From 30eef77241d1e58feed6d932101719b8a0d50145 Mon Sep 17 00:00:00 2001 From: JoryGriffith <83308254+JoryGriffith@users.noreply.github.com> Date: Tue, 15 Oct 2024 14:27:45 -0400 Subject: [PATCH 01/17] Fixed an error in the conda downloading packages instructions. (#143) --- docs/how_to_contribute.html | 26 +- docs/search.json | 102 ++- .../docs/DefaultApi.html | 452 ++++++------ .../docs/GetHistory200ResponseInner.html | 643 ++++++++++++++++++ how_to_contribute.qmd | 4 +- 5 files changed, 1023 insertions(+), 204 deletions(-) create mode 100644 docs/ui/BonInABoxScriptService/docs/GetHistory200ResponseInner.html diff --git a/docs/how_to_contribute.html b/docs/how_to_contribute.html index f2b4d61a..58279ceb 100644 --- a/docs/how_to_contribute.html +++ b/docs/how_to_contribute.html @@ -237,6 +237,7 @@

Instructions for adapting your code to an analysis pipeline

Step 1: Creating a YAML file

Each script should be accompanied by a YAML file (.yml extension) that specifies inputs and outputs of that step of the pipeline.

+

Markdown is supported for pipeline, script, input and output descriptions. See this CommonMark quick reference for allowed markups.

Name and description

YAML files should begin with a name, description, and authors of the script. The name should be the same as the script that it describes but with a .yml extension.

@@ -273,9 +274,9 @@

Inputs

There are several different types of user inputs that can be specified in the YAML file:

---+++ @@ -377,26 +378,31 @@

Outputs

+ + + + + - + - + - + - + @@ -414,7 +420,7 @@

Outputs

Specifying R package dependencies with conda

“Conda provides package, dependency, and environment management for any language.” If a script is dependent on a specific package version, conda will load that package version to prevent breaking changes when packages are updated. BON in a Box uses a central conda environment that includes commonly used libraries, and supports dedicated environments for the scripts that need it.

-

This means that instead of installing packages in R scripts, they are installed in the R environment in conda. Note that you still need to load the packages in your scripts.

+

This means that instead of installing packages in R scripts, they are installed in the R environment in Conda. Note that you still need to load the packages in your scripts.

Check if the libraries you need are in conda

    @@ -444,7 +450,7 @@

    +R -e 'install.packages(c("<packages>""), repos="https://cloud.r-project.org/")'

    • You can use devtools::install_github() in a similar fashion:

      docker exec -it biab-runner-conda bash
@@ -585,7 +591,7 @@ 
      Receiving inputs
      
         "/output/data/loadFromStac/6af2ccfcd4b0ffe243ff01e3b7eccdc3/bio2_7333b3d111981-01-01.tif"
     ],
     "presence_background": "/output/SDM/setupDataSdm/edb9492031df9e063a5ec5c325bacdb1/presence_background.tsv",
-    "proj": "EPSG:6623",
+    "proj": "EPSG:6622",
     "rm": [0.5, 1.0, 2.0]
 }

      The script reads the input.json file that is in the run folder. This JSON file is automatically created from the BON in a Box pipeline. Here is an example of how to read the input folder in the R script:

