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Add new schematic parameters data_model_labels, annotation_keys, and …
…table_column_names to README (#159) Signed-off-by: Anthony Williams <[email protected]>
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| # Project configurations for the [Data Curator App](github.com/sage-Bionetworks/data_curator) | ||
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| The file [tenants.json](tenants.json) controls which DCCs appear in DCA. It contains a json object `tenants` which holds one json object per DCC. Each DCC object requires:\ | ||
| The file [tenants.json](tenants.json) controls which DCCs appear in DCA. It contains a json object `tenants` which holds one json object per DCC. Each DCC object requires: | ||
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| - `name`: The name of the DCC to appear in the DCA selection menu\ | ||
| - `synapse_asset_view`: The synapse ID of the DCCs fileview for DCA. Must include "syn"\ | ||
| - `config_location`: Filepath to the DCC's DCA config file. More details below.\ | ||
| - `name`: The name of the DCC to appear in the DCA selection menu | ||
| - `synapse_asset_view`: The synapse ID of the DCCs fileview for DCA. Must include "syn" | ||
| - `config_location`: Filepath to the DCC's DCA config file. More details below. | ||
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| Each DCC will have its own directory to store configuration files. At minimum it will have [dca_config.json](demo/dca_config.json). This file can be validated against [schemas/dca_config.schema.json](schemas/dca_config.schema.json). At the top level it contains three json objects, `dcc`, `dca`, and `schematic`.\ | ||
| Each DCC will have its own directory to store configuration files. At minimum it will have [dca_config.json](demo/dca_config.json). This file can be validated against [schemas/dca_config.schema.json](schemas/dca_config.schema.json). At the top level it contains three json objects, `dcc`, `dca`, and `schematic`. | ||
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| `dcc` contains various configurations about your DCC and data model:\ | ||
| `dcc` contains various configurations about your DCC and data model: | ||
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| - `name` - name of DCC in dropdown menu | ||
| - `synapse_asset_view` - synapse ID of asset view. | ||
| - `data_model_url` - data model URL (**RAW** github file). | ||
| - `data_model_info` - URL to a description of the data model, such as release notes. | ||
| - `template_menu_config_file` - URL to DCA template dropdown file. | ||
| - `logo_location` - URL to logo file. | ||
| - `logo_link` - link to DCC website. | ||
| - `dcc_help_link` - link for users to find help about DCA. | ||
| - `portal_help_link` - link for users to find help about their portal. | ||
| - `name`: name of DCC in dropdown menu | ||
| - `synapse_asset_view`: synapse ID of asset view. | ||
| - `data_model_url`: data model URL (**RAW** github file). | ||
| - `data_model_info`: URL to a description of the data model, such as release notes. | ||
| - `template_menu_config_file`: URL to DCA template dropdown file. | ||
| - `logo_location`: URL to logo file. | ||
| - `logo_link`: link to DCC website. | ||
| - `dcc_help_link`: link for users to find help about DCA. | ||
| - `portal_help_link`: link for users to find help about their portal. | ||
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| `dca` contains DCA-specific customizations:\ | ||
| `dca` contains DCA-specific customizations: | ||
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| - `use_compliance_dashboard` - `TRUE` or `FALSE`. Only FALSE currently supported. Data compliance dashboard. | ||
| - `primary_col` - center header color hex code. | ||
| - `secondary_col` - right header color hex code. | ||
| - `sidebar_col` - left header color hex code. | ||
| - `use_compliance_dashboard`: `TRUE` or `FALSE`. Only FALSE currently supported. Data compliance dashboard. | ||
| - `primary_col`: center header color hex code. | ||
| - `secondary_col`: right header color hex code. | ||
| - `sidebar_col`: left header color hex code. | ||
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| `schematic` contains several objects for passing parameters to schematic commands:\ | ||
| `schematic` contains several objects for passing parameters to schematic commands: | ||
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| - `global` | ||
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| - `data_model_labels`: `class_label` or `display_label` [Schema labelling option](https://sagebionetworks.jira.com/wiki/spaces/SCHEM/pages/3089498257/How+to+Define+Display+Name+Labeling) | ||
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| - `manifest_generate` | ||
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| - `output_format`-`excel`or`google_sheets\`. [Schemtic manifest get ption](https://sage-schematic.readthedocs.io/en/develop/cli_reference.html#schematic-manifest-get). | ||
