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Merge branch 'caps-cli'
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‎README.md‎

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@@ -56,6 +56,11 @@ Help functionality in the CLI
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caps-cli --help
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```
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Use this command to configure username and password for the Model Catalog API
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```
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caps-cli configure --profile=<NAME_OF_PROFILE>
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```
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Use this command to know the details of each CLI function (options, arguments)
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```
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caps-cli <initialize, push, validate> --help
@@ -65,13 +70,13 @@ Run this command to test the template creation functionality (with 2 inputs, 3 o
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```
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caps-cli initialize -i 2 -o 3 -p 1
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```
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Running the above command will generate a yaml outline. By default this will create the outline in the current directory, use `-d path/to/location` to speciy a location. By default the yaml will be named `example_yaml.yaml`, user can also use `-d fileName.yaml` to name the output (note the user must specify .yaml after the name. Otherwise the program does not know if it is a directory or filename). By default this will not override an existing file if they share the same name. use flag `-f` to force override.
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Running the above command will generate a yaml outline. By default this will create the outline in the current directory, use -d path/to/location to speciy a location. By default the yaml will be named example_yaml.yaml, user can also use -d fileName.yaml to name the output (note the user must specify .yaml after the name. Otherwise the program does not know if it is a directory or filename). By default this will not override an existing file if they share the same name. use flag -f to force override.
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Run this command to transform the input YAML into a postable JSON object
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```
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caps-cli push <path_of_yaml_file_from_root_of_the_project>
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caps-cli push --profile=<NAME_OF_PROFILE> <path_of_yaml_file_from_root_of_the_project>
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```
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Run this command to validate the JSON schema obtained by using the above command

‎examples/ModelConfigExample-WithoutVariable.yaml‎

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#This is an example. The model here is a simplification of an existing one.
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modelName: EACS #URI: https://w3id.org/okn/i/mint/EACS
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#modelVersion: v7 #URI: https://w3id.org/okn/i/mint/EACS_v7
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#configuration with no setup ->is modelConfig. Setup is model setup
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configuration: EACS_v7_ethiopia
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#short_name maps to label. I think it's easier to understand
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short_name: Basic configuration of the economic aggregate crop supply model (EACS) v2
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description:
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- Aggregate crop supply response model for the country of South Sudan (version 2)
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author:
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- name: Rajiv Mayani #Assume type is person unless a type:Organization is added.
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contributor: #optional
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- name: Deborah Khider
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- name: Zeya Zhang
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email: blah@b.com
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hasComponentLocation:
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- https://github.com/mintproject/MINT-WorkflowDomain/raw/master/WINGSWorkflowComponents/economic-v2/economic-v2.zip
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hasImplementationScriptLocation: #Optional
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- https://github.com/mintproject/MINT-WorkflowDomain/raw/master/WINGSWorkflowComponents/economic-v2/run
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keywords:
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- economy; land use; crop production; fertilizer costs
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hasGrid: #optional
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- short_name: Grid from the economic crop supply model
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description:
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- Grid from the economic crop supply model
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hasDimension: 0D
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hasShape: Point
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hasSpatialResolution: Point
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hasModelCategory: #optional
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- Economy
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hasRegion: #Optional
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- description:
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- Area of the Pongo Basin in South Sudan
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short_name: Pongo basin region (South Sudan)
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hasSoftwareImage: mintproject/economic:v2
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hasSourceCode: #optional
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- codeRepository: https://github.com/mintproject/MINT-WorkflowDomain/tree/master/WINGSWorkflowComponents/economic-v2
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description:
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- Code for creating an encapsulation of EACS for a model configuration (version 2)
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short_name: EACS configuration component (version 2 of code)
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programmingLanguage:
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- shell
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hasOutputTimeInterval:
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- short_name: Simple economic time interval
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description:
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- Time interval used in the aggregate crop supply response model for the country
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of South Sudan configuration
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hasProcess: #each has to be mapped to an object.
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- Supply of Crop
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- Use of Fertilizer
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- Use of land
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hasInput:
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#input1
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- short_name: economic-sim #start always with the name of the input/output/param
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description: #should always follow the short name
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- Contains the economic data used in the simulation analysis
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position: 1
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type: #By default these are all datasetSpecifications. The type below is an additional aid
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- https://w3id.org/wings/export/MINT#EconomicSimData
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hasDimensionality: 0 #If this is not specified, assume 0
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hasFormat: csv
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#input2
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- short_name: economic-subsidies
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description:
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- File indicating the economic subsidies to use on each iteration of the model
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hasDimensionality: 0
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hasFormat: txt
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position: 2
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type:
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- https://w3id.org/wings/export/MINT#EconomicSubsidies
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hasOutput:
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#output 1
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- short_name: crop-yield
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description:
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- Contains the yield elasticities to fertilizer use that are derived from Cycles
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output
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hasDimensionality: 0
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hasFormat: csv
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position: 1
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type:
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- https://w3id.org/wings/export/MINT#CropYield
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#output 2
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- short_name: economic-data
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description:
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- Contains data on observed prices for each crop and supply elasticities and the
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costs of production for each crop
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position: 2
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type:
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- https://w3id.org/wings/export/MINT#EconomicData
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hasParameter:
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- short_name: maize-crop-price-adjustment
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description:
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- Change in market price by crop
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usesUnit: "%"
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dataType: float #maps to hasDataType
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defaultvalue: 0 #maps to hasDefaultValue
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maxValue: 50 #optional. Maps to hasMaximumAcceptedValue
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minValue: -50 #optional. Maps to hasMinimumAcceptedValue