      diff --git a/docs/search.json b/docs/search.json index b2f9b0e7..741afac0 100644 --- a/docs/search.json +++ b/docs/search.json @@ -144,14 +144,14 @@ "href": "how_to_contribute.html#step-1-creating-a-yaml-file", "title": "How to Contribute", "section": "Step 1: Creating a YAML file", - "text": "Step 1: Creating a YAML file\nEach script should be accompanied by a YAML file (.yml extension) that specifies inputs and outputs of that step of the pipeline.\n\nName and description\nYAML files should begin with a name, description, and authors of the script. The name should be the same as the script that it describes but with a .yml extension.\nExample:\nscript: script_name.R\nname: Script Name\ndescription: Describe what the script does\nauthor:\n - name: John Doe (john.doe@gmail.com)\n - name: Jane Doe (jane.doe@gmail.com)\n\n\nInputs\nNext, the YAML file should specify the inputs of the script. These inputs will either be outputs from the previous script, which can be connected by lines in the pipeline editor, or specified by the user in the input form.\nHere is an example where the input is a raster file of land cover pulled from a public database and a coordinate reference system that is specified by the user:\ninputs:\n landcover_raster:\n label: Raster of landcover\n description: Landcover data pulled from EarthEnv database with 1x1km resolution\n type: application/geo+json\n crs:\n label: coordinate reference system for output\n description: ESPG coordinate reference system for output\n type: int\n example: 4326\n unit_distance:\n label: unit for distance measurement\n description: String value of\n type: options\n options:\n - \"m2\"\n - \"km2\"\nSpecifying an example will autofill that input with the example unless changed by the user. Not specifying an example will leave that input blank (null).\nThere are several different types of user inputs that can be specified in the YAML file:\n\n\n\n\n\n\n\n\n“Type” attribute in the yaml\nIU rendering\nDescription\n\n\n\n\nboolean\nPlain text\ntrue/false\n\n\nfloat, float[]\nPlain text\npositive and negative numbers with a decimal point\n\n\nint, int[]\nPlain text\ninteger\n\n\noptions1\nPlain text\ndropdown menu\n\n\ntext, text[]\nPlain text\ntext input (words)\n\n\n(any unknown type)\nPlain text\n\n\n\n\n1options type requires an additioal options attribute to be added with the available options.\noptions_example:\n label: Options example\n description: The user has to select between a fixed number of text options. Also called select or enum. The script receives the selected option as text.\n type: options\n options:\n - first option\n - second option\n - third option\n example: third option\n\n\nOutputs\nAfter specifying the inputs, you can specify what you want the script to output.\nHere is an example:\noutputs:\n result:\n label: Analysis result\n description: The result of the analysis, in CSV form\n type: text/csv\n result_plot:\n label: Result plot\n description: Plot of results\n type: image/png\nThere are also several types of outputs that can be created\n\n\n\n\n\n\n\n\nFile Type\nMIME type to use in the yaml\nUI rendering\n\n\n\n\nCSV\ntext/csv\nHTML table (partial content)\n\n\nGeoJSON\napplication/geo+json\nMap\n\n\nGeoPackage\napplication/geopackage+sqlite3\nLink\n\n\nGeoTIFF2\nimage/tiff;application=geotiff\nMap widget (leaflet)\n\n\nJPG\nimage/jpg\ntag\n\n\nShapefile\napplication/dbf\nLink\n\n\nText\ntext/plain\nPlain text\n\n\nTSV\ntext/tab-separated-values\nHTML table (partial content)\n\n\n\n(any unknown type)\nPlain text or link\n\n\n\n2When used as an output, image/tiff;application=geotiff type allows an additional range attribute to be added with the min and max values that the tiff should hold. This will be used for display purposes.\nmap:\n label: My map\n description: Some map that shows something\n type: image/tiff;application=geotiff\n range: [0.1, 254]\n example: https://example.com/mytiff.tif\n\n\nSpecifying R package dependencies with conda\n“Conda provides package, dependency, and environment management for any language.” If a script is dependent on a specific package version, conda will load that package version to prevent breaking changes when packages are updated. BON in a Box uses a central conda environment that includes commonly used libraries, and supports dedicated environments for the scripts that need it.\nThis means that instead of installing packages in R scripts, they are installed in the R environment in conda. Note that you still need to load the packages in your scripts.\n\nCheck if the libraries you need are in conda\n\nTo check if the packages you need are already in the R environment in conda, go to runners/r-environment.yml in the BON in a Box project folder. The list of packages already installed will be under “dependencies”.\n\n\n\nInstall any libraries that are not already in the environment\n\nIf your package is not already in the R environment, you will need to add it.\nFirst, search for the package name on anaconda. Packages that are in anaconda will be recognized and easily loaded by conda. If it is there:\n\nAdd it to the runners/r-environment.yml file\nAdd it to your local environment, replacing <package name> in: docker exec -it biab-runner-conda mamba install -n rbase <package name> in the terminal. Make sure the program is in front of the package name (e.g. r-tidyverse)\n\nIf it is not found in anaconda\n\nGo to the runners/conda-dockerfile and add it to the install command. Replace <package> with your package name.\nRUN bash --login -c \"mamba activate rbase; R -e 'install.packages(c(\\<package 1>\\\", \\\n \\\"<package 2>\\\", \\\n \\\"<package 3>\\\"\\\n ), repos=\\\"https://cloud.r-project.org/\\\")'\"\nOr for packages in development loaded from github.\nRUN bash --login -c \"mamba activate rbase; R -e 'devtools::install_github(\\\"<user>/<package>\\\")'\"\nInstall in in your local environment by typing this in the terminal, replacing <packages> (three commands should be pasted separately):\ndocker exec -it biab-runner-conda bash\n\nmamba activate rbase\n\nR -e 'install.packages(c(<packages>), repose=\"https://cloud.r-project.org/\")\n\nYou can use devtools::install_github() in a similar fashion:\ndocker exec -it biab-runner-conda bash\n\nmamba activate rbase\n\nR -e 'devtools::install_github(\"<user>/<package>\")'\n\nDo not add these packages to the r-environment file or the conda portion of the yml file because conda will not be able to recognize them\n\nTo refresh the R environment to match the r-environment.yml file, run docker exec -u root -it biab-runner-conda mamba env update –file r-environment.yml in the terminal.\n\n\n\nAdd any version dependencies to your yml file\n\nIf your script does not require a specific version, you do not need to include a conda section to the yml file. The environment will be the default R environment.\nIf you need a specific version of an already installed library, such as when a breaking change occurs and the script cannot be adapted to use the new version, you can use conda to specify a specific package version in your yml file.\n\nIf you include a conda section, make sure you list all your dependencies. This is creating a new separate environment, not a supplement to the base environment. This means that all of the packages that you need need to be specified in here, even if they are in the r-environment.yml file.\n\n\nconda: # Optional: if you script requires specific versions of packages.\n channels:\n - conda-forge\n - r\n dependencies:\n - r-rjson # read inputs and save outputs for R scripts\n - package=version\nFor more information, refer to the conda documentation.\n\n\n\nExamples\nHere is an example of a complete YAML file with inputs and outputs:\nscript: script_name.R\nname: Script Name\ndescription: Describe what the script does\nauthor:\n - name: John Doe (john.doe@gmail.com)\n - name: Jane Doe (jane.doe@gmail.com)\ninputs:\n landcover_raster:\n label: Raster of landcover\n description: Landcover data pulled from EarthEnv database with 1x1km resolution\n type: application/geo+json\n crs:\n label: coordinate reference system for output\n description: ESPG coordinate reference system for output\n type: int\n example: 4326\n unit_distance:\n label: unit for distance measurement\n description: String value of\n type: options\n options:\n - \"m2\"\n - \"km2\"\noutputs:\n result:\n label: Analysis result\n description: The result of the analysis, in CSV form\n type: text/csv\n result_plot:\n label: Result plot\n description: Plot of results\n type: image/png\nconda: # Optional, only needed if your script has specific package dependencies\n channels:\n - r\n dependencies:\n - r-rjson=0.2.22 #package=version\nYAML is a space sensitive format, so make sure all the tab sets are correct in the file.\nIf inputs are outputs from a previous step in the pipeline, make sure to give the inputs and outputs the same name and they will be automatically linked in the pipeline.\nHere is an empty commented sample that can be filled in\nscript: # script file with extension, such as \"myScript.R\".\nname: # short name, such as My Script\ndescription: # Targeted to those who will interpret pipeline results and edit pipelines.\nauthor: # 1 to many\n - name: # Full name\n email: # Optional, email address of the author. This will be publicly available.\n identifier: # Optional, full URL of a unique digital identifier, such as an ORCID.\nlicense: # Optional. If unspecified, the project's MIT license will apply.\nexternal_link: # Optional, link to a separate project, github repo, etc.\ntimeout: # Optional, in minutes. By defaults steps time out after 1h to avoid hung process to consume resources. It can be made longer for heavy processes.\n\ninputs: # 0 to many\n key: # replace the word \"key\" by a snake case identifier for this input\n label: # Human-readable version of the name\n description: # Targetted to those who will interpret pipeline results and edit pipelines.\n type: # see below\n example: # will also be used as default value, can be null\n\noutputs: # 1 to many\n key:\n label:\n description:\n type:\n example: # optional, for documentation purpose only\n\nreferences: # 0 to many\n - text: # plain text reference\n doi: # link\n\nconda: # Optional, only needed if your script has specific package dependencies\n channels: # programs that you need\n - # list here\n dependencies: # any packages that are dependent on a specfic version\n - # list here\nSee example" + "text": "Step 1: Creating a YAML file\nEach script should be accompanied by a YAML file (.yml extension) that specifies inputs and outputs of that step of the pipeline.\nMarkdown is supported for pipeline, script, input and output descriptions. See this CommonMark quick reference for allowed markups.\n\nName and description\nYAML files should begin with a name, description, and authors of the script. The name should be the same as the script that it describes but with a .yml extension.\nExample:\nscript: script_name.R\nname: Script Name\ndescription: Describe what the script does\nauthor:\n - name: John Doe (john.doe@gmail.com)\n - name: Jane Doe (jane.doe@gmail.com)\n\n\nInputs\nNext, the YAML file should specify the inputs of the script. These inputs will either be outputs from the previous script, which can be connected by lines in the pipeline editor, or specified by the user in the input form.\nHere is an example where the input is a raster file of land cover pulled from a public database and a coordinate reference system that is specified by the user:\ninputs:\n landcover_raster:\n label: Raster of landcover\n description: Landcover data pulled from EarthEnv database with 1x1km resolution\n type: application/geo+json\n crs:\n label: coordinate reference system for output\n description: ESPG coordinate reference system for output\n type: int\n example: 4326\n unit_distance:\n label: unit for distance measurement\n description: String value of\n type: options\n options:\n - \"m2\"\n - \"km2\"\nSpecifying an example will autofill that input with the example unless changed by the user. Not specifying an example will leave that input blank (null).\nThere are several different types of user inputs that can be specified in the YAML file:\n\n\n\n\n\n\n\n\n“Type” attribute in the yaml\nIU rendering\nDescription\n\n\n\n\nboolean\nPlain text\ntrue/false\n\n\nfloat, float[]\nPlain text\npositive and negative numbers with a decimal point\n\n\nint, int[]\nPlain text\ninteger\n\n\noptions1\nPlain text\ndropdown menu\n\n\ntext, text[]\nPlain text\ntext input (words)\n\n\n(any unknown type)\nPlain text\n\n\n\n\n1options type requires an additioal options attribute to be added with the available options.\noptions_example:\n label: Options example\n description: The user has to select between a fixed number of text options. Also called select or enum. The script receives the selected option as text.\n type: options\n options:\n - first option\n - second option\n - third option\n example: third option\n\n\nOutputs\nAfter specifying the inputs, you can specify what you want the script to output.