| - `use_annotations` - `TRUE` or `FALSE`. [Schemtic manifest get option](https://sage-schematic.readthedocs.io/en/develop/cli_reference.html#schematic-manifest-get). | ||
| - `output_format`: `excel`or`google_sheets`. [Schemtic manifest get option](https://sage-schematic.readthedocs.io/en/develop/cli_reference.html#schematic-manifest-get). | ||
| - `use_annotations`: `TRUE` or `FALSE`. [Schemtic manifest get option](https://sage-schematic.readthedocs.io/en/develop/cli_reference.html#schematic-manifest-get). | ||
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| - `model_validate` | ||
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| - `restrict_rules` - `TRUE` or `FALSE`. [Schematic model validate and submit option](https://sage-schematic.readthedocs.io/en/develop/cli_reference.html#schematic-model-validate). | ||
| - `restrict_rules`: `TRUE` or `FALSE`. [Schematic model validate and submit option](https://sage-schematic.readthedocs.io/en/develop/cli_reference.html#schematic-model-validate). | ||
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| - `model_submit` | ||
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| - `use_schema_labels` - `TRUE` or `FALSE`. [Schematic model submit option](https://sage-schematic.readthedocs.io/en/develop/cli_reference.html#schematic-model-submit). | ||
| - `table_manipulation` - `replace` or `upsert`. [Schematic model submit option](https://sage-schematic.readthedocs.io/en/develop/cli_reference.html#schematic-model-submit). | ||
| - `manifest_record_type` - One of `table_and_file`, `file_only` , `file_and_entities` or `table_file_and_entities`. [Schematic model submit option](https://sage-schematic.readthedocs.io/en/develop/cli_reference.html#schematic-model-submit). | ||
| - `hide_blanks` - `TRUE` or `FALSE`. [Schematic model submit option](https://sage-schematic.readthedocs.io/en/develop/cli_reference.html#schematic-model-submit). | ||
| - `table_column_names`: `class_label`, `display_label`, or `display_name` [Schema labelling option](https://sagebionetworks.jira.com/wiki/spaces/SCHEM/pages/3089498257/How+to+Define+Display+Name+Labeling) | ||
| - `annotation_keys`: `class_label` or `display_label` [Schema labelling option](https://sagebionetworks.jira.com/wiki/spaces/SCHEM/pages/3089498257/How+to+Define+Display+Name+Labeling) | ||
| - `table_manipulation`: `replace` or `upsert`. [Schematic model submit option](https://sage-schematic.readthedocs.io/en/develop/cli_reference.html#schematic-model-submit). | ||
| - `manifest_record_type`: One of `table_and_file`, `file_only` , `file_and_entities` or `table_file_and_entities`. [Schematic model submit option](https://sage-schematic.readthedocs.io/en/develop/cli_reference.html#schematic-model-submit). | ||
| - `hide_blanks`: `TRUE` or `FALSE`. [Schematic model submit option](https://sage-schematic.readthedocs.io/en/develop/cli_reference.html#schematic-model-submit). | ||
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| Each DCC also needs a template configuration file. This controls which data types are accessible to users and if they contain record-based or file-based data. It can be generated by hand or automatically from a data model using the [dca-template-config-action github action](https://github.com/Sage-Bionetworks/dca-template-config-action). See an [example workflow in a data model repo](https://github.com/Sage-Bionetworks/data-models/blob/main/.github/workflows/create-template-config.yml). This json file can be validated against [schemas/dca_template_config.schema.json](schemas/dca_template_config.schema.json). The top level of the file needs a json array of objects named `manifest_schemas`. Each object in the array requires: | ||
| Each DCC also needs a template configuration file. This controls which data types are accessible to users and if they contain record-based or file-based data. It can be generated by hand or automatically from a data model using the [dca-template-config-action github action](https://github.com/Sage-Bionetworks/dca-template-config-action). See an [example workflow in a data model repo](https://github.com/Sage-Bionetworks/data-models/blob/main/.github/workflows/create-template-config.yml). This json file can be validated against [schemas/dca_template_config.schema.json](schemas/dca_template_config.schema.json). The top level of the file needs a json array of objects named `manifest_schemas`. Each object in the array requires the strings: | ||
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| - `display_name`: Display name of the data type | ||
| - `schema_name`: Name of the schema | ||
| - `type`: record or file | ||
| - `project_scope`: Array of Synapse IDs for cross manifest validation. Optional. | ||
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| Project scope is only needed for data types that use cross manifest validation. In most cases it can be ommitted. | ||
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| See our [example dca_template_config.json](https://github.com/Sage-Bionetworks/data-models/blob/main/dca-template-config.json) |