diff --git a/doc/list_action_software.md b/doc/list_action_software.md index b0ad91e8..71662076 100644 --- a/doc/list_action_software.md +++ b/doc/list_action_software.md @@ -12,7 +12,8 @@ workflows - List of actions and softwares | [**geometa-create-iso-19110**](#geometa-create-iso-19110)
| Metadata production | Produce an ISO 19110/19139 metadata object | entity | metadata | FALSE | geometa | | [**ows4R-publish-iso-19139**](#ows4R-publish-iso-19139)
| Metadata publication | Publish/Update an ISO/OGC 19139 metadata object using OGC CSW Protocol | NA | NA | FALSE | ows4R | | [**geonapi-publish-iso-19139**](#geonapi-publish-iso-19139)
| Metadata publication | Publish/Update an ISO/OGC 19139 metadata object with GeoNetwork API | NA | NA | FALSE | geonapi | -| [**geosapi-publish-ogc-services**](#geosapi-publish-ogc-services)
| Data upload,Data publication,Metadata publication | Publish vector data to GeoServer OGC web-services (WMS/WFS/WCS) | NA | NA | FALSE | geosapi | +| [**geosapi-publish-ogc-services**](#geosapi-publish-ogc-services)
| Data upload,Data publication,Metadata publication | Publish data to GeoServer OGC web-services (WMS/WFS/WCS) | NA | NA | FALSE | geosapi | +| [**geonode4R-publish-ogc-services**](#geonode4R-publish-ogc-services)
| Data upload,Data publication,Metadata publication | Publish data to GeoNode OGC web-services (WMS/WFS/WCS) | NA | NA | FALSE | geonode4R | | [**zen4R-deposit-record**](#zen4R-deposit-record)
| Data upload,Data publication,Metadata publication,DOI assignment | Deposits/Publish data and/or metadata in the Zenodo infrastructure | job | zenodo | TRUE | zen4R | | [**atom4R-dataverse-deposit-record**](#atom4R-dataverse-deposit-record)
| Data upload,Data publication,Metadata publication,DOI assignment | Deposits/Publish data and/or metetadata on a Dataverse using the Sword API | job | dataverse | TRUE | atom4R | | [**dataone-upload-datapackage**](#dataone-upload-datapackage)
| Data upload,Data publication,Metadata publication,DOI assignment | Uploads a data package to a DataOne metacat node | job | dataone | TRUE | mime,datapack,dataone | @@ -21,6 +22,7 @@ workflows - List of actions and softwares | [**sf-write-shp**](#sf-write-shp)
| Data writing | Import features data and zip files | entity | data | FALSE | sf | | [**eml-create-eml**](#eml-create-eml)
| Metadata production | Produce an EML metadata object | entity | metadata | FALSE | EML,emld | | [**d4storagehub4R-upload-data**](#d4storagehub4R-upload-data)
| Data upload | Upload data/metadata to a D4Science Workspace | NA | NA | FALSE | d4storagehub4R | +| [**ocs4R-upload-data**](#ocs4R-upload-data)
| Data upload | Upload data to an OCS Cloud (NextCloud/Owncloud) Workspace | NA | NA | FALSE | ocs4R | | [**create-metadata-rmd**](#create-metadata-rmd)
| Metadata production | Generate a Markdown out of a entity | entity | markdown | FALSE | rmarkdown | ### 1.1.1 List of geometa-create-iso-19115 options @@ -35,6 +37,7 @@ workflows - List of actions and softwares | addfeatures | Add entity data features - if defined - as metadata bounding polygon(s) | FALSE | | featureid | ID of entity data features used to identify bounding polygon(s) with option ‘addfeatures’ | NA | | subject_geography | Identifier of the subject handling a Geographic coverage. | geography | +| include_service_identification | Include service identification info metadata block | FALSE | | include_coverage_data_dimension_values | Include data dimensions’s range values to coverage description | FALSE | | include_coverage_service_dimension_values | Include ogc dimensions’s range values to coverage description | FALSE | @@ -58,13 +61,13 @@ workflows - List of actions and softwares ### 1.1.4 List of geonapi-publish-iso-19139 options -| name | definition | default | -|:-------------------|:-------------------------------------------------------------------------------------------|:----------------------| -| geometa_inspire | Validates ISO 19139 metadata with INSPIRE reference validator before publication | FALSE | -| privileges | Geonetwork privileges to set for the metadata to be