\nHere is an example:\noutputs:\n result:\n label: Analysis result\n description: The result of the analysis, in CSV form\n type: text/csv\n result_plot:\n label: Result plot\n description: Plot of results\n type: image/png\nThere are also several types of outputs that can be created\n\n\n\n\n\n\n\n\nFile Type\nMIME type to use in the yaml\nUI rendering\n\n\n\n\nCSV\ntext/csv\nHTML table (partial content)\n\n\nGeoJSON\napplication/geo+json\nMap\n\n\nGeoPackage\napplication/geopackage+sqlite3\nLink\n\n\nGeoTIFF2\nimage/tiff;application=geotiff\nMap widget (leaflet)\n\n\nHTML\ntext/html\nOpen in new tab\n\n\nJPG\nimage/jpg\ntag\n\n\nShapefile\napplication/dbf\nLink\n\n\nText\ntext/plain\nPlain text\n\n\nTSV\ntext/tab-separated-values\nHTML table (partial content)\n\n\n\n(any unknown type)\nPlain text or link\n\n\n\n2When used as an output, image/tiff;application=geotiff type allows an additional range attribute to be added with the min and max values that the tiff should hold. This will be used for display purposes.\nmap:\n label: My map\n description: Some map that shows something\n type: image/tiff;application=geotiff\n range: [0.1, 254]\n example: https://example.com/mytiff.tif\n\n\nSpecifying R package dependencies with conda\n“Conda provides package, dependency, and environment management for any language.” If a script is dependent on a specific package version, conda will load that package version to prevent breaking changes when packages are updated. BON in a Box uses a central conda environment that includes commonly used libraries, and supports dedicated environments for the scripts that need it.\nThis means that instead of installing packages in R scripts, they are installed in the R environment in Conda. Note that you still need to load the packages in your scripts.\n\nCheck if the libraries you need are in conda\n\nTo check if the packages you need are already in the R environment in conda, go to runners/r-environment.yml in the BON in a Box project folder. The list of packages already installed will be under “dependencies”.\n\n\n\nInstall any libraries that are not already in the environment\n\nIf your package is not already in the R environment, you will need to add it.\nFirst, search for the package name on anaconda. Packages that are in anaconda will be recognized and easily loaded by conda. If it is there:\n\nAdd it to the runners/r-environment.yml file\nAdd it to your local environment, replacing <package name> in: docker exec -it biab-runner-conda mamba install -n rbase <package name> in the terminal. Make sure the program is in front of the package name (e.g. r-tidyverse)\n\nIf it is not found in anaconda\n\nGo to the runners/conda-dockerfile and add it to the install command. Replace <package> with your package name.\nRUN bash --login -c \"mamba activate rbase; R -e 'install.packages(c(\\<package 1>\\\", \\\n \\\"<package 2>\\\", \\\n \\\"<package 3>\\\"\\\n ), repos=\\\"https://cloud.r-project.org/\\\")'\"\nOr for packages in development loaded from github.\nRUN bash --login -c \"mamba activate rbase; R -e 'devtools::install_github(\\\"<user>/<package>\\\")'\"\nInstall in in your local environment by typing this in the terminal, replacing <packages> (three commands should be pasted separately):\ndocker exec -it biab-runner-conda bash\n\nmamba activate rbase\n\nR -e 'install.packages(c(\"<packages>\"\"), repos=\"https://cloud.r-project.org/\")'\n\nYou can use devtools::install_github() in a similar fashion:\ndocker exec -it biab-runner-conda bash\n\nmamba activate rbase\n\nR -e 'devtools::install_github(\"<user>/<package>\")'\n\nDo not add these packages to the r-environment file or the conda portion of the yml file because conda will not be able to recognize them\n\nTo refresh the R environment to match the r-environment.yml file, run docker exec -u root -it biab-runner-conda mamba env update –file r-environment.yml in the terminal.\n\n\n\nAdd any version dependencies to your yml file\n\nIf your script does not require a specific version, you do not need to include a conda section to the yml file. The environment will be the default R environment.\nIf you need a specific version of an already installed library, such as when a breaking change occurs and the script cannot be adapted to use the new version, you can use conda to specify a specific package version in your yml file.\n\nIf you include a conda section, make sure you list all your dependencies. This is creating a new separate environment, not a supplement to the base environment. This means that all of the packages that you need need to be specified in here, even if they are in the r-environment.yml file.\n\n\nconda: # Optional: if you script requires specific versions of packages.\n channels:\n - conda-forge\n - r\n dependencies:\n - r-rjson # read inputs and save outputs for R scripts\n - package=version\nFor more information, refer to the conda documentation.\n\n\n\nExamples\nHere is an example of a complete YAML file with inputs and outputs:\nscript: script_name.R\nname: Script Name\ndescription: Describe what the script does\nauthor:\n - name: John Doe (john.doe@gmail.com)\n - name: Jane Doe (jane.doe@gmail.com)\ninputs:\n landcover_raster:\n label: Raster of landcover\n description: Landcover data pulled from EarthEnv database with 1x1km resolution\n type: application/geo+json\n crs:\n label: coordinate reference system for output\n description: ESPG coordinate reference system for output\n type: int\n example: 4326\n unit_distance:\n label: unit for distance measurement\n description: String value of\n type: options\n options:\n - \"m2\"\n - \"km2\"\noutputs:\n result:\n label: Analysis result\n description: The result of the analysis, in CSV form\n type: text/csv\n result_plot:\n label: Result plot\n description: Plot of results\n type: image/png\nconda: # Optional, only needed if your script has specific package dependencies\n channels:\n - r\n dependencies:\n - r-rjson=0.2.22 #package=version\nYAML is a space sensitive format, so make sure all the tab sets are correct in the file.\nIf inputs are outputs from a previous step in the pipeline, make sure to give the inputs and outputs the same name and they will be automatically linked in the pipeline.\nHere is an empty commented sample that can be filled in\nscript: # script file with extension, such as \"myScript.R\".\nname: # short name, such as My Script\ndescription: # Targeted to those who will interpret pipeline results and edit pipelines.\nauthor: # 1 to many\n - name: # Full name\n email: # Optional, email address of the author. This will be publicly available.\n identifier: # Optional, full URL of a unique digital identifier, such as an ORCID.\nlicense: # Optional. If unspecified, the project's MIT license will apply.\nexternal_link: # Optional, link to a separate project, github repo, etc.\ntimeout: # Optional, in minutes. By defaults steps time out after 1h to avoid hung process to consume resources. It can be made longer for heavy processes.\n\ninputs: # 0 to many\n key: # replace the word \"key\" by a snake case identifier for this input\n label: # Human-readable version of the name\n description: # Targetted to those who will interpret pipeline results and edit pipelines.\n type: # see below\n example: # will also be used as default value, can be null\n\noutputs: # 1 to many\n key:\n label:\n description:\n type:\n example: # optional, for documentation purpose only\n\nreferences: # 0 to many\n - text: # plain text reference\n doi: # link\n\nconda: # Optional, only needed if your script has specific package dependencies\n channels: # programs that you need\n - # list here\n dependencies: # any packages that are dependent on a specfic version\n - # list here\nSee example" }, { "objectID": "how_to_contribute.html#step-2-integrating-yaml-inputs-and-outputs-into-your-script", "href": "how_to_contribute.html#step-2-integrating-yaml-inputs-and-outputs-into-your-script", "title": "How to Contribute", "section": "Step 2: Integrating YAML inputs and outputs into your script", - "text": "Step 2: Integrating YAML inputs and outputs into your script\nNow that you have created your YAML file, the inputs and outputs need to be integrated into your scripts.\nThe scripts perform the actual work behind the scenes. They are located in /scripts folder\nCurrently supported : - R v4.3.1 - Julia v1.9.3 - Python3 v3.9.2 - sh\nScript lifecycle:\n\nScript launched with output folder as a parameter. (In R, an outputFolder variable in the R session. In Julia, Shell and Python, the output folder is received as an argument.)\nScript reads input.json to get execution parameters (ex. species, area, data source, etc.)\nScript performs its task\nScript generates output.json containing links to result files, or native values (number, string, etc.)\n\nSee empty R script for a minimal script lifecycle example.\n\nReceiving inputs\nWhen running a script, a folder is created for each given set of parameters. The same parameters result in the same folder, different parameters result in a different folder. The inputs for a given script are saved in an input.json file in this unique run folder.\nThe file contains the id of the parameters that were specified in the yaml script description, associated to the values for this run. Example:\n{\n \"fc\": [\"L\", \"LQ\", \"LQHP\"],\n \"method_select_params\": \"AUC\",\n \"n_folds\": 2,\n \"orientation_block\": \"lat_lon\",\n \"partition_type\": \"block\",\n \"predictors\": [\n \"/output/data/loadFromStac/6af2ccfcd4b0ffe243ff01e3b7eccdc3/bio1_75548ca61981-01-01.tif\",\n \"/output/data/loadFromStac/6af2ccfcd4b0ffe243ff01e3b7eccdc3/bio2_7333b3d111981-01-01.tif\"\n ],\n \"presence_background\": \"/output/SDM/setupDataSdm/edb9492031df9e063a5ec5c325bacdb1/presence_background.tsv\",\n \"proj\": \"EPSG:6623\",\n \"rm\": [0.5, 1.0, 2.0]\n}\nThe script reads the input.json file that is in the run folder. This JSON file is automatically created from the BON in a Box pipeline. Here is an example of how to read the input folder in the R script:\nFirst, set the environment for the script:\nSys.getenv(\"SCRIPT_LOCATION\")\nAnd then set the ‘input’ environment variables. The ‘input’ environment contains the specified inputs from the BON in a Box platform.\ninput <- rjson::fromJSON(file=file.path(outputFolder, \"input.json\")) # Load input file\nNext, for any functions that are using these inputs, they need to be specified.\nInputs are specified by input$input_name.\nFor example, to create a function to take the square root of a number that was input by the user in the UI:\nresult <- sqrt(input$number)\nThis means if the user inputs the number 144, this will be run in the function and output 12.\nHere is another example to read in an output from a previous step of the pipeline, which was output in csv format.\ndat <- read.csv(input$csv_file)\nNext, you have to specify the outputs, which can be saved in a variety of formats. The format must be accurately specified in the YAML file.\nHere is an example of an output with a csv file and a plot in png format.\nresult_path <- file.path(outputFolder, \"result.csv\")\nwrite.csv(result, result_path, row.names = F )\n\nresult_plot_path <- file.path(outputFolder, \"result_plot.png\")\nggsave(result_path, result)\n\noutput <- list(result = result_path,\nresult_plot = result_plot_path)\nLastly, write the output as a JSON file:\nsetwd(outputFolder)\njsonlite::write_json(output, \"output.json\", auto_unbox = TRUE, pretty = TRUE)\n\n\nScript validation\nThe syntax and structure of the script description file will be validated on push. To run the validation locally, run validate.sh\nThis validates that the syntax and structure are correct, but not that it’s content is correct. Hence, peer review of the scripts and the description files is mandatory before accepting a pull requests.\n\n\nReporting problems\nThe output keys info, warning and error can be used to report problems in script execution. They do not need to be described in the outputs section of the description. They will be displayed specially in the UI.\nAny error message will halt the rest of the pipeline.\nTo code an error so it prints in the pipeline step, you will need to wrap your script in a try catch function and then code it to print errors.\n{r}\noutput<- tryCatch({\n\nSCRIPT BODY HERE\n\n}, error = function(e) { list(error= conditionMessage(e)) })\nThis will print any errors in the output of the script in the UI.\nYou can also code specific error messages. For example, if a user wanted the analysis to stop if the result was less than 0:\noutput<- tryCatch({\n\nif (result < 0){\nstop(\"Analysis was halted because result is less than 0.\")\n}\n\n}, error = function(e) { list(error= conditionMessage(e)) })\nAnd then the customized error message would appear in the UI." + "text": "Step 2: Integrating YAML inputs and outputs into your script\nNow that you have created your YAML file, the inputs and outputs need to be integrated into your scripts.\nThe scripts perform the actual work behind the scenes. They are located in /scripts folder\nCurrently supported : - R v4.3.1 - Julia v1.9.3 - Python3 v3.9.2 - sh\nScript lifecycle:\n\nScript launched with output folder as a parameter. (In R, an outputFolder variable in the R session. In Julia, Shell and Python, the output folder is received as an argument.)\nScript reads input.json to get execution parameters (ex. species, area, data source, etc.)\nScript performs its task\nScript generates output.json containing links to result files, or native values (number, string, etc.)