schematicpy
Installation
Installation Requirements
Installation Guide For: Users
1. Verify your python version
2. Set up your virtual environment
2a. Set up your virtual environment with
venv
2b. Set up your virtual environment with
conda
3. Install
schematic
dependencies
4. Get your data model as a
JSON-LD
schema file
5. Obtain Google credential files
6. Set up configuration files
Installation Guide For: Developers
1. Clone the
schematic
package repository
2. Install
poetry
3. Start the virtual environment
4. Install
schematic
dependencies
5. Set up configuration files
6. Obtain Google credential files
7. Verify your setup
Setting up your asset store
Option 1: Distributed Synapse Projects
Access & Project Setup - Multiple Contributing Projects
Option 2: Single Synapse Project
Access & Project Setup - Single Contributing Project
Synapse External Cloud Buckets Setup
Configure Schematic
Asset Store
Synapse
Manifest
Model
Google Sheets
Validation Rules
Overview
Validation Types
Rule Implementation
Rule Types and Details
List Validation Type
list
Regex Validation Type
regex
Type Validation Type
float
int
num
str
URL Validation Type
url
Required Validation Type
required
Cross-manifest Validation Type
Value Scope
Set scope
Content Validation Type
recommended
protectAges
unique
inRange
date
Filename Validation
filenameExists
Rule Combinations
Component-Based Rule Setting
Generate a manifest
Prerequisites
Run help command
Generate an empty manifest
Option 1: Use the CLI
Option 2: Use the API
Generate a manifest using a dataset on synapse
Option 1: Use the CLI
Option 2: Use the API
Generate a manifest using a dataset on synapse and pull annotations
Option 1: Use the CLI
Option 2: Use the API
Validating a Metadata Manifest
Prerequisites
Requirements
Authentication
File Format
Required Column Headers
Restricted Column Headers
Manifest Validation
Overview
With the CLI
Authentication
Parameters
With the API
Authentication
Parameters
Request Body
Response
With the Library
Submit a manifest to Synapse
Prerequisites
Run help command
Submit a Manifest File to Synapse
Option 1: Use the CLI
Option 2: Use the API
Submit a Manifest file and Add Annotations
Option 1: Use the CLI
Option 2: Use the API
Expedite submission process (Optional)
Option 1: Use the CLI
Option 2: Use the API
Enable upsert for manifest submission
Pre-requisite
Option 1: Use the CLI
Option 2: Use the API
Tutorials
Contributing your manifest with the CLI
Prerequisites
Steps to Contribute a Manifest
Step 1: Generate a Manifest
Step 2: Validate the Manifest (Optional)
Step 3: Submit the Manifest to Synapse
Troubleshooting
Debugging
Manifest Submit:
RuntimeError: failed with SynapseHTTPError(‘400 Client Error: nan is not a valid Synapse ID.’)
Manifest Submit:
TypeError: boolean value of NA is ambiguous
Manifest Submit:
AssertionError: input_df lacks Id column.