published | view,dynamic,featured | -| group | Geonetwork user group to which the metadata should be associated | 2 | -| category | Category of metadata resources to which the metadata record should be associated | datasets | -| publish_thumbnails | Uploads local thumbnails as attachments and publish them as thumbnails / graphic overviews | TRUE | +| name | definition | default | +|:-------------------|:-------------------------------------------------------------------------------------------|:-------------------------------| +| geometa_inspire | Validates ISO 19139 metadata with INSPIRE reference validator before publication | FALSE | +| privileges | Geonetwork privileges to set for the metadata to be published | view,dynamic,download,featured | +| group | Geonetwork user group to which the metadata should be associated | 2 | +| category | Category of metadata resources to which the metadata record should be associated | datasets | +| publish_thumbnails | Uploads local thumbnails as attachments and publish them as thumbnails / graphic overviews | TRUE | ### 1.1.5 List of geosapi-publish-ogc-services options @@ -81,7 +84,11 @@ workflows - List of actions and softwares | enrich_with_relation_wcs | When enabled, enrichs entity with a base WCS link relation (applies to ‘grid’ only) | TRUE | | enrich_with_relation_wcs_download_links | When enabled, enrichs entity with WCS format-specific links for download purpose (applies to ‘grid’ only). Only GeoTIFF at now. | TRUE | -### 1.1.6 List of zen4R-deposit-record options +### 1.1.6 List of geonode4R-publish-ogc-services options + +*No options available for this action* + +### 1.1.7 List of zen4R-deposit-record options | name | definition | default | |:-----------------------|:--------------------------------------------------------------------------------------------|:-----------| @@ -96,7 +103,7 @@ workflows - List of actions and softwares | update_files | For an existing deposit, indicates if files should be updated | TRUE | | communities | One or more communities to which the deposit should be associated | NA | -### 1.1.7 List of atom4R-dataverse-deposit-record options +### 1.1.8 List of atom4R-dataverse-deposit-record options | name | definition | default | |:-----------------|:--------------------------------------------------------------------------------------------|:--------| @@ -106,11 +113,11 @@ workflows - List of actions and softwares | update_metadata | For an existing deposit, indicates if metadata elements should be updated | TRUE | | update_files | For an existing deposit, indicates if files should be updated | TRUE | -### 1.1.8 List of dataone-upload-datapackage options +### 1.1.9 List of dataone-upload-datapackage options *No options available for this action* -### 1.1.9 List of sf-write-generic options +### 1.1.10 List of sf-write-generic options | name | definition | default | |:--------------|:------------------------------------------------------------------------------|:--------| @@ -120,7 +127,7 @@ workflows - List of actions and softwares | append | Append policy | FALSE | | chunk.size | Size of DB upload data chunk. Default is 0L, meaning no chunking is operated. | 0 | -### 1.1.10 List of sf-write-dbi options +### 1.1.11 List of sf-write-dbi options | name | definition | default | |:--------------|:------------------------------------------------------------------------------|:--------| @@ -129,24 +136,28 @@ workflows - List of actions and softwares | append | Append policy | FALSE | | chunk.size | Size of DB upload data chunk. Default is 0L, meaning no chunking is operated. | 0 | -### 1.1.11 List of sf-write-shp options +### 1.1.12 List of sf-write-shp options *No options available for this action* -### 1.1.12 List of eml-create-eml options +### 1.1.13 List of eml-create-eml options | name | definition | default | |:-----------------|:-----------------------------------------------------------|:---------| | subject_taxonomy | Identifier of the subject handling the Taxonomic coverage. | taxonomy | -### 1.1.13 List of d4storagehub4R-upload-data options +### 1.1.14 