\n\nSee empty R script for a minimal script lifecycle example.\n\nReceiving inputs\nWhen running a script, a folder is created for each given set of parameters. The same parameters result in the same folder, different parameters result in a different folder. The inputs for a given script are saved in an input.json file in this unique run folder.\nThe file contains the id of the parameters that were specified in the yaml script description, associated to the values for this run. Example:\n{\n \"fc\": [\"L\", \"LQ\", \"LQHP\"],\n \"method_select_params\": \"AUC\",\n \"n_folds\": 2,\n \"orientation_block\": \"lat_lon\",\n \"partition_type\": \"block\",\n \"predictors\": [\n \"/output/data/loadFromStac/6af2ccfcd4b0ffe243ff01e3b7eccdc3/bio1_75548ca61981-01-01.tif\",\n \"/output/data/loadFromStac/6af2ccfcd4b0ffe243ff01e3b7eccdc3/bio2_7333b3d111981-01-01.tif\"\n ],\n \"presence_background\": \"/output/SDM/setupDataSdm/edb9492031df9e063a5ec5c325bacdb1/presence_background.tsv\",\n \"proj\": \"EPSG:6622\",\n \"rm\": [0.5, 1.0, 2.0]\n}\nThe script reads the input.json file that is in the run folder. This JSON file is automatically created from the BON in a Box pipeline. Here is an example of how to read the input folder in the R script:\nFirst, set the environment for the script:\nSys.getenv(\"SCRIPT_LOCATION\")\nAnd then set the ‘input’ environment variables. The ‘input’ environment contains the specified inputs from the BON in a Box platform.\ninput <- rjson::fromJSON(file=file.path(outputFolder, \"input.json\")) # Load input file\nNext, for any functions that are using these inputs, they need to be specified.\nInputs are specified by input$input_name.\nFor example, to create a function to take the square root of a number that was input by the user in the UI:\nresult <- sqrt(input$number)\nThis means if the user inputs the number 144, this will be run in the function and output 12.\nHere is another example to read in an output from a previous step of the pipeline, which was output in csv format.\ndat <- read.csv(input$csv_file)\nNext, you have to specify the outputs, which can be saved in a variety of formats. The format must be accurately specified in the YAML file.\nHere is an example of an output with a csv file and a plot in png format.\nresult_path <- file.path(outputFolder, \"result.csv\")\nwrite.csv(result, result_path, row.names = F )\n\nresult_plot_path <- file.path(outputFolder, \"result_plot.png\")\nggsave(result_path, result)\n\noutput <- list(result = result_path,\nresult_plot = result_plot_path)\nLastly, write the output as a JSON file:\nsetwd(outputFolder)\njsonlite::write_json(output, \"output.json\", auto_unbox = TRUE, pretty = TRUE)\n\n\nScript validation\nThe syntax and structure of the script description file will be validated on push. To run the validation locally, run validate.sh\nThis validates that the syntax and structure are correct, but not that it’s content is correct. Hence, peer review of the scripts and the description files is mandatory before accepting a pull requests.\n\n\nReporting problems\nThe output keys info, warning and error can be used to report problems in script execution. They do not need to be described in the outputs section of the description. They will be displayed specially in the UI.\nAny error message will halt the rest of the pipeline.\nTo code an error so it prints in the pipeline step, you will need to wrap your script in a try catch function and then code it to print errors.\n{r}\noutput<- tryCatch({\n\nSCRIPT BODY HERE\n\n}, error = function(e) { list(error= conditionMessage(e)) })\nThis will print any errors in the output of the script in the UI.\nYou can also code specific error messages. For example, if a user wanted the analysis to stop if the result was less than 0:\noutput<- tryCatch({\n\nif (result < 0){\nstop(\"Analysis was halted because result is less than 0.\")\n}\n\n}, error = function(e) { list(error= conditionMessage(e)) })\nAnd then the customized error message would appear in the UI." }, { "objectID": "how_to_contribute.html#step-3-connect-your-scripts-with-the-bon-in-a-box-pipeline-editor.", @@ -306,5 +306,103 @@ "title": "Developer documentation", "section": "", "text": "Since runner-r and runner-julia run in a separate docker, when the user stops the pipeline, the signal must go from the script-server, to the runner, to the running script. Docker does not allow this by default, this is why we save the PID in a file and use a separate exec command to kill the process.\nThe PID file is called .pid and is located in the output folder of the run. It is deleted when the script completes. For details, see ScriptRun.kt." + }, + { + "objectID": "ui/BonInABoxScriptService/docs/DefaultApi.html", + "href": "ui/BonInABoxScriptService/docs/DefaultApi.html", + "title": "BonInABoxScriptService.DefaultApi", + "section": "", + "text": "All URIs are relative to http://localhost\n\n\n\nMethod\nHTTP request\nDescription\n\n\n\n\ngetHistory\nGET /api/history\nGet the history of runs for all pipelines on this server\n\n\ngetInfo\nGET /{type}/{descriptionPath}/info\nGet metadata about this script or pipeline.\n\n\ngetListOf\nGET /{type}/list\nGet a list of available steps of given type and their names.\n\n\ngetOutputFolders\nGET /{type}/{id}/outputs\nGet the output folders of the scripts composing this pipeline\n\n\ngetPipeline\nGET /pipeline/{descriptionPath}/get\nGet JSON file that describes the pipeline.\n\n\ngetVersions\nGET /api/versions\nReturns the version of system components.\n\n\nrun\nPOST /{type}/{descriptionPath}/run\nRuns the script or pipeline matching `descriptionPath`.\n\n\nsavePipeline\nPOST /pipeline/save/{filename}\nSave a json file to the pipeline folder.\n\n\nstop\nGET /{type}/{id}/stop\nStop the specified pipeline run.\n\n\n\n\n\n\n[GetHistory200ResponseInner] getHistory()\n\nGet the history of runs for all pipelines on this server\n\n\nimport BonInABoxScriptService from 'bon_in_a_box_script_service';\n\nlet apiInstance = new BonInABoxScriptService.DefaultApi();\napiInstance.getHistory((error, data, response) => {\n if (error) {\n console.error(error);\n } else {\n console.log('API called successfully. Returned data: ' + data);\n }\n});\n\n\n\nThis endpoint does not need any parameter.\n\n\n\n[GetHistory200ResponseInner]\n\n\n\nNo authorization required\n\n\n\n\nContent-Type: Not defined\nAccept: application/json\n\n\n\n\n\n\nInfo getInfo(type, descriptionPath)\n\nGet metadata about this script or pipeline.\n\n\nimport BonInABoxScriptService from 'bon_in_a_box_script_service';\n\nlet apiInstance = new BonInABoxScriptService.DefaultApi();\nlet type = \"type_example\"; // String | Script or pipeline\nlet descriptionPath = \"descriptionPath_example\"; // String | Where to find the step. For scripts, paths are relative to the /script folder. For pipelines, paths are relative to the /pipeline folder.\napiInstance.getInfo(type, descriptionPath, (error, data, response) => {\n if (error) {\n console.error(error);\n } else {\n console.log('API called successfully. Returned data: ' + data);\n }\n});\n\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nNotes\n\n\n\n\ntype\nString\nScript or pipeline\n\n\n\ndescriptionPath\nString\nWhere to find the step. For scripts, paths are relative to the /script folder. For pipelines, paths are relative to the /pipeline folder.\n\n\n\n\n\n\n\nInfo\n\n\n\nNo authorization required\n\n\n\n\nContent-Type: Not defined\nAccept: application/json\n\n\n\n\n\n\n{String: String} getListOf(type)\n\nGet a list of available steps of given type and their names.\n\n\nimport BonInABoxScriptService from 'bon_in_a_box_script_service';\n\nlet apiInstance = new BonInABoxScriptService.DefaultApi();\nlet type = \"type_example\"; // String | Script or pipeline\napiInstance.getListOf(type, (error, data, response) => {\n if (error) {\n console.error(error);\n } else {\n console.log('API called successfully. Returned data: ' + data);\n }\n});\n\n\n\n\n\n\nName\nType\nDescription\nNotes\n\n\n\n\ntype\nString\nScript or pipeline\n\n\n\n\n\n\n\n{String: String}\n\n\n\nNo authorization required\n\n\n\n\nContent-Type: Not defined\nAccept: application/json\n\n\n\n\n\n\n{String: String} getOutputFolders(type, id)\n\nGet the output folders of the scripts composing this pipeline\n\n\nimport BonInABoxScriptService from 'bon_in_a_box_script_service';\n\nlet apiInstance = new BonInABoxScriptService.DefaultApi();\nlet type = \"type_example\"; // String | Script or pipeline\nlet id = \"id_example\"; // String | Where to find the pipeline or step outputs in ./output folder. It also acts as a handle to stop the run. \napiInstance.getOutputFolders(type, id, (error, data, response) => {\n if (error) {\n console.error(error);\n } else {\n console.log('API called successfully. Returned data: ' + data);\n }\n});\n\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nNotes\n\n\n\n\ntype\nString\nScript or pipeline\n\n\n\nid\nString\nWhere to find the pipeline or step outputs in ./output folder. It also acts as a handle to stop the run.\n\n\n\n\n\n\n\n{String: String}\n\n\n\nNo authorization required\n\n\n\n\nContent-Type: Not defined\nAccept: application/json\n\n\n\n\n\n\nObject getPipeline(descriptionPath)\n\nGet JSON file that describes the pipeline.\n\n\nimport BonInABoxScriptService from 'bon_in_a_box_script_service';\n\nlet apiInstance = new BonInABoxScriptService.DefaultApi();\nlet descriptionPath = \"descriptionPath_example\"; // String | Where to find the step. For scripts, paths are relative to the /script folder. For pipelines, paths are relative to the /pipeline folder.\napiInstance.getPipeline(descriptionPath, (error, data, response) => {\n if (error) {\n console.error(error);\n } else {\n console.log('API called successfully. Returned data: ' + data);\n }\n});\n\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nNotes\n\n\n\n\ndescriptionPath\nString\nWhere to find the step. For scripts, paths are relative to the /script folder. For pipelines, paths are relative to the /pipeline folder.\n\n\n\n\n\n\n\nObject\n\n\n\nNo authorization required\n\n\n\n\nContent-Type: Not defined\nAccept: application/json\n\n\n\n\n\n\nString getVersions()\n\nReturns the version of system components.\n\n\nimport BonInABoxScriptService from 'bon_in_a_box_script_service';\n\nlet apiInstance = new BonInABoxScriptService.DefaultApi();\napiInstance.getVersions((error, data, response) => {\n if (error) {\n console.error(error);\n } else {\n console.log('API called successfully. Returned data: ' + data);\n }\n});\n\n\n\nThis endpoint does not need any parameter.\n\n\n\nString\n\n\n\nNo authorization required\n\n\n\n\nContent-Type: Not defined\nAccept: text/plain\n\n\n\n\n\n\nString run(type, descriptionPath, opts)\n\nRuns the script or pipeline matching `descriptionPath`.\n\n\nimport BonInABoxScriptService from 'bon_in_a_box_script_service';\n\nlet apiInstance = new BonInABoxScriptService.DefaultApi();\nlet type = \"type_example\"; // String | Script or pipeline\nlet descriptionPath = \"descriptionPath_example\"; // String | Where to find the step. For scripts, paths are relative to the /script folder. For pipelines, paths are relative to the /pipeline folder.\nlet opts = {\n 'body': \"body_example\" // String | Content of input.json for this run\n};\napiInstance.run(type, descriptionPath, opts, (error, data, response) => {\n if (error) {\n console.error(error);\n } else {\n console.log('API called successfully. Returned data: ' + data);\n }\n});\n\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nNotes\n\n\n\n\ntype\nString\nScript or pipeline\n\n\n\ndescriptionPath\nString\nWhere to find the step. For scripts, paths are relative to the /script folder. For pipelines, paths are relative to the /pipeline folder.\n\n\n\nbody\nString\nContent of input.json for this run\n[optional]\n\n\n\n\n\n\nString\n\n\n\nNo authorization required\n\n\n\n\nContent-Type: text/plain\nAccept: text/plain\n\n\n\n\n\n\nString savePipeline(filename, requestBody)\n\nSave a json file to the pipeline folder.\n\n\nimport BonInABoxScriptService from 'bon_in_a_box_script_service';\n\nlet apiInstance = new BonInABoxScriptService.DefaultApi();\nlet filename = \"filename_example\"; // String | The name of the JSON file (without extension).\nlet requestBody = {key: null}; // {String: Object} | Content of pipeline.json to save\napiInstance.savePipeline(filename, requestBody, (error, data, response) => {\n if (error) {\n console.error(error);\n } else {\n console.log('API called successfully. Returned data: ' + data);\n }\n});\n\n\n\n\n\n\nName\nType\nDescription\nNotes\n\n\n\n\nfilename\nString\nThe name of the JSON file (without extension).\n\n\n\nrequestBody\n{String: Object}\nContent of pipeline.json to save\n\n\n\n\n\n\n\nString\n\n\n\nNo authorization required\n\n\n\n\nContent-Type: application/json\nAccept: text/plain\n\n\n\n\n\n\nstop(type, id)\n\nStop the specified pipeline run.\n\n\nimport BonInABoxScriptService from 'bon_in_a_box_script_service';\n\nlet apiInstance = new BonInABoxScriptService.DefaultApi();\nlet type = \"type_example\"; // String | Script or pipeline\nlet id = \"id_example\"; // String | Where to find the pipeline or step outputs in ./output folder. It also acts as a handle to stop the run. \napiInstance.stop(type, id, (error, data, response) => {\n if (error) {\n console.error(error);\n } else {\n console.log('API called successfully.');\n }\n});\n\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nNotes\n\n\n\n\ntype\nString\nScript or pipeline\n\n\n\nid\nString\nWhere to find the pipeline or step outputs in ./output folder. It also acts as a handle to stop the run.