ -84,7 +84,7 @@ Provide the data required for your `study_description` file in this paramater. | ------ | ------------- | -------- | ------------------------------------------ | | Object | {} | yes | Data object following the required schemas | -More information about the required data can be found in the [study_description](../schemas/study_description.md) schema. +More information about the required data can be found in the [study_description](https://github.com/AI-READI/pyfairdatatools/blob/main/pyfairdatatools/schemas/study_description.schema.json) schema. ##### file_path @@ -138,7 +138,7 @@ Provide the data required for your readme file in this paramater. | ------ | ------------- | -------- | ------------------------------------------ | | Object | {} | yes | Data object following the required schemas | -More information about the required data can be found in the [readme](../schemas/readme.md) schema. +More information about the required data can be found in the [readme](https://github.com/AI-READI/pyfairdatatools/blob/main/pyfairdatatools/schemas/readme.schema.json) schema. ##### file_path diff --git a/docs/modules/validate.md b/docs/modules/validate.md index 987e95d..5ee5de2 100644 --- a/docs/modules/validate.md +++ b/docs/modules/validate.md @@ -30,7 +30,7 @@ Provide the data required for your `dataset_description` file in this paramater. | ------ | ------------- | -------- | ------------------------------------------ | | Object | {} | yes | Data object following the required schemas | -More information about the required data can be found in the [dataset_description](https://github.com/AI-READI/cds-specification/tree/main/docs/schemas/dataset_description.schema.json) schema. +More information about the required data can be found in the [dataset_description](https://github.com/AI-READI/pyfairdatatools/blob/main/pyfairdatatools/schemas/dataset_description.schema.json) schema. You can the hosted validator [here](https://www.jsonschemavalidator.net/s/Uaohwh1p) if you want a better understanding or visualization of the schema for the input. @@ -70,7 +70,7 @@ Provide the data required for your `study_description` file in this paramater. | ------ | ------------- | -------- | ------------------------------------------ | | Object | {} | yes | Data object following the required schemas | -More information about the required data can be found in the [study_description](https://github.com/AI-READI/cds-specification/tree/main/docs/schemas/study_description.schema.json) schema. +More information about the required data can be found in the [study_description](https://github.com/AI-READI/pyfairdatatools/blob/main/pyfairdatatools/schemas/study_description.schema.json) schema. You can host the validator [here](https://www.jsonschemavalidator.net/s/pfpR4Klf) if you want a better understanding or visualization of the schema for the input. From 9ce1ba783792c417633cdfae12ecb2d5d0de44d5 Mon Sep 17 00:00:00 2001 From: aydawka Date: Fri, 29 Aug 2025 21:59:10 -0700 Subject: [PATCH 3/4] fix: typo --- docs/modules/generate.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/modules/generate.md b/docs/modules/generate.md index 9950b10..09b8cc5 100644 --- a/docs/modules/generate.md +++ b/docs/modules/generate.md @@ -60,9 +60,9 @@ Provide the file type of the file where you want to save the generated dataset_d from pyfairdatatools import generate data = { - "Title": "My Dataset", - "Identifier": "10.5281/zenodo.1234567", - "IdentifierType": "DOI" + "title": "My Dataset", + "identifier": "10.5281/zenodo.1234567", + "identifierType": "DOI" } output = generate.generate_dataset_description(data = data, file_path = "dataset_description.json", file_type = "json") @@ -114,9 +114,9 @@ Provide the file type of the file where you want to save the generated study_des from pyfairdatatools import generate data = { - "Title": "My Dataset", - "Identifier": "10.5281/zenodo.1234567", - "IdentifierType": "DOI" + "title": "My Dataset", + "identifier": "10.5281/zenodo.1234567", + "identifierType": "DOI" } output = generate.generate_study_description(data = data, file_path = "study_description.json", file_type = "json") From 0e81272fbe397a592d09a74bbe58d27b30ff6a9e Mon Sep 17 00:00:00 2001 From: aydawka Date: Wed, 3 Sep 2025 12:29:56 -0700 Subject: [PATCH 4/4] feat: adsd clinical trials info --- docs/modules/generate.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/modules/generate.md b/docs/modules/generate.md index 09b8cc5..2e7f5ad 100644 --- a/docs/modules/generate.md +++ b/docs/modules/generate.md @@ -74,6 +74,10 @@ print(output) # dataset_description.json You can call the `generate_study_description` method to generate a study_description file. +#### Generate Study Description from Clinical Trial integration + +You can call the `generate_study_description_from_clinical_trials` method to generate an initial study_description file. + #### Parameters ##### data