Manifest validation:
The submitted metadata does not contain all required column(s)
Manifest validation:
The submitted metadata contains << ‘string’ >> in the Component column, but requested validation for << expected string >>
Manifest Generate:
KeyError: entityId
Manifest Generate:
ValueError: cannot insert eTag, already exists
CLI Reference
Generate a new manifest as a Google Sheet
Generate an existing manifest from Synapse
Validate a manifest
Submit a manifest as a file
In depth guide
schematic
manifest
model
schema
viz
LinkML
Background
Links
Generate JSON Schema from Data Models
JSONSchema Components and How to Set from Data Model
Property Keys
Description
Type
Explicit Type Setting
Implicit Type Inference
Validation Checks
Type Checks
Valid Values
Required Attributes
Validation Rules
Conditional Dependencies
schematicpy
Index
Index
Symbols
|
S
Symbols
--alphabetize_valid_values
schematic-manifest-get command line option
--annotation_keys
schematic-model-submit command line option
--archive_project
schematic-manifest-migrate command line option
--config
schematic-manifest command line option
schematic-model command line option
schematic-viz command line option
--data_model_labels
schematic-manifest-get command line option
schematic-model-submit command line option
schematic-model-validate command line option
schematic-schema-convert command line option
schematic-schema-generate-jsonschema command line option
schematic-viz-attributes command line option
schematic-viz-tangled_tree_layers command line option
schematic-viz-tangled_tree_text command line option
--data_model_source
schematic-schema-generate-jsonschema command line option
--data_type
schematic-manifest-get command line option
schematic-model-validate command line option
schematic-schema-generate-jsonschema command line option
--dataset_id
schematic-manifest-download command line option
schematic-manifest-get command line option
schematic-model-submit command line option
--dataset_scope
schematic-model-submit command line option
schematic-model-validate command line option
--dry_run
schematic-manifest-migrate command line option
--figure_type
schematic-viz-tangled_tree_layers command line option
schematic-viz-tangled_tree_text command line option
--file_annotations_upload
schematic-model-submit command line option
--hide_blanks
schematic-model-submit command line option
--json_schema
schematic-manifest-get command line option
schematic-model-validate command line option
--jsonld
schematic-manifest-migrate command line option
--manifest_path
schematic-model-submit command line option
schematic-model-validate command line option
--manifest_record_type
schematic-model-submit command line option
--new_manifest_name
schematic-manifest-download command line option
--no-file_annotations_upload
schematic-model-submit command line option
--output_csv
schematic-manifest-get command line option
--output_directory
schematic-schema-generate-jsonschema command line option
--output_jsonld
schematic-schema-convert command line option
--output_xlsx
schematic-manifest-get command line option
--path_to_data_model
schematic-manifest-get command line option
--project_scope
schematic-manifest-migrate command line option
schematic-model-submit command line option
schematic-model-validate command line option
--restrict_rules
schematic-model-submit command line option
schematic-model-validate command line option
--return_entities
schematic-manifest-migrate command line option
--sheet_url
schematic-manifest-get command line option
--table_column_names
schematic-model-submit command line option
--table_manipulation
schematic-model-submit command line option
--text_format
schematic-viz-tangled_tree_text command line option
--title
schematic-manifest-get command line option
--use_annotations
schematic-manifest-get command line option
--validate_component
schematic-model-submit command line option
--verbosity
schematic command line option
schematic-manifest command line option
schematic-manifest-download command line option
schematic-manifest-get command line option
schematic-manifest-migrate command line option
schematic-model command line option
schematic-model-submit command line option
schematic-model-validate command line option
schematic-schema-convert command line option
schematic-schema-generate-jsonschema command line option
schematic-viz command line option
schematic-viz-attributes command line option
schematic-viz-tangled_tree_layers command line option
schematic-viz-tangled_tree_text command line option
--version
schematic command line option
-a
schematic-manifest-get command line option
-ak
schematic-model-submit command line option
-ap
schematic-manifest-migrate command line option
-av
schematic-manifest-get command line option
-c
schematic-manifest command line option
schematic-model command line option
schematic-viz command line option
-d
schematic-manifest-download command line option