\n\n\n\n\n\n\n\nnull (empty response body)\n\n\n\nNo authorization required\n\n\n\n\nContent-Type: Not defined\nAccept: Not defined" + }, + { + "objectID": "ui/BonInABoxScriptService/docs/DefaultApi.html#gethistory", + "href": "ui/BonInABoxScriptService/docs/DefaultApi.html#gethistory", + "title": "BonInABoxScriptService.DefaultApi", + "section": "", + "text": "[GetHistory200ResponseInner] getHistory()\n\nGet the history of runs for all pipelines on this server\n\n\nimport BonInABoxScriptService from 'bon_in_a_box_script_service';\n\nlet apiInstance = new BonInABoxScriptService.DefaultApi();\napiInstance.getHistory((error, data, response) => {\n if (error) {\n console.error(error);\n } else {\n console.log('API called successfully. Returned data: ' + data);\n }\n});\n\n\n\nThis endpoint does not need any parameter.\n\n\n\n[GetHistory200ResponseInner]\n\n\n\nNo authorization required\n\n\n\n\nContent-Type: Not defined\nAccept: application/json" + }, + { + "objectID": "ui/BonInABoxScriptService/docs/DefaultApi.html#getinfo", + "href": "ui/BonInABoxScriptService/docs/DefaultApi.html#getinfo", + "title": "BonInABoxScriptService.DefaultApi", + "section": "", + "text": "Info getInfo(type, descriptionPath)\n\nGet metadata about this script or pipeline.\n\n\nimport BonInABoxScriptService from 'bon_in_a_box_script_service';\n\nlet apiInstance = new BonInABoxScriptService.DefaultApi();\nlet type = \"type_example\"; // String | Script or pipeline\nlet descriptionPath = \"descriptionPath_example\"; // String | Where to find the step. For scripts, paths are relative to the /script folder. For pipelines, paths are relative to the /pipeline folder.\napiInstance.getInfo(type, descriptionPath, (error, data, response) => {\n if (error) {\n console.error(error);\n } else {\n console.log('API called successfully. Returned data: ' + data);\n }\n});\n\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nNotes\n\n\n\n\ntype\nString\nScript or pipeline\n\n\n\ndescriptionPath\nString\nWhere to find the step. For scripts, paths are relative to the /script folder. For pipelines, paths are relative to the /pipeline folder.\n\n\n\n\n\n\n\nInfo\n\n\n\nNo authorization required\n\n\n\n\nContent-Type: Not defined\nAccept: application/json" + }, + { + "objectID": "ui/BonInABoxScriptService/docs/DefaultApi.html#getlistof", + "href": "ui/BonInABoxScriptService/docs/DefaultApi.html#getlistof", + "title": "BonInABoxScriptService.DefaultApi", + "section": "", + "text": "{String: String} getListOf(type)\n\nGet a list of available steps of given type and their names.\n\n\nimport BonInABoxScriptService from 'bon_in_a_box_script_service';\n\nlet apiInstance = new BonInABoxScriptService.DefaultApi();\nlet type = \"type_example\"; // String | Script or pipeline\napiInstance.getListOf(type, (error, data, response) => {\n if (error) {\n console.error(error);\n } else {\n console.log('API called successfully. Returned data: ' + data);\n }\n});\n\n\n\n\n\n\nName\nType\nDescription\nNotes\n\n\n\n\ntype\nString\nScript or pipeline\n\n\n\n\n\n\n\n{String: String}\n\n\n\nNo authorization required\n\n\n\n\nContent-Type: Not defined\nAccept: application/json" + }, + { + "objectID": "ui/BonInABoxScriptService/docs/DefaultApi.html#getoutputfolders", + "href": "ui/BonInABoxScriptService/docs/DefaultApi.html#getoutputfolders", + "title": "BonInABoxScriptService.DefaultApi", + "section": "", + "text": "{String: String} getOutputFolders(type, id)\n\nGet the output folders of the scripts composing this pipeline\n\n\nimport BonInABoxScriptService from 'bon_in_a_box_script_service';\n\nlet apiInstance = new BonInABoxScriptService.DefaultApi();\nlet type = \"type_example\"; // String | Script or pipeline\nlet id = \"id_example\"; // String | Where to find the pipeline or step outputs in ./output folder. It also acts as a handle to stop the run. \napiInstance.getOutputFolders(type, id, (error, data, response) => {\n if (error) {\n console.error(error);\n } else {\n console.log('API called successfully. Returned data: ' + data);\n }\n});\n\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nNotes\n\n\n\n\ntype\nString\nScript or pipeline\n\n\n\nid\nString\nWhere to find the pipeline or step outputs in ./output folder. It also acts as a handle to stop the run.\n\n\n\n\n\n\n\n{String: String}\n\n\n\nNo authorization required\n\n\n\n\nContent-Type: Not defined\nAccept: application/json" + }, + { + "objectID": "ui/BonInABoxScriptService/docs/DefaultApi.html#getpipeline", + "href": "ui/BonInABoxScriptService/docs/DefaultApi.html#getpipeline", + "title": "BonInABoxScriptService.DefaultApi", + "section": "", + "text": "Object getPipeline(descriptionPath)\n\nGet JSON file that describes the pipeline.\n\n\nimport BonInABoxScriptService from 'bon_in_a_box_script_service';\n\nlet apiInstance = new BonInABoxScriptService.DefaultApi();\nlet descriptionPath = \"descriptionPath_example\"; // String | Where to find the step. For scripts, paths are relative to the /script folder. For pipelines, paths are relative to the /pipeline folder.\napiInstance.getPipeline(descriptionPath, (error, data, response) => {\n if (error) {\n console.error(error);\n } else {\n console.log('API called successfully. Returned data: ' + data);\n }\n});\n\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nNotes\n\n\n\n\ndescriptionPath\nString\nWhere to find the step. For scripts, paths are relative to the /script folder. For pipelines, paths are relative to the /pipeline folder.\n\n\n\n\n\n\n\nObject\n\n\n\nNo authorization required\n\n\n\n\nContent-Type: Not defined\nAccept: application/json" + }, + { + "objectID": "ui/BonInABoxScriptService/docs/DefaultApi.html#getversions", + "href": "ui/BonInABoxScriptService/docs/DefaultApi.html#getversions", + "title": "BonInABoxScriptService.DefaultApi", + "section": "", + "text": "String getVersions()\n\nReturns the version of system components.\n\n\nimport BonInABoxScriptService from 'bon_in_a_box_script_service';\n\nlet apiInstance = new BonInABoxScriptService.DefaultApi();\napiInstance.getVersions((error, data, response) => {\n if (error) {\n console.error(error);\n } else {\n console.log('API called successfully. Returned data: ' + data);\n }\n});\n\n\n\nThis endpoint does not need any parameter.\n\n\n\nString\n\n\n\nNo authorization required\n\n\n\n\nContent-Type: Not defined\nAccept: text/plain" + }, + { + "objectID": "ui/BonInABoxScriptService/docs/DefaultApi.html#run", + "href": "ui/BonInABoxScriptService/docs/DefaultApi.html#run", + "title": "BonInABoxScriptService.DefaultApi", + "section": "", + "text": "String run(type, descriptionPath, opts)\n\nRuns the script or pipeline matching `descriptionPath`.\n\n\nimport BonInABoxScriptService from 'bon_in_a_box_script_service';\n\nlet apiInstance = new BonInABoxScriptService.DefaultApi();\nlet type = \"type_example\"; // String | Script or pipeline\nlet descriptionPath = \"descriptionPath_example\"; // String | Where to find the step. For scripts, paths are relative to the /script folder. For pipelines, paths are relative to the /pipeline folder.\nlet opts = {\n 'body': \"body_example\" // String | Content of input.json for this run\n};\napiInstance.run(type, descriptionPath, opts, (error, data, response) => {\n if (error) {\n console.error(error);\n } else {\n console.log('API called successfully. Returned data: ' + data);\n }\n});\n\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nNotes\n\n\n\n\ntype\nString\nScript or pipeline\n\n\n\ndescriptionPath\nString\nWhere to find the step. For scripts, paths are relative to the /script folder. For pipelines, paths are relative to the /pipeline folder.\n\n\n\nbody\nString\nContent of input.json for this run\n[optional]\n\n\n\n\n\n\nString\n\n\n\nNo authorization required\n\n\n\n\nContent-Type: text/plain\nAccept: text/plain" + }, + { + "objectID": "ui/BonInABoxScriptService/docs/DefaultApi.html#savepipeline", + "href": "ui/BonInABoxScriptService/docs/DefaultApi.html#savepipeline", + "title": "BonInABoxScriptService.DefaultApi", + "section": "", + "text": "String savePipeline(filename, requestBody)\n\nSave a json file to the pipeline folder.\n\n\nimport BonInABoxScriptService from 'bon_in_a_box_script_service';\n\nlet apiInstance = new BonInABoxScriptService.DefaultApi();\nlet filename = \"filename_example\"; // String | The name of the JSON file (without extension).\nlet requestBody = {key: null}; // {String: Object} | Content of pipeline.json to save\napiInstance.savePipeline(filename, requestBody, (error, data, response) => {\n if (error) {\n console.error(error);\n } else {\n console.log('API called successfully. Returned data: ' + data);\n }\n});\n\n\n\n\n\n\nName\nType\nDescription\nNotes\n\n\n\n\nfilename\nString\nThe name of the JSON file (without extension).\n\n\n\nrequestBody\n{String: Object}\nContent of pipeline.json to save\n\n\n\n\n\n\n\nString\n\n\n\nNo authorization required\n\n\n\n\nContent-Type: application/json\nAccept: text/plain" + }, + { + "objectID": "ui/BonInABoxScriptService/docs/DefaultApi.html#stop", + "href": "ui/BonInABoxScriptService/docs/DefaultApi.html#stop", + "title": "BonInABoxScriptService.DefaultApi", + "section": "", + "text": "stop(type, id)\n\nStop the specified pipeline run.\n\n\nimport BonInABoxScriptService from 'bon_in_a_box_script_service';\n\nlet apiInstance = new BonInABoxScriptService.DefaultApi();\nlet type = \"type_example\"; // String | Script or pipeline\nlet id = \"id_example\"; // String | Where to find the pipeline or step outputs in ./output folder. It also acts as a handle to stop the run. \napiInstance.stop(type, id, (error, data, response) => {\n if (error) {\n console.error(error);\n } else {\n console.log('API called successfully.');\n }\n});\n\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nNotes\n\n\n\n\ntype\nString\nScript or pipeline\n\n\n\nid\nString\nWhere to find the pipeline or step outputs in ./output folder. It also acts as a handle to stop the run.\n\n\n\n\n\n\n\nnull (empty response body)\n\n\n\nNo authorization required\n\n\n\n\nContent-Type: Not defined\nAccept: Not defined" + }, + { + "objectID": "ui/BonInABoxScriptService/docs/GetHistory200ResponseInner.html", + "href": "ui/BonInABoxScriptService/docs/GetHistory200ResponseInner.html", + "title": "BonInABoxScriptService.GetHistory200ResponseInner", + "section": "", + "text": "Name\nType\nDescription\nNotes\n\n\n\n\nname\nString\nHuman readable name of the pipeline.\n[optional]\n\n\nrunId\nString\nWhere to find the pipeline outputs in ./output folder.\n[optional]\n\n\ntype\nString\nIf it's a script or a pipeline\n[optional]\n\n\nstartTime\nDate\nUTC date and time when the run was started\n[optional]\n\n\nstatus\nString\nInformation on the completion status\n[optional]\n\n\ninputs\nObject\nInputs that were given to the pipeline form for this run.\n[optional]\n\n\n\n\n\n\n\nscript (value: \"script\")\npipeline (value: \"pipeline\")\n\n\n\n\n\nrunning (value: \"running\")\nerror (value: \"error\")\ncancelled (value: \"cancelled\")\ncompleted (value: \"completed\")" + }, + { + "objectID": "ui/BonInABoxScriptService/docs/GetHistory200ResponseInner.html#properties", + "href": "ui/BonInABoxScriptService/docs/GetHistory200ResponseInner.html#properties", + "title": "BonInABoxScriptService.GetHistory200ResponseInner", + "section": "", + "text": "Name\nType\nDescription\nNotes\n\n\n\n\nname\nString\nHuman readable name of the pipeline.\n[optional]\n\n\nrunId\nString\nWhere to find the pipeline outputs in ./output folder.\n[optional]\n\n\ntype\nString\nIf it's a script or a pipeline\n[optional]\n\n\nstartTime\nDate\nUTC date and time when the run was started\n[optional]\n\n\nstatus\nString\nInformation on the completion status\n[optional]\n\n\ninputs\nObject\nInputs that were given to the pipeline form for this run.\n[optional]" + }, + { + "objectID": "ui/BonInABoxScriptService/docs/GetHistory200ResponseInner.html#enum-typeenum", + "href": "ui/BonInABoxScriptService/docs/GetHistory200ResponseInner.html#enum-typeenum", + "title": "BonInABoxScriptService.GetHistory200ResponseInner", + "section": "", + "text": "script (value: \"script\")\npipeline (value: \"pipeline\")" + }, + { + "objectID": "ui/BonInABoxScriptService/docs/GetHistory200ResponseInner.html#enum-statusenum", + "href": "ui/BonInABoxScriptService/docs/GetHistory200ResponseInner.html#enum-statusenum", + "title": "BonInABoxScriptService.GetHistory200ResponseInner", + "section": "", + "text": "running (value: \"running\")\nerror (value: \"error\")\ncancelled (value: \"cancelled\")\ncompleted (value: \"completed\")" } ] \ No newline at end of file diff --git a/docs/ui/BonInABoxScriptService/docs/DefaultApi.html b/docs/ui/BonInABoxScriptService/docs/DefaultApi.html index 92b3f560..809873ed 100644 --- a/docs/ui/BonInABoxScriptService/docs/DefaultApi.html +++ b/docs/ui/BonInABoxScriptService/docs/DefaultApi.html @@ -7,7 +7,7 @@ -defaultapi – bon-in-a-box-pipeline-engine +defaultapi – BON in a Box + + + + + + + + + + + + + + + + + + + + + + + + + + +
      +
      + +
      + +
      + + + + +
      + + + + +
      +

