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Merge pull request #39 from nextflow-io/feat/nested-params
Feat/nested params
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| .nextflow | ||
| .nextflow.log* | ||
| .nextflow.pid | ||
| null | ||
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| # Ignore Gradle build output directory | ||
| build | ||
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| @@ -1,2 +1,2 @@ | ||
| nextflowVersion = 22.10.0 | ||
| nextflowVersion = 23.10.0 | ||
| groovyVersion = 3.0.14 |
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255
plugins/nf-schema/src/main/nextflow/validation/HelpMessage.groovy
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| package nextflow.validation | ||
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| import groovy.util.logging.Slf4j | ||
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| import java.nio.file.Path | ||
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| import nextflow.Session | ||
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| /** | ||
| * This class contains methods to write a help message | ||
| * | ||
| * @author : nvnieuwk <[email protected]> | ||
| * | ||
| */ | ||
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| @Slf4j | ||
| class HelpMessage { | ||
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| private final ValidationConfig config | ||
| private final Map colors | ||
| private Integer hiddenParametersCount = 0 | ||
| private Map<String,Map> paramsMap | ||
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| // The length of the terminal | ||
| private Integer terminalLength = System.getenv("COLUMNS")?.toInteger() ?: 100 | ||
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| HelpMessage(ValidationConfig inputConfig, Session session) { | ||
| config = inputConfig | ||
| colors = Utils.logColours(config.monochromeLogs) | ||
| paramsMap = Utils.paramsLoad( Path.of(Utils.getSchemaPath(session.baseDir.toString(), config.parametersSchema)) ) | ||
| addHelpParameters() | ||
| } | ||
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| public String getShortHelpMessage(String param) { | ||
| def String helpMessage = "" | ||
| if (param) { | ||
| def List<String> paramNames = param.tokenize(".") as List<String> | ||
| def Map paramOptions = [:] | ||
| paramsMap.each { String group, Map groupParams -> | ||
| if (groupParams.containsKey(paramNames[0])) { | ||
| paramOptions = groupParams.get(paramNames[0]) as Map | ||
| } | ||
| } | ||
| if (paramNames.size() > 1) { | ||
| paramNames.remove(0) | ||
| paramNames.each { | ||
| paramOptions = (Map) paramOptions?.properties?[it] ?: [:] | ||
| } | ||
| } | ||
| if (!paramOptions) { | ||
| throw new Exception("Unable to create help message: Specified param '${param}' does not exist in JSON schema.") | ||
| } | ||
| if(paramOptions.containsKey("properties")) { | ||
| paramOptions.properties = removeHidden(paramOptions.properties) | ||
| } | ||
| helpMessage = getDetailedHelpString(param, paramOptions) | ||
| } else { | ||
| helpMessage = getGroupHelpString() | ||
| } | ||
| return helpMessage | ||
| } | ||
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| public String getFullHelpMessage() { | ||
| return getGroupHelpString(true) | ||
| } | ||
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| public String getBeforeText() { | ||
| def String beforeText = config.help.beforeText | ||
| if (config.help.command) { | ||
| beforeText += "Typical pipeline command:\n\n" | ||
| beforeText += " ${colors.cyan}${config.help.command}${colors.reset}\n\n" | ||
| } | ||
| return beforeText | ||
| } | ||
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| public String getAfterText() { | ||
| def String afterText = "" | ||
| if (hiddenParametersCount > 0) { | ||
| afterText += " ${colors.dim}!! Hiding ${hiddenParametersCount} param(s), use the `--${config.help.showHiddenParameter}` parameter to show them !!${colors.reset}\n" | ||
| } | ||
