mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-23 21:29:55 +00:00
529 lines
22 KiB
Groovy
Executable file
529 lines
22 KiB
Groovy
Executable file
//
|
|
// This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template.
|
|
//
|
|
|
|
import org.everit.json.schema.Schema
|
|
import org.everit.json.schema.loader.SchemaLoader
|
|
import org.everit.json.schema.ValidationException
|
|
import org.json.JSONObject
|
|
import org.json.JSONTokener
|
|
import org.json.JSONArray
|
|
import groovy.json.JsonSlurper
|
|
import groovy.json.JsonBuilder
|
|
|
|
class NfcoreSchema {
|
|
|
|
//
|
|
// Resolve Schema path relative to main workflow directory
|
|
//
|
|
public static String getSchemaPath(workflow, schema_filename='nextflow_schema.json') {
|
|
return "${workflow.projectDir}/${schema_filename}"
|
|
}
|
|
|
|
//
|
|
// Function to loop over all parameters defined in schema and check
|
|
// whether the given parameters adhere to the specifications
|
|
//
|
|
/* groovylint-disable-next-line UnusedPrivateMethodParameter */
|
|
public static void validateParameters(workflow, params, log, schema_filename='nextflow_schema.json') {
|
|
def has_error = false
|
|
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~//
|
|
// Check for nextflow core params and unexpected params
|
|
def json = new File(getSchemaPath(workflow, schema_filename=schema_filename)).text
|
|
def Map schemaParams = (Map) new JsonSlurper().parseText(json).get('definitions')
|
|
def nf_params = [
|
|
// Options for base `nextflow` command
|
|
'bg',
|
|
'c',
|
|
'C',
|
|
'config',
|
|
'd',
|
|
'D',
|
|
'dockerize',
|
|
'h',
|
|
'log',
|
|
'q',
|
|
'quiet',
|
|
'syslog',
|
|
'v',
|
|
'version',
|
|
|
|
// Options for `nextflow run` command
|
|
'ansi',
|
|
'ansi-log',
|
|
'bg',
|
|
'bucket-dir',
|
|
'c',
|
|
'cache',
|
|
'config',
|
|
'dsl2',
|
|
'dump-channels',
|
|
'dump-hashes',
|
|
'E',
|
|
'entry',
|
|
'latest',
|
|
'lib',
|
|
'main-script',
|
|
'N',
|
|
'name',
|
|
'offline',
|
|
'params-file',
|
|
'pi',
|
|
'plugins',
|
|
'poll-interval',
|
|
'pool-size',
|
|
'profile',
|
|
'ps',
|
|
'qs',
|
|
'queue-size',
|
|
'r',
|
|
'resume',
|
|
'revision',
|
|
'stdin',
|
|
'stub',
|
|
'stub-run',
|
|
'test',
|
|
'w',
|
|
'with-charliecloud',
|
|
'with-conda',
|
|
'with-dag',
|
|
'with-docker',
|
|
'with-mpi',
|
|
'with-notification',
|
|
'with-podman',
|
|
'with-report',
|
|
'with-singularity',
|
|
'with-timeline',
|
|
'with-tower',
|
|
'with-trace',
|
|
'with-weblog',
|
|
'without-docker',
|
|
'without-podman',
|
|
'work-dir'
|
|
]
|
|
def unexpectedParams = []
|
|
|
|
// Collect expected parameters from the schema
|
|
def expectedParams = []
|
|
def enums = [:]
|
|
for (group in schemaParams) {
|
|
for (p in group.value['properties']) {
|
|
expectedParams.push(p.key)
|
|
if (group.value['properties'][p.key].containsKey('enum')) {
|
|
enums[p.key] = group.value['properties'][p.key]['enum']
|
|
}
|
|
}
|
|
}
|
|
|
|
for (specifiedParam in params.keySet()) {
|
|
// nextflow params
|
|
if (nf_params.contains(specifiedParam)) {
|
|
log.error "ERROR: You used a core Nextflow option with two hyphens: '--${specifiedParam}'. Please resubmit with '-${specifiedParam}'"
|
|
has_error = true
|
|
}
|
|
// unexpected params
|
|
def params_ignore = params.schema_ignore_params.split(',') + 'schema_ignore_params'
|
|
def expectedParamsLowerCase = expectedParams.collect{ it.replace("-", "").toLowerCase() }
|
|
def specifiedParamLowerCase = specifiedParam.replace("-", "").toLowerCase()
|
|
def isCamelCaseBug = (specifiedParam.contains("-") && !expectedParams.contains(specifiedParam) && expectedParamsLowerCase.contains(specifiedParamLowerCase))