schematic-manifest-get command line option
schematic-model-submit command line option
-dml
schematic-manifest-get command line option
schematic-model-submit command line option
schematic-model-validate command line option
schematic-schema-convert command line option
schematic-schema-generate-jsonschema command line option
schematic-viz-attributes command line option
schematic-viz-tangled_tree_layers command line option
schematic-viz-tangled_tree_text command line option
-dms
schematic-schema-generate-jsonschema command line option
-dr
schematic-manifest-migrate command line option
-ds
schematic-model-submit command line option
schematic-model-validate command line option
-dt
schematic-manifest-get command line option
schematic-model-validate command line option
schematic-schema-generate-jsonschema command line option
-fa
schematic-model-submit command line option
-ft
schematic-viz-tangled_tree_layers command line option
schematic-viz-tangled_tree_text command line option
-hb
schematic-model-submit command line option
-js
schematic-manifest-get command line option
schematic-model-validate command line option
-mp
schematic-model-submit command line option
schematic-model-validate command line option
-mrt
schematic-model-submit command line option
-nmn
schematic-manifest-download command line option
-no-fa
schematic-model-submit command line option
-o
schematic-manifest-get command line option
schematic-schema-convert command line option
-od
schematic-schema-generate-jsonschema command line option
-oxlsx
schematic-manifest-get command line option
-p
schematic-manifest-get command line option
schematic-manifest-migrate command line option
-ps
schematic-manifest-migrate command line option
schematic-model-submit command line option
schematic-model-validate command line option
-re
schematic-manifest-migrate command line option
-rr
schematic-model-submit command line option
schematic-model-validate command line option
-s
schematic-manifest-get command line option
-t
schematic-manifest-get command line option
-tcn
schematic-model-submit command line option
-tf
schematic-viz-tangled_tree_text command line option
-tm
schematic-model-submit command line option
-v
schematic command line option
schematic-manifest command line option
schematic-manifest-download command line option
schematic-manifest-get command line option
schematic-manifest-migrate command line option
schematic-model command line option
schematic-model-submit command line option
schematic-model-validate command line option
schematic-schema-convert command line option
schematic-schema-generate-jsonschema command line option
schematic-viz command line option
schematic-viz-attributes command line option
schematic-viz-tangled_tree_layers command line option
schematic-viz-tangled_tree_text command line option
-vc
schematic-model-submit command line option
<DATA_MODEL_CSV>
schematic-schema-convert command line option
S
schematic command line option
--verbosity
--version
-v
schematic-manifest command line option
--config
--verbosity
-c
-v
schematic-manifest-download command line option
--dataset_id
--new_manifest_name
--verbosity
-d
-nmn
-v
schematic-manifest-get command line option
--alphabetize_valid_values
--data_model_labels
--data_type
--dataset_id
--json_schema
--output_csv
--output_xlsx
--path_to_data_model
--sheet_url
--title
--use_annotations
--verbosity
-a
-av
-d
-dml
-dt
-js
-o
-oxlsx
-p
-s
-t
-v
schematic-manifest-migrate command line option
--archive_project
--dry_run
--jsonld
--project_scope
--return_entities
--verbosity
-ap
-dr
-p
-ps
-re
-v
schematic-model command line option
--config
--verbosity
-c
-v
schematic-model-submit command line option
--annotation_keys
--data_model_labels
--dataset_id
--dataset_scope
--file_annotations_upload
--hide_blanks
--manifest_path
--manifest_record_type
--no-file_annotations_upload
--project_scope
--restrict_rules
--table_column_names
--table_manipulation
--validate_component
--verbosity
-ak
-d
-dml
-ds
-fa
-hb
-mp
-mrt
-no-fa
-ps
-rr
-tcn
-tm
-v
-vc
schematic-model-validate command line option
--data_model_labels
--data_type
--dataset_scope
--json_schema
--manifest_path
--project_scope
--restrict_rules
--verbosity
-dml
-ds
-dt
-js
-mp
-ps
-rr
-v
schematic-schema-convert command line option
--data_model_labels
--output_jsonld
--verbosity
-dml
-o
-v
<DATA_MODEL_CSV>
schematic-schema-generate-jsonschema command line option
--data_model_labels
--data_model_source
--data_type
--output_directory
--verbosity
-dml
-dms
-dt
-od
-v
schematic-viz command line option
--config
--verbosity
-c
-v
schematic-viz-attributes command line option
--data_model_labels
--verbosity
-dml
-v
schematic-viz-tangled_tree_layers command line option
--data_model_labels
--figure_type
--verbosity
-dml
-ft
-v
schematic-viz-tangled_tree_text command line option
--data_model_labels
--figure_type
--text_format
--verbosity
-dml
-ft
-tf
-v