| afterText += "-${colors.dim}----------------------------------------------------${colors.reset}-\n" | ||
| afterText += config.help.afterText | ||
| return afterText | ||
| } | ||
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| // | ||
| // Get a detailed help string from one parameter | ||
| // | ||
| private String getDetailedHelpString(String paramName, Map paramOptions) { | ||
| def String helpMessage = "${colors.underlined}${colors.bold}--${paramName}${colors.reset}\n" | ||
| def Integer optionMaxChars = Utils.longestStringLength(paramOptions.keySet().collect { it == "properties" ? "options" : it } as List<String>) | ||
| for (option in paramOptions) { | ||
| def String key = option.key | ||
| if (key == "fa_icon" || (key == "type" && option.value == "object")) { | ||
| continue | ||
| } | ||
| if (key == "properties") { | ||
| def Map subParamsOptions = [:] | ||
| flattenNestedSchemaMap(option.value as Map).each { String subParam, Map value -> | ||
| subParamsOptions.put("${paramName}.${subParam}" as String, value) | ||
| } | ||
| def Integer maxChars = Utils.longestStringLength(subParamsOptions.keySet() as List<String>) + 1 | ||
| def String subParamsHelpString = getHelpListParams(subParamsOptions, maxChars, paramName) | ||
| .collect { | ||
| " --" + it[4..it.length()-1] | ||
| } | ||
| .join("\n") | ||
| helpMessage += " " + colors.dim + "options".padRight(optionMaxChars) + ": " + colors.reset + "\n" + subParamsHelpString + "\n\n" | ||
| continue | ||
| } | ||
| def String value = option.value | ||
| if (value.length() > terminalLength) { | ||
| value = wrapText(value) | ||
| } | ||
| helpMessage += " " + colors.dim + key.padRight(optionMaxChars) + ": " + colors.reset + value + '\n' | ||
| } | ||
| return helpMessage | ||
| } | ||
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| // | ||
| // Get the full help message for a grouped params structure in list format | ||
| // | ||
| private String getGroupHelpString(Boolean showNested = false) { | ||
| def String helpMessage = "" | ||
| def Map<String,Map> visibleParamsMap = paramsMap.collectEntries { key, Map value -> [key, removeHidden(value)]} | ||
| def Map<String,Map> parsedParams = showNested ? visibleParamsMap.collectEntries { key, Map value -> [key, flattenNestedSchemaMap(value)] } : visibleParamsMap | ||
| def Integer maxChars = Utils.paramsMaxChars(parsedParams) + 1 | ||
| if (parsedParams.containsKey(null)) { | ||
| def Map ungroupedParams = parsedParams[null] | ||
| parsedParams.remove(null) | ||
| helpMessage += getHelpListParams(ungroupedParams, maxChars + 2).collect { | ||
| it[2..it.length()-1] | ||
| }.join("\n") + "\n\n" | ||
| } | ||
| parsedParams.each { String group, Map groupParams -> | ||
| def List<String> helpList = getHelpListParams(groupParams, maxChars) | ||
| if (helpList.size() > 0) { | ||
| helpMessage += "${colors.underlined}${colors.bold}${group}${colors.reset}\n" as String | ||
| helpMessage += helpList.join("\n") + "\n\n" | ||
| } | ||
| } | ||
| return helpMessage | ||
| } | ||
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| private Map<String,Map> removeHidden(Map<String,Map> map) { | ||
| if (config.help.showHidden) { | ||
| return map | ||
| } | ||
| def Map<String,Map> returnMap = [:] | ||
| map.each { String key, Map value -> | ||
| if(!value.hidden) { | ||
| returnMap[key] = value | ||
| } else if(value.containsKey("properties")) { | ||
| value.properties = removeHidden(value.properties) | ||
| returnMap[key] = value | ||
| } else { | ||
| hiddenParametersCount++ | ||
| } | ||
| } | ||
| return returnMap | ||
| } | ||
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| // | ||
| // Get help for params in list format | ||
| // | ||
| private List<String> getHelpListParams(Map<String,Map> params, Integer maxChars, String parentParameter = "") { | ||
| def List helpMessage = [] | ||
| def Integer typeMaxChars = Utils.longestStringLength(params.collect { key, value -> value.type instanceof String ? "[${value.type}]" : value.type as String}) | ||