‎examples/ModelConfigExample.yaml‎

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#This is an example. The model here is a simplification of an existing one.
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modelName: EACS #URI: https://w3id.org/okn/i/mint/EACS
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modelVersion: v7 #URI: https://w3id.org/okn/i/mint/EACS_v7
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#modelVersion: v7 #URI: https://w3id.org/okn/i/mint/EACS_v7
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#configuration with no setup ->is modelConfig. Setup is model setup
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configuration: EACS_v7_ethiopia
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#short_name maps to label. I think it's easier to understand

‎examples/SetupExample-WithoutVariable.yaml‎

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#This is an example. The model here is a simplification of an existing one.
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modelName: EACS #URI: https://w3id.org/okn/i/mint/EACS
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#modelVersion: v7 #URI: https://w3id.org/okn/i/mint/EACS_v7
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configuration: EACS_v7_ethiopia
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setup: EACS_v7_ethiopia_2018
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#short_name maps to label. I think it's easier to understand
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short_name: Basic configuration of the economic aggregate crop supply model (EACS) v2
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description:
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- Aggregate crop supply response model for the country of South Sudan (version 2)
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author:
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- name: Rajiv Mayani #Assume type is person unless a type:Organization is added.
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contributor: #optional
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- name: Deborah Khider
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- name: Zeya Zhang
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email: blah@b.com
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hasComponentLocation:
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- https://github.com/mintproject/MINT-WorkflowDomain/raw/master/WINGSWorkflowComponents/economic-v2/economic-v2.zip
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hasImplementationScriptLocation: #Optional
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- https://github.com/mintproject/MINT-WorkflowDomain/raw/master/WINGSWorkflowComponents/economic-v2/run
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keywords:
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- economy; land use; crop production; fertilizer costs
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hasGrid: #optional
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- short_name: Grid from the economic crop supply model
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description:
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- Grid from the economic crop supply model
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hasDimension: 0D
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hasShape: Point
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hasSpatialResolution: Point
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hasModelCategory: #optional
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- Economy
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hasRegion: #Optional
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- description:
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- Area of the Pongo Basin in South Sudan
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short_name: Pongo basin region (South Sudan)
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hasSoftwareImage: mintproject/economic:v2
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hasSourceCode: #optional
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- codeRepository: https://github.com/mintproject/MINT-WorkflowDomain/tree/master/WINGSWorkflowComponents/economic-v2
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description:
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- Code for creating an encapsulation of EACS for a model configuration (version 2)
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short_name: EACS configuration component (version 2 of code)
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programmingLanguage:
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- shell
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hasOutputTimeInterval:
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- short_name: Simple economic time interval
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description:
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- Time interval used in the aggregate crop supply response model for the country
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of South Sudan configuration
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49+
hasProcess: #each has to be mapped to an object.
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- Supply of Crop
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- Use of Fertilizer
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- Use of land
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hasInput:
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#input1
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- short_name: economic-sim #start always with the name of the input/output/param
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description: #should always follow the short name
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- Contains the economic data used in the simulation analysis
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position: 1
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hasValue: #maps to hasFixedResource
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- short_name: File for the Oromia region
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#below: maps to sd:value
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url: https://github.com/mintproject/MINT-WorkflowDomain/raw/master/WINGSWorkflowComponents/economic-v7/data/elasticity-cyclesdata.csv
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datacatalogId: FFF-e15c1f9e-c7ae-4cda-ba23-2e4f2286a18 #Optional
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- short_name: Second file for the Oromia region
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#below: maps to sd:value
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url: https://github.com/mintproject/MINT-WorkflowDomain/raw/master/WINGSWorkflowComponents/economic-v7/data/some_other_file
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type: #By default these are all datasetSpecifications. The type below is an additional aid
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- https://w3id.org/wings/export/MINT#EconomicSimData
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hasDimensionality: 0 #If this is not specified, assume 0
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#input2
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- short_name: economic-subsidies
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description:
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- File indicating the economic subsidies to use on each iteration of the model
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hasDimensionality: 0
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hasFormat: txt
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position: 2
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type:
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- https://w3id.org/wings/export/MINT#EconomicSubsidies
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hasOutput:
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#output 1
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- short_name: crop-yield
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description:
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- Contains the yield elasticities to fertilizer use that are derived from Cycles
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output
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hasDimensionality: 0
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hasFormat: csv
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position: 1
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type:
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- https://w3id.org/wings/export/MINT#CropYield
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#output 2
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- short_name: economic-data
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description:
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- Contains data on observed prices for each crop and supply elasticities and the
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costs of production for each crop
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position: 2
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type:
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- https://w3id.org/wings/export/MINT#EconomicData
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hasParameter:
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- short_name: maize-crop-price-adjustment
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description:
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- Change in market price by crop
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usesUnit: "%"
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value: 0 #maps to hasFixedValue