      BonInABoxScriptService.GetHistory200ResponseInner

      +
      +

      Properties

      +

Map widget (leaflet)
HTMLtext/htmlOpen in new tab
JPG image/jpg tag
Shapefile application/dbf Link
Text text/plain Plain text
TSV text/tab-separated-values HTML table (partial content)
(any unknown type) Plain text or link
++++++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameTypeDescriptionNotes
nameStringHuman readable name of the pipeline.[optional]
runIdStringWhere to find the pipeline outputs in ./output folder.[optional]
typeStringIf it's a script or a pipeline[optional]
startTimeDateUTC date and time when the run was started[optional]
statusStringInformation on the completion status[optional]
inputsObjectInputs that were given to the pipeline form for this run.[optional]
+
+
+

Enum: TypeEnum

+ +
+
+

Enum: StatusEnum

+ + + +
+
+ + + + + + + + + \ No newline at end of file diff --git a/how_to_contribute.qmd b/how_to_contribute.qmd index 662f4121..9dea5f9e 100644 --- a/how_to_contribute.qmd +++ b/how_to_contribute.qmd @@ -92,7 +92,7 @@ Specifying an example will autofill that input with the example unless changed b There are several different types of user inputs that can be specified in the YAML file: | "Type" attribute in the yaml | IU rendering | Description | -|----|----|----| +|------------------------|------------------------|------------------------| | boolean | Plain text | true/false | | float, float\[\] | Plain text | positive and negative numbers with a decimal point | | int, int\[\] | Plain text | integer | @@ -202,7 +202,7 @@ This means that instead of installing packages in R scripts, they are installed mamba activate rbase - R -e 'install.packages(c(), repose="https://cloud.r-project.org/") + R -e 'install.packages(c("""), repos="https://cloud.r-project.org/")' ``` - You can use `devtools::install_github()` in a similar fashion: From 267b676d465ccb2e5e44e853558e52d72c431585 Mon Sep 17 00:00:00 2001 From: Jean-Michel Lord Date: Tue, 15 Oct 2024 16:19:29 -0400 Subject: [PATCH 02/17] fix warning about missing examples appearing with 0, null or false examples --- ui/src/components/PipelineEditor/PipelineEditor.jsx | 3 +++ ui/src/components/form/InputFileInput.jsx | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/ui/src/components/PipelineEditor/PipelineEditor.jsx b/ui/src/components/PipelineEditor/PipelineEditor.jsx index 56ba63c1..bda6a96e 100644 --- a/ui/src/components/PipelineEditor/PipelineEditor.jsx +++ b/ui/src/components/PipelineEditor/PipelineEditor.jsx @@ -640,6 +640,9 @@ export default function PipelineEditor(props) { // Destructuring copy to leave out fields that are not part of the input description spec. const { file, nodeId, inputId, ...copy } = input; copy.weight = i + if(copy.example === undefined) + copy.example = null; + flow.inputs[id] = copy; }); diff --git a/ui/src/components/form/InputFileInput.jsx b/ui/src/components/form/InputFileInput.jsx index d0db25e1..13a3d76f 100644 --- a/ui/src/components/form/InputFileInput.jsx +++ b/ui/src/components/form/InputFileInput.jsx @@ -96,7 +96,7 @@ const InputForm = ({ inputs, inputFileContent, setInputFileContent }) => { } {!isEmptyObject(theRest) && yaml.dump(theRest)} - {example + {example !== undefined ? <> Example:
From e5bcf003fb83429d17f0fe6ae71ab85a9623b845 Mon Sep 17 00:00:00 2001 From: Jean-Michel Lord Date: Wed, 16 Oct 2024 16:33:42 -0400 Subject: [PATCH 03/17] update description --- ui/index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ui/index.html b/ui/index.html index aab355f9..807ff21b 100644 --- a/ui/index.html +++ b/ui/index.html @@ -5,7 +5,7 @@ - + From a73a9dab491102b8d087ab3b04aac6231adf425d Mon Sep 17 00:00:00 2001 From: Jean-Michel Lord Date: Wed, 16 Oct 2024 16:46:36 -0400 Subject: [PATCH 04/17] Fix snake_case warning appearing for user-defined inputs. --- ui/src/components/StepResult.jsx | 4 ++-- ui/src/components/form/InputFileInput.jsx | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/ui/src/components/StepResult.jsx b/ui/src/components/StepResult.jsx index 2e099e44..4a61b8b9 100644 --- a/ui/src/components/StepResult.jsx +++ b/ui/src/components/StepResult.jsx @@ -209,8 +209,8 @@ export const SingleIOResult = memo(({ ioId, value, ioMetadata, componentId, sect icon = Error } - if(! /^(.*\|)?[a-z0-9]+(?:_[a-z0-9]+)*$/.test(ioId) && !ioId.startsWith("pipeline@")) { - errorMsg =