| for (String paramName in params.keySet()) { | ||
| def Map paramOptions = params.get(paramName) as Map | ||
| def String type = paramOptions.type instanceof String ? '[' + paramOptions.type + ']' : paramOptions.type as String | ||
| def String enumsString = "" | ||
| if (paramOptions.enum != null) { | ||
| def List enums = (List) paramOptions.enum | ||
| def String chopEnums = enums.join(", ") | ||
| if(chopEnums.length() > terminalLength){ | ||
| chopEnums = chopEnums.substring(0, terminalLength-5) | ||
| chopEnums = chopEnums.substring(0, chopEnums.lastIndexOf(",")) + ", ..." | ||
| } | ||
| enumsString = " (accepted: " + chopEnums + ") " | ||
| } | ||
| def String description = paramOptions.description ? paramOptions.description as String + " " : "" | ||
| def defaultValue = paramOptions.default != null ? "[default: " + paramOptions.default.toString() + "] " : '' | ||
| def String nestedParamName = parentParameter ? parentParameter + "." + paramName : paramName | ||
| def String nestedString = paramOptions.properties ? "(This parameter has sub-parameters. Use '--help ${nestedParamName}' to see all sub-parameters) " : "" | ||
| def descriptionDefault = description + colors.dim + enumsString + defaultValue + colors.reset + nestedString | ||
| // Wrap long description texts | ||
| // Loosely based on https://dzone.com/articles/groovy-plain-text-word-wrap | ||
| if (descriptionDefault.length() > terminalLength){ | ||
| descriptionDefault = wrapText(descriptionDefault) | ||
| } | ||
| helpMessage.add(" --" + paramName.padRight(maxChars) + colors.dim + type.padRight(typeMaxChars + 1) + colors.reset + descriptionDefault) | ||
| } | ||
| return helpMessage | ||
| } | ||
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| // | ||
| // Flattens the schema params map so all nested parameters are shown as their full name | ||
| // | ||
| private Map<String,Map> flattenNestedSchemaMap(Map params) { | ||
| def Map returnMap = [:] | ||
| params.each { String key, Map value -> | ||
| if (value.containsKey("properties")) { | ||
| def flattenedMap = flattenNestedSchemaMap(value.properties) | ||
| flattenedMap.each { String k, Map v -> | ||
| returnMap.put(key + "." + k, v) | ||
| } | ||
| } else { | ||
| returnMap.put(key, value) | ||
| } | ||
| } | ||
| return returnMap | ||
| } | ||
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| // | ||
| // This function adds the help parameters to the main parameters map as ungrouped parameters | ||
| // | ||
| private void addHelpParameters() { | ||
| if (!paramsMap.containsKey(null)) { | ||
| paramsMap[null] = [:] | ||
| } | ||
| paramsMap[null][config.help.shortParameter] = [ | ||
| "type": ["boolean", "string"], | ||
| "description": "Show the help message for all top level parameters. When a parameter is given to `--${config.help.shortParameter}`, the full help message of that parameter will be printed." | ||
| ] | ||
| paramsMap[null][config.help.fullParameter] = [ | ||
| "type": "boolean", | ||
| "description": "Show the help message for all non-hidden parameters." | ||
| ] | ||
| paramsMap[null][config.help.showHiddenParameter] = [ | ||
| "type": "boolean", | ||
| "description": "Show all hidden parameters in the help message. This needs to be used in combination with `--${config.help.shortParameter}` or `--${config.help.fullParameter}`." | ||
| ] | ||
| } | ||
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| // | ||
| // Wrap too long text | ||
| // | ||
| private String wrapText(String text) { | ||
| def List olines = [] | ||
| def String oline = "" | ||
| text.split(" ").each() { wrd -> | ||
| if ((oline.size() + wrd.size()) <= terminalLength) { | ||
| oline += wrd + " " | ||
| } else { | ||
| olines += oline | ||
| oline = wrd + " " | ||
| } | ||
| } | ||
| olines += oline | ||
| return olines.join("\n") | ||
| } | ||
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| } |
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