List of d4storagehub4R-upload-data options | name | definition | default | |:-------------------|:----------------------------------------------------------------------------------------------------------------------------|:--------| | depositWithFiles | Indicates if the action is uploading files | FALSE | | otherUploadFolders | List of Folders (other than ‘data’ and ‘metadata’) to upload and which may contain files which should enrich others actions | | -### 1.1.14 List of create-metadata-rmd options +### 1.1.15 List of ocs4R-upload-data options + +*No options available for this action* + +### 1.1.16 List of create-metadata-rmd options | name | definition | default | |:--------------|:-----------------------------------------------------------------|:--------| @@ -169,12 +180,14 @@ workflows - List of actions and softwares | [**geoserver**](#218-geoserver)
| GeoServer REST API Client, powered by ‘geosapi’ package | geosapi | | [**zenodo**](#219-zenodo)
| Zenodo client powered by ‘zen4R’ package | zen4R | | [**sword_for_dataverse**](#2110-sword_for_dataverse)
| Dataverse SWORD API Client powered by ‘atom4R’ package | atom4R | -| [**dataone**](#2111-dataone)
| DataONe API Client powered by ‘dataone’ package | dataone | -| [**d4storagehub**](#2112-d4storagehub)
| D4science storage hub API Client powered by ‘d4storagehub4R’ package | d4storagehub4R | -| [**gbif**](#2113-gbif)
| Gbif API Client powered by ‘rgbif’ package | rgbif | -| [**thredds**](#2114-thredds)
| Thredds data server API Client powered by ‘thredds’ package | thredds | -| [**openapi**](#2115-openapi)
| OpenAPI client powered by ‘rapiclient’ package | rapiclient | -| [**ocs**](#2116-ocs)
| Open Collaboration Services (OCS) client powered by ‘ocs4R’ package | ocs4R | +| [**dataverse**](#2111-dataverse)
| Dataverse Native API Client powered by ‘dataverse’ package | dataverse | +| [**dataone**](#2112-dataone)
| DataONe API Client powered by ‘dataone’ package | dataone | +| [**d4storagehub**](#2113-d4storagehub)
| D4science storage hub API Client powered by ‘d4storagehub4R’ package | d4storagehub4R | +| [**gbif**](#2114-gbif)
| Gbif API Client powered by ‘rgbif’ package | rgbif | +| [**thredds**](#2115-thredds)
| Thredds data server API Client powered by ‘thredds’ package | thredds | +| [**openapi**](#2116-openapi)
| OpenAPI client powered by ‘rapiclient’ package | rapiclient | +| [**ocs**](#2117-ocs)
| Open Collaboration Services (OCS) client powered by ‘ocs4R’ package | ocs4R | +| [**geonode**](#2118-geonode)
| GeoNode client powered by ‘geonode4R’ package | geonode4R | ### 2.1.1 dbi @@ -202,11 +215,11 @@ workflows - List of actions and softwares #### 2.1.2.1 List of googledrive parameters -| name | label | definition | -|:------|:-----------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| email | Email | User email to authenticate in Google Drive | -| path | Path | An optional path within the Google drive repository. Default will be the root | -| token | User token | The user authentication token. To get your token in R: gargle::token_fetch()![credentials](https://latex.codecogs.com/png.image?%5Cdpi%7B110%7D&space;%5Cbg_white&space;credentials "credentials")access_token | +| name | label | definition | +|:------|:-----------|:------------------------------------------------------------------------------------------------------| +| email | Email | User email to authenticate in Google Drive | +| path | Path | An optional path within the Google drive repository. Default will be the root | +| token | User token | The user authentication token. To get your token in R: gargle::token_fetch()$credentials$access_token | #### 2.1.2.2 List of googledrive properties @@ -339,9 +352,23 @@ workflows - List of actions and softwares |:----------|:-------------|:----------------------------------------------| | dataverse | Dataverse ID | Dataverse id where to deposit/publish records | -### 2.1.11 dataone +### 2.1.11 dataverse + +#### 2.1.11.1 List of dataverse parameters + +| name | label | definition | +|:-------|:------|:---------------------| +| server | URL | Dataverse server URL | -#### 2.1.11.1 List of dataone parameters +#### 2.1.11.2 List of dataverse properties + +| name | label | definition | +|:----------|:-------------|:----------------------------------------------| +| dataverse | Dataverse ID | Dataverse id where to deposit/publish records | + +### 2.1.12 dataone + +#### 2.1.12.1 List of dataone parameters | name | label | definition | |:------|:----------------------|:-------------------------| @@ -349,28 +376,28 @@ workflows - List of actions and softwares | y | Member Node URL | Member Node URL | | token | User token | User Authorization token | -#### 2.1.11.2 List of dataone properties +#### 2.1.12.2 List of dataone properties *No properties available for this software* -### 2.1.12 d4storagehub +### 2.1.13 d4storagehub -#### 2.1.12.1 List of d4storagehub parameters +#### 2.1.13.1 List of d4storagehub parameters | name | label | definition | |:-------|:-----------|:---------------------------------------------------------------------| | token | User token | D4Science storage hub user authentication token | | logger | Logger | Level for ‘d4storagehub4R’ logger messages (NULL, ‘INFO’ or ‘DEBUG’) | -#### 2.1.12.2 List of d4storagehub properties +#### 2.1.13.2 List of d4storagehub properties | name | label | definition | |:----------|:----------|:-------------------------------------| | workspace | Workspace | D4Science storage hub workspace name | -### 2.1.13 gbif +### 2.1.14 gbif -#### 2.1.13.1 List of gbif parameters +#### 2.1.14.1 List of gbif parameters | name | label | definition | |:------|:---------|:---------------------------------------| @@ -378,26 +405,26 @@ workflows - List of actions and softwares | pwd | Password | Password for Gbif authentication | | email | Email | Email address for sending notification | -#### 2.1.13.2 List of gbif properties +#### 2.1.14.2 List of gbif properties *No properties available for this software* -### 2.1.14 thredds +### 2.1.15 thredds -#### 2.1.14.1 List of thredds parameters +#### 2.1.15.1 List of thredds parameters | name | label | definition | |:-------|:------------|:---------------------------------| | x | Catalog URL | url of top level catalog request | | prefix | Namespace | the namespace to examine | -#### 2.1.14.2 List of thredds properties +#### 2.1.15.2 List of thredds properties *No properties available for this software* -### 2.1.15 openapi +### 2.1.16 openapi -#### 2.1.15.1 List of openapi parameters +#### 2.1.16.1 List of openapi parameters | name | label | definition | |:--------------|:-------------------|:---------------------------------------------------------------| @@ -405,13 +432,13 @@ workflows - List of actions and softwares | api_key_name | Open API key name | Name of the API key for registered uses | | api_key_value | Open API key value | Value of the API key for registered uses (typically a token) | -#### 2.1.15.2 List of openapi properties +#### 2.1.16.2 List of openapi properties *No properties available for this software* -### 2.1.16 ocs +### 2.1.17 ocs -#### 2.1.16.1 List of ocs parameters +#### 2.1.17.1 List of ocs parameters | name | label | definition | |:-------|:---------|:-------------------------------------------------------| @@ -420,6 +447,23 @@ workflows - List of actions and softwares | pwd | Password | Password for user authentication | | logger | Logger | Level for ‘ows4R’ logger messages (NULL,INFO or DEBUG) | -#### 2.1.16.2 List of ocs properties +#### 2.1.17.2 List of ocs properties + +| name | label | definition | +|:----------|:----------|:---------------------| +| workspace | Workspace | Cloud workspace name | + +### 2.1.18 geonode + +#### 2.1.18.1 List of geonode parameters + +| name | label | definition | +|:-------|:---------|:-----------------------------------------------------------| +| url | URL | GeoNode endpoint URL | +| user | Username | Username for user authentication | +| pwd | Password | Password for user authentication | +| logger | Logger | Level for ‘geonode4R’ logger messages (NULL,INFO or DEBUG) | + +#### 2.1.18.2 List of geonode properties *No properties available for this software*