{ioId} should be a snake_case id

+ if(! /^(.*\|)?[a-z0-9]+(?:_[a-z0-9]+)*$/.test(ioId) && !/pipeline@\d+$/.test(ioId)) { + errorMsg =

Output id {ioId.replace(/^(.*\|)/, '')} should be a snake_case id

icon = Warning } } else { diff --git a/ui/src/components/form/InputFileInput.jsx b/ui/src/components/form/InputFileInput.jsx index 13a3d76f..bf84a835 100644 --- a/ui/src/components/form/InputFileInput.jsx +++ b/ui/src/components/form/InputFileInput.jsx @@ -73,8 +73,8 @@ const InputForm = ({ inputs, inputFileContent, setInputFileContent }) => { Date: Thu, 17 Oct 2024 11:50:59 -0400 Subject: [PATCH 05/17] Fixes for protconn and SHI --- viewer/src/components/Main/index.tsx | 22 ++++++++++----- .../Sidebar/PipelineOutput/index.tsx | 28 +++++++++++++------ viewer/src/components/Sidebar/index.tsx | 13 ++++++--- 3 files changed, 43 insertions(+), 20 deletions(-) diff --git a/viewer/src/components/Main/index.tsx b/viewer/src/components/Main/index.tsx index d72b24d9..c9b2e431 100644 --- a/viewer/src/components/Main/index.tsx +++ b/viewer/src/components/Main/index.tsx @@ -95,24 +95,32 @@ export default function Main(props: any) { if (logTransform) { expression = `sqrt(${selectedLayer.band_id})`; } - const obj = { - assets: selectedLayerAssetName, - colormap_name: colormap, - bidx: "1", - expression: expression, - }; + let min = data.percentile_2; let max = data.percentile_98; + let colmap = colormap; if (min === max) { min = data.min; max = data.max; + if (data.min == data.max) { + if (colormap == "inferno" || colormap == "hot") { + colmap = "spectral"; + setColormap(colmap); + } + } } + const obj = { + assets: selectedLayerAssetName, + colormap_name: colmap, + bidx: "1", + expression: expression, + }; const rescale = `${min},${max}`; const params = new URLSearchParams(obj).toString(); setSelectedLayerTiles( `${tiler}?url=${selectedLayer.url}&rescale=${rescale}&${params}&expression=${expression}` ); - setLegend(createRangeLegendControl(min, max, cmap(colormap))); + setLegend(createRangeLegendControl(min, max, cmap(colmap))); } ); GetCOGBounds(selectedLayer.url).then((b: any) => { diff --git a/viewer/src/components/Sidebar/PipelineOutput/index.tsx b/viewer/src/components/Sidebar/PipelineOutput/index.tsx index 60d0b5d6..0b697538 100644 --- a/viewer/src/components/Sidebar/PipelineOutput/index.tsx +++ b/viewer/src/components/Sidebar/PipelineOutput/index.tsx @@ -182,13 +182,13 @@ export function PipelineOutput(props: any) { }} > - Choose layer + Choose table handleSelect(event.target.value)} - label="Layer" + label="Table" > {outs.map((o: any) => ( @@ -200,7 +200,7 @@ export function PipelineOutput(props: any) { { - handleClick(event, "", "table"); + handleClick(event, "", outputObj?.type); }} > See table @@ -209,9 +209,14 @@ export function PipelineOutput(props: any) { )} {!Array.isArray(outs) && - ["image/png", "image/jpeg", "image/jpg", "image/svg", "image/gif", "image/bmp"].includes( - outputObj?.type - ) && + [ + "image/png", + "image/jpeg", + "image/jpg", + "image/svg", + "image/gif", + "image/bmp", + ].includes(outputObj?.type) && "type" in outputObj && ( )} {Array.isArray(outs) && - ["image/png", "image/jpeg", "image/jpg", "image/svg", "image/gif", "image/bmp"].includes( - outputObj?.type - ) && + [ + "image/png[]", + "image/jpeg[]", + "image/jpg[]", + "image/svg[]", + "image/gif[]", + "image/bmp[]", + ].includes(outputObj?.type) && "type" in outputObj && ( { if (type.includes("geotiff")) { - setSelectedLayer(output); + setSelectedLayer(output); } else if (type.includes("points/")) { let crs = "EPSG:4326"; GetPipelineRunInputs(pipeline_run_id).then((p: any) => { @@ -70,7 +70,9 @@ export default function Sidebar(props: any) { if ( pipelineData.pipeline_inputs_desc[m].label.includes("proj") || pipelineData.pipeline_inputs_desc[m].label.includes("crs") || - pipelineData.pipeline_inputs_desc[m].label.toLowerCase().includes("coordinate reference system") + pipelineData.pipeline_inputs_desc[m].label + .toLowerCase() + .includes("coordinate reference system") ) { crs = p[m]; } @@ -105,9 +107,10 @@ export default function Sidebar(props: any) { @@ -351,7 +354,9 @@ export default function Sidebar(props: any) { onClose={modalClose} sx={{ width: "60vw", height: "80vh", margin: "auto" }} > - {modalContent} + + {modalContent} + ); From c8ec4f38390e3b6fbcd6c83094f2d88d1eb65448 Mon Sep 17 00:00:00 2001 From: Guillaume Larocque Date: Sun, 20 Oct 2024 11:22:30 -0400 Subject: [PATCH 06/17] Fixes for protconn and SHI (#145) --- viewer/src/components/Main/index.tsx | 22 ++++++++++----- .../Sidebar/PipelineOutput/index.tsx | 28 +++++++++++++------ viewer/src/components/Sidebar/index.tsx | 13 ++++++--- 3 files changed, 43 insertions(+), 20 deletions(-) diff --git a/viewer/src/components/Main/index.tsx b/viewer/src/components/Main/index.tsx index d72b24d9..c9b2e431 100644 --- a/viewer/src/components/Main/index.tsx +++ b/viewer/src/components/Main/index.tsx @@ -95,24 +95,32 @@ export default function Main(props: any) { if (logTransform) { expression = `sqrt(${selectedLayer.band_id})`; } - const obj = { - assets: selectedLayerAssetName, - colormap_name: colormap, - bidx: "1", - expression: expression, - }; + let min = data.percentile_2; let max = data.percentile_98; + let colmap = colormap; if (min === max) { min = data.min; max = data.max; + if (data.min == data.max) { + if (colormap == "inferno" || colormap == "hot") { + colmap = "spectral"; + setColormap(colmap); + } + } } + const obj = { + assets: selectedLayerAssetName, + colormap_name: colmap, + bidx: "1", + expression: expression, + }; const rescale = `${min},${max}`; const params = new URLSearchParams(obj).toString(); setSelectedLayerTiles( `${tiler}?url=${selectedLayer.url}&rescale=${rescale}&${params}&expression=${expression}` ); - setLegend(createRangeLegendControl(min, max, cmap(colormap))); + setLegend(createRangeLegendControl(min, max, cmap(colmap))); } ); GetCOGBounds(selectedLayer.url).then((b: any) => { diff --git a/viewer/src/components/Sidebar/PipelineOutput/index.tsx b/viewer/src/components/Sidebar/PipelineOutput/index.tsx index 60d0b5d6..0b697538 100644 --- a/viewer/src/components/Sidebar/PipelineOutput/index.tsx +++ b/viewer/src/components/Sidebar/PipelineOutput/index.tsx @@ -182,13 +182,13 @@ export function PipelineOutput(props: any) { }} > - Choose layer + Choose table handleSelect(event.target.value)} - label="Layer" + label="Table" > {outs.map((o: any) => ( @@ -200,7 +200,7 @@ export function PipelineOutput(props: any) { { - handleClick(event, "", "table"); + handleClick(event, "", outputObj?.type); }} > See table @@ -209,9 +209,14 @@ export function PipelineOutput(props: any) { )} {!Array.isArray(outs) && - ["image/png", "image/jpeg", "image/jpg", "image/svg", "image/gif", "image/bmp"].includes( - outputObj?.type - ) && + [ + "image/png", + "image/jpeg", + "image/jpg", + "image/svg", + "image/gif", + "image/bmp", + ].includes(outputObj?.type) && "type" in outputObj && ( )} {Array.isArray(outs) && - ["image/png", "image/jpeg", "image/jpg", "image/svg", "image/gif", "image/bmp"].includes( - outputObj?.type - ) && + [ + "image/png[]", + "image/jpeg[]", + "image/jpg[]", + "image/svg[]", + "image/gif[]", + "image/bmp[]", + ].includes(outputObj?.type) && "type" in outputObj && ( { if (type.includes("geotiff")) { - setSelectedLayer(output); + setSelectedLayer(output); } else if (type.includes("points/")) { let crs = "EPSG:4326"; GetPipelineRunInputs(pipeline_run_id).then((p: any) => { @@ -70,7 +70,9 @@ export default function Sidebar(props: any) { if ( pipelineData.pipeline_inputs_desc[m].label.includes("proj") || pipelineData.pipeline_inputs_desc[m].label.includes("crs") || - pipelineData.pipeline_inputs_desc[m].label.toLowerCase().includes("coordinate reference system") + pipelineData.pipeline_inputs_desc[m].label + .toLowerCase() + .includes("coordinate reference system") ) { crs = p[m]; } @@ -105,9 +107,10 @@ export default function Sidebar(props: any) { @@ -351,7 +354,9 @@ export default function Sidebar(props: any) { onClose={modalClose} sx={{ width: "60vw", height: "80vh", margin: "auto" }} > - {modalContent} + + {modalContent} + ); From 6fed522f8b8a7fd7c66529753a05a32c2da5b6c8 Mon Sep 17 00:00:00 2001 From: Guillaume Larocque Date: Tue, 22 Oct 2024 08:53:10 -0400 Subject: [PATCH 07/17] Update LICENSE GNU GPLv3 --- LICENSE | 252 +++++++++++++++++++++++++++++++++++++++++++++++++++----- 1 file changed, 231 insertions(+), 21 deletions(-) diff --git a/LICENSE b/LICENSE index 778afd54..70830022 100644 --- a/LICENSE +++ b/LICENSE @@ -1,21 +1,231 @@ -MIT License - -Copyright (c) 2023 GEO-BON - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. +GNU GENERAL PUBLIC LICENSE +Version 3, 29 June 2007 +Copyright © 2007 Free Software Foundation, Inc. + +Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. + +Preamble + +The GNU General Public License is a free, copyleft license for software and other kinds of works. + +The licenses for most software and other practical works are designed to take away your freedom to share and change the works. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program--to make sure it remains free software for all its users. We, the Free Software Foundation, use the GNU General Public License for most of our software; it applies also to any other work released this way by its authors. You can apply it to your programs, too. + +When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for them if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs, and that you know you can do these things. + +To protect your rights, we need to prevent others from denying you these rights or asking you to surrender the rights. Therefore, you have certain responsibilities if you distribute copies of the software, or if you modify it: responsibilities to respect the freedom of others. + +For example, if you distribute copies of such a program, whether gratis or for a fee, you must pass on to the recipients the same freedoms that you received. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. + +Developers that use the GNU GPL protect your rights with two steps: (1) assert copyright on the software, and (2) offer you this License giving you legal permission to copy, distribute and/or modify it. + +For the developers' and authors' protection, the GPL clearly explains that there is no warranty for this free software. For both users' and authors' sake, the GPL requires that modified versions be marked as changed, so that their problems will not be attributed erroneously to authors of previous versions. + +Some devices are designed to deny users access to install or run modified versions of the software inside them, although the manufacturer can do so. This is fundamentally incompatible with the aim of protecting users' freedom to change the software. The systematic pattern of such abuse occurs in the area of products for individuals to use, which is precisely where it is most unacceptable. Therefore, we have designed this version of the GPL to prohibit the practice for those products. If such problems arise substantially in other domains, we stand ready to extend this provision to those domains in future versions of the GPL, as needed to protect the freedom of users. + +Finally, every program is threatened constantly by software patents. States should not allow patents to restrict development and use of software on general-purpose computers, but in those that do, we wish to avoid the special danger that patents applied to a free program could make it effectively proprietary. To prevent this, the GPL assures that patents cannot be used to render the program non-free. + +The precise terms and conditions for copying, distribution and modification follow. + +TERMS AND CONDITIONS + +0. Definitions. + +“This License” refers to version 3 of the GNU General Public License. + +“Copyright” also means copyright-like laws that apply to other kinds of works, such as semiconductor masks. + +“The Program” refers to any copyrightable work licensed under this License. Each licensee is addressed as “you”. “Licensees” and “recipients” may be individuals or organizations. + +To “modify” a work means to copy from or adapt all or part of the work in a fashion requiring copyright permission, other than the making of an exact copy. The resulting work is called a “modified version” of the earlier work or a work “based on” the earlier work. + +A “covered work” means either the unmodified Program or a work based on the Program. + +To “propagate” a work means to do anything with it that, without permission, would make you directly or secondarily liable for infringement under applicable copyright law, except executing it on a computer or modifying a private copy. Propagation includes copying, distribution (with or without modification), making available to the public, and in some countries other activities as well. + +To “convey” a work means any kind of propagation that enables other parties to make or receive copies. Mere interaction with a user through a computer network, with no transfer of a copy, is not conveying. + +An interactive user interface displays “Appropriate Legal Notices” to the extent that it includes a convenient and prominently visible feature that (1) displays an appropriate copyright notice, and (2) tells the user that there is no warranty for the work (except to the extent that warranties are provided), that licensees may convey the work under this License, and how to view a copy of this License. If the interface presents a list of user commands or options, such as a menu, a prominent item in the list meets this criterion. + +1. Source Code. +The “source code” for a work means the preferred form of the work for making modifications to it. “Object code” means any non-source form of a work. + +A “Standard Interface” means an interface that either is an official standard defined by a recognized standards body, or, in the case of interfaces specified for a particular programming language, one that is widely used among developers working in that language. + +The “System Libraries” of an executable work include anything, other than the work as a whole, that (a) is included in the normal form of packaging a Major Component, but which is not part of that Major Component, and (b) serves only to enable use of the work with that Major Component, or to implement a Standard Interface for which an implementation is available to the public in source code form. A “Major Component”, in this context, means a major essential component (kernel, window system, and so on) of the specific operating system (if any) on which the executable work runs, or a compiler used to produce the work, or an object code interpreter used to run it. + +The “Corresponding Source” for a work in object code form means all the source code needed to generate, install, and (for an executable work) run the object code and to modify the work, including scripts to control those activities. However, it does not include the work's System Libraries, or general-purpose tools or generally available free programs which are used unmodified in performing those activities but which are not part of the work. For example, Corresponding Source includes interface definition files associated with source files for the work, and the source code for shared libraries and dynamically linked subprograms that the work is specifically designed to require, such as by intimate data communication or control flow between those subprograms and other parts of the work. + +The Corresponding Source need not include anything that users can regenerate automatically from other parts of the Corresponding Source. + +The Corresponding Source for a work in source code form is that same work. + +2. Basic Permissions. +All rights granted under this License are granted for the term of copyright on the Program, and are irrevocable provided the stated conditions are met. This License explicitly affirms your unlimited permission to run the unmodified Program. The output from running a covered work is covered by this License only if the output, given its content, constitutes a covered work. This License acknowledges your rights of fair use or other equivalent, as provided by copyright law. + +You may make, run and propagate covered works that you do not convey, without conditions so long as your license otherwise remains in force. You may convey covered works to others for the sole purpose of having them make modifications exclusively for you, or provide you with facilities for running those works, provided that you comply with the terms of this License in conveying all material for which you do not control copyright. Those thus making or running the covered works for you must do so exclusively on your behalf, under your direction and control, on terms that prohibit them from making any copies of your copyrighted material outside their relationship with you. + +Conveying under any other circumstances is permitted solely under the conditions stated below. Sublicensing is not allowed; section 10 makes it unnecessary. + +3. Protecting Users' Legal Rights From Anti-Circumvention Law. +No covered work shall be deemed part of an effective technological measure under any applicable law fulfilling obligations under article 11 of the WIPO copyright treaty adopted on 20 December 1996, or similar laws prohibiting or restricting circumvention of such measures. + +When you convey a covered work, you waive any legal power to forbid circumvention of technological measures to the extent such circumvention is effected by exercising rights under this License with respect to the covered work, and you disclaim any intention to limit operation or modification of the work as a means of enforcing, against the work's users, your or third parties' legal rights to forbid circumvention of technological measures. + +4. Conveying Verbatim Copies. +You may convey verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice; keep intact all notices stating that this License and any non-permissive terms added in accord with section 7 apply to the code; keep intact all notices of the absence of any warranty; and give all recipients a copy of this License along with the Program. + +You may charge any price or no price for each copy that you convey, and you may offer support or warranty protection for a fee. + +5. Conveying Modified Source Versions. +You may convey a work based on the Program, or the modifications to produce it from the Program, in the form of source code under the terms of section 4, provided that you also meet all of these conditions: + +a) The work must carry prominent notices stating that you modified it, and giving a relevant date. + +b) The work must carry prominent notices stating that it is released under this License and any conditions added under section 7. This requirement modifies the requirement in section 4 to “keep intact all notices”. + +c) You must license the entire work, as a whole, under this License to anyone who comes into possession of a copy. This License will therefore apply, along with any applicable section 7 additional terms, to the whole of the work, and all its parts, regardless of how they are packaged. This License gives no permission to license the work in any other way, but it does not invalidate such permission if you have separately received it. + +d) If the work has interactive user interfaces, each must display Appropriate Legal Notices; however, if the Program has interactive interfaces that do not display Appropriate Legal Notices, your work need not make them do so. + +A compilation of a covered work with other separate and independent works, which are not by their nature extensions of the covered work, and which are not combined with it such as to form a larger program, in or on a volume of a storage or distribution medium, is called an “aggregate” if the compilation and its resulting copyright are not used to limit the access or legal rights of the compilation's users beyond what the individual works permit. Inclusion of a covered work in an aggregate does not cause this License to apply to the other parts of the aggregate. + +6. Conveying Non-Source Forms. +You may convey a covered work in object code form under the terms of sections 4 and 5, provided that you also convey the machine-readable Corresponding Source under the terms of this License, in one of these ways: + +a) Convey the object code in, or embodied in, a physical product (including a physical distribution medium), accompanied by the Corresponding Source fixed on a durable physical medium customarily used for software interchange. + +b) Convey the object code in, or embodied in, a physical product (including a physical distribution medium), accompanied by a written offer, valid for at least three years and valid for as long as you offer spare parts or customer support for that product model, to give anyone who possesses the object code either (1) a copy of the Corresponding Source for all the software in the product that is covered by this License, on a durable physical medium customarily used for software interchange, for a price no more than your reasonable cost of physically performing this conveying of source, or (2) access to copy the Corresponding Source from a network server at no charge. + +c) Convey individual copies of the object code with a copy of the written offer to provide the Corresponding Source. This alternative is allowed only occasionally and noncommercially, and only if you received the object