‎examples/SetupExample_new.yaml‎

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#This is an example. The model here is a simplification of an existing one.
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modelName: EACS #URI: https://w3id.org/okn/i/mint/EACS
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modelVersion: v7 #URI: https://w3id.org/okn/i/mint/EACS_v7
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#modelVersion: v7 #URI: https://w3id.org/okn/i/mint/EACS_v7
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configuration: EACS_v7_ethiopia
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setup: EACS_v7_ethiopia_2018
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#short_name maps to label. I think it's easier to understand
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description:
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- Change in market price by crop
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usesUnit: "%"
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value: 0 #maps to hasFixedValue
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value: 0 #maps to hasFixedValue

‎insertion_template.json‎

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This file was deleted.

‎setup.py‎

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"jsonschema>=3.0.0",
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"semver>=2.8.1",
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"requests",
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"ruamel.yaml",
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"modelcatalog-api"
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]
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zip_safe=False,
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install_requires=install_requires,
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python_requires=">=3.5.0",
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)
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)

‎src/caps/__init__.py‎

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__version__ = "0.2.1"
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__version__ = "0.3.0"

‎src/caps/__main__.py‎

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from caps import _utils, _metadata_schema, _transform_data, _initialize, _push, _validate
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__DEFAULT_CAPS_CLI_CREDENTIALS_FILE__ = "~/.caps-cli/credentials"
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__DEFAULT_MINT_API_CREDENTIALS_FILE__ = "~/.mint_api/credentials"
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@click.group()
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click.echo(f"{Path(sys.argv[0]).name} v{caps.__version__}")
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@cli.command(help="Configure Model Catalog API credentials")
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@click.option(
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"--profile",
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"-p",
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envvar="CAPS_PROFILE",
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type=str,
45+
default="default",
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metavar="<profile-name>",
47+
)
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def configure(profile="default"):
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api_username = click.prompt("Model Catalog API Username")
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api_password = click.prompt("Model Catalog API Password", hide_input=True)
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credentials_file = Path(
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os.getenv("MINT_API_CREDENTIALS_FILE", __DEFAULT_MINT_API_CREDENTIALS_FILE__)
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).expanduser()
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os.makedirs(str(credentials_file.parent), exist_ok=True)
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57+
credentials = configparser.ConfigParser()
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credentials.optionxform = str
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if credentials_file.exists():
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credentials.read(credentials_file)
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credentials[profile] = {
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"api_username": api_username,
65+
"api_password": api_password
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}
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68+
with credentials_file.open("w") as fh:
69+
credentials_file.parent.chmod(0o700)
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credentials_file.chmod(0o600)
71+
credentials.write(fh)
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click.secho(f"Success", fg="green")
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@cli.command(short_help="Create an empty JSON template to fill the data to be inserted in Model Catalog")
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@click.option(
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"--inputs",
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type=int,
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default=0,
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)
57-
def initialize(inputs=0, outputs=0, parameters=0):
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@click.option(
95+
"--directory",
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"-d",
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type=str,
98+
default="",
99+
help="Specify folder to generate new component in. Entering a filename will initialize the yaml with that name"
100+
)
101+
@click.option(
102+
"--force",
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"-f",
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is_flag=True,
105+
help="Force file creation. This will override a file with the same name. Use with caution"
106+
)
107+
def initialize(inputs=0, outputs=0, parameters=0, directory="", force=False):
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logging.info("Initializing YAML")
60-
_initialize.initialize(inputs, outputs, parameters)
110+
_initialize.initialize(inputs, outputs, parameters, directory, force)
61111
click.secho(f"Success", fg="green")
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@cli.command(short_help="Transform the input YAML into a Valid JSON for posting the file to Model Catalog")
115+
@click.option(
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"--profile",
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"-m",
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envvar="MINT_API_PROFILE",
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type=str,
120+
default="default",
121+
metavar="<profile-name>",
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)
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@click.argument("is_setup", default="false", type=str)
65124
@click.argument("yaml_file_path", default=None, type=str)
66-
def push(yaml_file_path):
125+
def push(is_setup, yaml_file_path, profile="default"):
67126
logging.info("Pushing yaml")
68-
_push.push(yaml_file_path)
127+
_push.push(is_setup, yaml_file_path, profile=profile)
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click.secho(f"Success", fg="green")
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