code with such an offer, in accord with subsection 6b. + +d) Convey the object code by offering access from a designated place (gratis or for a charge), and offer equivalent access to the Corresponding Source in the same way through the same place at no further charge. You need not require recipients to copy the Corresponding Source along with the object code. If the place to copy the object code is a network server, the Corresponding Source may be on a different server (operated by you or a third party) that supports equivalent copying facilities, provided you maintain clear directions next to the object code saying where to find the Corresponding Source. Regardless of what server hosts the Corresponding Source, you remain obligated to ensure that it is available for as long as needed to satisfy these requirements. + +e) Convey the object code using peer-to-peer transmission, provided you inform other peers where the object code and Corresponding Source of the work are being offered to the general public at no charge under subsection 6d. + +A separable portion of the object code, whose source code is excluded from the Corresponding Source as a System Library, need not be included in conveying the object code work. + +A “User Product” is either (1) a “consumer product”, which means any tangible personal property which is normally used for personal, family, or household purposes, or (2) anything designed or sold for incorporation into a dwelling. In determining whether a product is a consumer product, doubtful cases shall be resolved in favor of coverage. For a particular product received by a particular user, “normally used” refers to a typical or common use of that class of product, regardless of the status of the particular user or of the way in which the particular user actually uses, or expects or is expected to use, the product. A product is a consumer product regardless of whether the product has substantial commercial, industrial or non-consumer uses, unless such uses represent the only significant mode of use of the product. + +“Installation Information” for a User Product means any methods, procedures, authorization keys, or other information required to install and execute modified versions of a covered work in that User Product from a modified version of its Corresponding Source. The information must suffice to ensure that the continued functioning of the modified object code is in no case prevented or interfered with solely because modification has been made. + +If you convey an object code work under this section in, or with, or specifically for use in, a User Product, and the conveying occurs as part of a transaction in which the right of possession and use of the User Product is transferred to the recipient in perpetuity or for a fixed term (regardless of how the transaction is characterized), the Corresponding Source conveyed under this section must be accompanied by the Installation Information. But this requirement does not apply if neither you nor any third party retains the ability to install modified object code on the User Product (for example, the work has been installed in ROM). + +The requirement to provide Installation Information does not include a requirement to continue to provide support service, warranty, or updates for a work that has been modified or installed by the recipient, or for the User Product in which it has been modified or installed. Access to a network may be denied when the modification itself materially and adversely affects the operation of the network or violates the rules and protocols for communication across the network. + +Corresponding Source conveyed, and Installation Information provided, in accord with this section must be in a format that is publicly documented (and with an implementation available to the public in source code form), and must require no special password or key for unpacking, reading or copying. + +7. Additional Terms. +“Additional permissions” are terms that supplement the terms of this License by making exceptions from one or more of its conditions. Additional permissions that are applicable to the entire Program shall be treated as though they were included in this License, to the extent that they are valid under applicable law. If additional permissions apply only to part of the Program, that part may be used separately under those permissions, but the entire Program remains governed by this License without regard to the additional permissions. + +When you convey a copy of a covered work, you may at your option remove any additional permissions from that copy, or from any part of it. (Additional permissions may be written to require their own removal in certain cases when you modify the work.) You may place additional permissions on material, added by you to a covered work, for which you have or can give appropriate copyright permission. + +Notwithstanding any other provision of this License, for material you add to a covered work, you may (if authorized by the copyright holders of that material) supplement the terms of this License with terms: + +a) Disclaiming warranty or limiting liability differently from the terms of sections 15 and 16 of this License; or + +b) Requiring preservation of specified reasonable legal notices or author attributions in that material or in the Appropriate Legal Notices displayed by works containing it; or + +c) Prohibiting misrepresentation of the origin of that material, or requiring that modified versions of such material be marked in reasonable ways as different from the original version; or + +d) Limiting the use for publicity purposes of names of licensors or authors of the material; or + +e) Declining to grant rights under trademark law for use of some trade names, trademarks, or service marks; or + +f) Requiring indemnification of licensors and authors of that material by anyone who conveys the material (or modified versions of it) with contractual assumptions of liability to the recipient, for any liability that these contractual assumptions directly impose on those licensors and authors. + +All other non-permissive additional terms are considered “further restrictions” within the meaning of section 10. If the Program as you received it, or any part of it, contains a notice stating that it is governed by this License along with a term that is a further restriction, you may remove that term. If a license document contains a further restriction but permits relicensing or conveying under this License, you may add to a covered work material governed by the terms of that license document, provided that the further restriction does not survive such relicensing or conveying. + +If you add terms to a covered work in accord with this section, you must place, in the relevant source files, a statement of the additional terms that apply to those files, or a notice indicating where to find the applicable terms. + +Additional terms, permissive or non-permissive, may be stated in the form of a separately written license, or stated as exceptions; the above requirements apply either way. + +8. Termination. +You may not propagate or modify a covered work except as expressly provided under this License. Any attempt otherwise to propagate or modify it is void, and will automatically terminate your rights under this License (including any patent licenses granted under the third paragraph of section 11). + +However, if you cease all violation of this License, then your license from a particular copyright holder is reinstated (a) provisionally, unless and until the copyright holder explicitly and finally terminates your license, and (b) permanently, if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation. + +Moreover, your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means, this is the first time you have received notice of violation of this License (for any work) from that copyright holder, and you cure the violation prior to 30 days after your receipt of the notice. + +Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License. If your rights have been terminated and not permanently reinstated, you do not qualify to receive new licenses for the same material under section 10. + +9. Acceptance Not Required for Having Copies. +You are not required to accept this License in order to receive or run a copy of the Program. Ancillary propagation of a covered work occurring solely as a consequence of using peer-to-peer transmission to receive a copy likewise does not require acceptance. However, nothing other than this License grants you permission to propagate or modify any covered work. These actions infringe copyright if you do not accept this License. Therefore, by modifying or propagating a covered work, you indicate your acceptance of this License to do so. + +10. Automatic Licensing of Downstream Recipients. +Each time you convey a covered work, the recipient automatically receives a license from the original licensors, to run, modify and propagate that work, subject to this License. You are not responsible for enforcing compliance by third parties with this License. + +An “entity transaction” is a transaction transferring control of an organization, or substantially all assets of one, or subdividing an organization, or merging organizations. If propagation of a covered work results from an entity transaction, each party to that transaction who receives a copy of the work also receives whatever licenses to the work the party's predecessor in interest had or could give under the previous paragraph, plus a right to possession of the Corresponding Source of the work from the predecessor in interest, if the predecessor has it or can get it with reasonable efforts. + +You may not impose any further restrictions on the exercise of the rights granted or affirmed under this License. For example, you may not impose a license fee, royalty, or other charge for exercise of rights granted under this License, and you may not initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging that any patent claim is infringed by making, using, selling, offering for sale, or importing the Program or any portion of it. + +11. Patents. +A “contributor” is a copyright holder who authorizes use under this License of the Program or a work on which the Program is based. The work thus licensed is called the contributor's “contributor version”. + +A contributor's “essential patent claims” are all patent claims owned or controlled by the contributor, whether already acquired or hereafter acquired, that would be infringed by some manner, permitted by this License, of making, using, or selling its contributor version, but do not include claims that would be infringed only as a consequence of further modification of the contributor version. For purposes of this definition, “control” includes the right to grant patent sublicenses in a manner consistent with the requirements of this License. + +Each contributor grants you a non-exclusive, worldwide, royalty-free patent license under the contributor's essential patent claims, to make, use, sell, offer for sale, import and otherwise run, modify and propagate the contents of its contributor version. + +In the following three paragraphs, a “patent license” is any express agreement or commitment, however denominated, not to enforce a patent (such as an express permission to practice a patent or covenant not to sue for patent infringement). To “grant” such a patent license to a party means to make such an agreement or commitment not to enforce a patent against the party. + +If you convey a covered work, knowingly relying on a patent license, and the Corresponding Source of the work is not available for anyone to copy, free of charge and under the terms of this License, through a publicly available network server or other readily accessible means, then you must either (1) cause the Corresponding Source to be so available, or (2) arrange to deprive yourself of the benefit of the patent license for this particular work, or (3) arrange, in a manner consistent with the requirements of this License, to extend the patent license to downstream recipients. “Knowingly relying” means you have actual knowledge that, but for the patent license, your conveying the covered work in a country, or your recipient's use of the covered work in a country, would infringe one or more identifiable patents in that country that you have reason to believe are valid. + +If, pursuant to or in connection with a single transaction or arrangement, you convey, or propagate by procuring conveyance of, a covered work, and grant a patent license to some of the parties receiving the covered work authorizing them to use, propagate, modify or convey a specific copy of the covered work, then the patent license you grant is automatically extended to all recipients of the covered work and works based on it. + +A patent license is “discriminatory” if it does not include within the scope of its coverage, prohibits the exercise of, or is conditioned on the non-exercise of one or more of the rights that are specifically granted under this License. You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software, under which you make payment to the third party based on the extent of your activity of conveying the work, and under which the third party grants, to any of the parties who would receive the covered work from you, a discriminatory patent license (a) in connection with copies of the covered work conveyed by you (or copies made from those copies), or (b) primarily for and in connection with specific products or compilations that contain the covered work, unless you entered into that arrangement, or that patent license was granted, prior to 28 March 2007. + +Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law. + +12. No Surrender of Others' Freedom. +If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program. + +13. Use with the GNU Affero General Public License. +Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such. + +14. Revised Versions of this License. +The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. + +Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU General Public License “or any later version” applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the GNU General Public License, you may choose any version ever published by the Free Software Foundation. + +If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used, that proxy's public statement of acceptance of a version permanently authorizes you to choose that version for the Program. + +Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version. + +15. Disclaimer of Warranty. +THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + +16. Limitation of Liability. +IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. + +17. Interpretation of Sections 15 and 16. +If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee. + +END OF TERMS AND CONDITIONS + +How to Apply These Terms to Your New Programs + +If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. + +To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the “copyright” line and a pointer to where the full notice is found. + + +Copyright (C) + +This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + +This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. + +You should have received a copy of the GNU General Public License along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + +If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode: + + Copyright (C) +This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. +This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an “about box”. + +You should also get your employer (if you work as a programmer) or school, if any, to sign a “copyright disclaimer” for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see . + +The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read . From e4c42bdefc73ea2a3a751fcd9aa65944f2aa158b Mon Sep 17 00:00:00 2001 From: Guillaume Larocque Date: Tue, 22 Oct 2024 09:09:02 -0400 Subject: [PATCH 08/17] Add options --- viewer/src/components/Sidebar/PipelineOutput/index.tsx | 1 + 1 file changed, 1 insertion(+) diff --git a/viewer/src/components/Sidebar/PipelineOutput/index.tsx b/viewer/src/components/Sidebar/PipelineOutput/index.tsx index 0b697538..b18b024e 100644 --- a/viewer/src/components/Sidebar/PipelineOutput/index.tsx +++ b/viewer/src/components/Sidebar/PipelineOutput/index.tsx @@ -274,6 +274,7 @@ export function PipelineOutput(props: any) { )} {(!("type" in outputObj) || outputObj.type == "text" || + outputObj.type == "options" || outputObj.type == "text[]") && ( {outputObj.outputs} )} From dc127e819e630f028f7f6d8c17aec21c2dd80842 Mon Sep 17 00:00:00 2001 From: Jean-Michel Date: Sat, 26 Oct 2024 13:05:12 -0500 Subject: [PATCH 09/17] added --offline param to start the server without pulling. --- how_to_install.qmd | 3 +++ 1 file changed, 3 insertions(+) diff --git a/how_to_install.qmd b/how_to_install.qmd index 08a5ee51..0752f417 100644 --- a/how_to_install.qmd +++ b/how_to_install.qmd @@ -70,6 +70,9 @@ When modifying scripts in the `/scripts` folder, servers do not need to be resta When modifying pipelines in the /pipelines folder, servers do not need to be restarted: - In the pipeline editor, click save, paste the file to your file in the pipeline folder and run it from the "pipeline run" page. - When adding or renaming pipelines, refresh the browser page. +### Deploying without pulling the new server +If the server has already been deployed at least once, and low bandwith does not allow to download the latest version (this can be a few gigabytes), the server can be started with option `./server-up.sh --offline`. Use with caution, since this may create errors if elements of the repository depend on new server features. + ## Deploying BON in a Box on a server {#deploying-the-servers-remotely} Installation steps on a server are the same as installing on a Linux computer, but some additional configurations need to be changed: From 1989f0d2fd51b1ae88e70063af95bd92ed51719c Mon Sep 17 00:00:00 2001 From: Jean-Michel Date: Mon, 4 Nov 2024 15:03:19 -0500 Subject: [PATCH 10/17] remove weight from run UI --- ui/src/components/form/InputFileInput.jsx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ui/src/components/form/InputFileInput.jsx b/ui/src/components/form/InputFileInput.jsx index bf84a835..5e11c73c 100644 --- a/ui/src/components/form/InputFileInput.jsx +++ b/ui/src/components/form/InputFileInput.jsx @@ -64,7 +64,7 @@ const InputForm = ({ inputs, inputFileContent, setInputFileContent }) => { {Object.entries(inputs) .sort((a, b) => a[1].weight - b[1].weight) .map(([inputId, inputDescription]) => { - const { label, description, options, example, ...theRest } = + const { label, description, options, example, weight, ...theRest } = inputDescription; return ( From f17537a15fd41f36ce438b691664058e7da1e835 Mon Sep 17 00:00:00 2001 From: Jean-Michel Date: Mon, 4 Nov 2024 16:23:23 -0500 Subject: [PATCH 11/17] Support run blocking --- how_to_install.qmd | 2 ++ .../main/kotlin/org/geobon/server/plugins/Routing.kt | 10 ++++++++++ 2 files changed, 12 insertions(+) diff --git a/how_to_install.qmd b/how_to_install.qmd index 0752f417..771fb7d6 100644 --- a/how_to_install.qmd +++ b/how_to_install.qmd @@ -81,6 +81,8 @@ Installation steps on a server are the same as installing on a Linux computer, b - In `runner.env`, select the "partial" cache cleaning mode. This will allow for calculated results to be long-lived on the server, as long as they are not run again with a new version of the script. The results in the output folder are always accessible by URL. +- In the case where a server is used for demonstration purpose only, set environment variable `BLOCK_RUNS=true` + - The outputs are precious, while the server machine can be re-generated anytime. Consider mounting an external backed-up drive to the output folder of your BON in a Box installation. - By default, BON in a Box listens for http. To enable https, we hide it behind a reverse proxy and activate https with certbot. How to do this is out of scope for this readme. diff --git a/script-server/src/main/kotlin/org/geobon/server/plugins/Routing.kt b/script-server/src/main/kotlin/org/geobon/server/plugins/Routing.kt index c2a62e0b..3757845a 100644 --- a/script-server/src/main/kotlin/org/geobon/server/plugins/Routing.kt +++ b/script-server/src/main/kotlin/org/geobon/server/plugins/Routing.kt @@ -207,6 +207,16 @@ fun Application.configureRouting() { } post("/{type}/{descriptionPath}/run") { + logger.debug("BLOCK_RUNS: ${System.getenv("BLOCK_RUNS")}") + + if (System.getenv("BLOCK_RUNS") == "true") { + call.respond( + HttpStatusCode.ServiceUnavailable, "This server does not allow running pipelines and scripts.\n" + + "It was configured to display results only." + ) + return@post + } + val singleScript = call.parameters["type"] == "script" val inputFileContent = call.receive() From 577267ebc812c729cd3f7ff723010911d3b098e6 Mon Sep 17 00:00:00 2001 From: Jean-Michel Lord Date: Thu, 7 Nov 2024 09:56:30 -0500 Subject: [PATCH 12/17] mend icon link --- ui/index.html | 2 +- ui/public/manifest.json | 5 ----- 2 files changed, 1 insertion(+), 6 deletions(-) diff --git a/ui/index.html b/ui/index.html index 807ff21b..06e6a70b 100644 --- a/ui/index.html +++ b/ui/index.html @@ -13,7 +13,7 @@ rel="stylesheet" href="https://fonts.googleapis.com/css2?family=Roboto:wght@300;400;500;600;700&display=swap" /> - +