|
|
if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam) && !isCamelCaseBug) {
|
|
// Temporarily remove camelCase/camel-case params #1035
|
|
def unexpectedParamsLowerCase = unexpectedParams.collect{ it.replace("-", "").toLowerCase()}
|
|
if (!unexpectedParamsLowerCase.contains(specifiedParamLowerCase)){
|
|
unexpectedParams.push(specifiedParam)
|
|
}
|
|
}
|
|
}
|
|
|
|
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~//
|
|
// Validate parameters against the schema
|
|
InputStream input_stream = new File(getSchemaPath(workflow, schema_filename=schema_filename)).newInputStream()
|
|
JSONObject raw_schema = new JSONObject(new JSONTokener(input_stream))
|
|
|
|
// Remove anything that's in params.schema_ignore_params
|
|
raw_schema = removeIgnoredParams(raw_schema, params)
|
|
|
|
Schema schema = SchemaLoader.load(raw_schema)
|
|
|
|
// Clean the parameters
|
|
def cleanedParams = cleanParameters(params)
|
|
|
|
// Convert to JSONObject
|
|
def jsonParams = new JsonBuilder(cleanedParams)
|
|
JSONObject params_json = new JSONObject(jsonParams.toString())
|
|
|
|
// Validate
|
|
try {
|
|
schema.validate(params_json)
|
|
} catch (ValidationException e) {
|
|
println ''
|
|
log.error 'ERROR: Validation of pipeline parameters failed!'
|
|
JSONObject exceptionJSON = e.toJSON()
|
|
printExceptions(exceptionJSON, params_json, log, enums)
|
|
println ''
|
|
has_error = true
|
|
}
|
|
|
|
// Check for unexpected parameters
|
|
if (unexpectedParams.size() > 0) {
|
|
Map colors = NfcoreTemplate.logColours(params.monochrome_logs)
|
|
println ''
|
|
def warn_msg = 'Found unexpected parameters:'
|
|
for (unexpectedParam in unexpectedParams) {
|
|
warn_msg = warn_msg + "\n* --${unexpectedParam}: ${params[unexpectedParam].toString()}"
|
|
}
|
|
log.warn warn_msg
|
|
log.info "- ${colors.dim}Ignore this warning: params.schema_ignore_params = \"${unexpectedParams.join(',')}\" ${colors.reset}"
|
|
println ''
|
|
}
|
|
|
|
if (has_error) {
|
|
System.exit(1)
|
|
}
|
|
}
|
|
|
|
//
|
|
// Beautify parameters for --help
|
|
//
|
|
public static String paramsHelp(workflow, params, command, schema_filename='nextflow_schema.json') {
|
|
Map colors = NfcoreTemplate.logColours(params.monochrome_logs)
|
|
Integer num_hidden = 0
|
|
String output = ''
|
|
output += 'Typical pipeline command:\n\n'
|
|
output += " ${colors.cyan}${command}${colors.reset}\n\n"
|
|
Map params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename))
|
|
Integer max_chars = paramsMaxChars(params_map) + 1
|
|
Integer desc_indent = max_chars + 14
|
|
Integer dec_linewidth = 160 - desc_indent
|
|
for (group in params_map.keySet()) {
|
|
Integer num_params = 0
|
|
String group_output = colors.underlined + colors.bold + group + colors.reset + '\n'
|
|
def group_params = params_map.get(group) // This gets the parameters of that particular group
|
|
for (param in group_params.keySet()) {
|
|
if (group_params.get(param).hidden && !params.show_hidden_params) {
|
|
num_hidden += 1
|
|
continue;
|
|
}
|
|
def type = '[' + group_params.get(param).type + ']'
|
|
def description = group_params.get(param).description
|
|
def defaultValue = group_params.get(param).default != null ? " [default: " + group_params.get(param).default.toString() + "]" : ''
|
|
def description_default = description + colors.dim + defaultValue + colors.reset
|
|
// Wrap long description texts
|
|
// Loosely based on https://dzone.com/articles/groovy-plain-text-word-wrap
|
|
if (description_default.length() > dec_linewidth){
|
|
List olines = []
|
|
String oline = "" // " " * indent
|
|
description_default.split(" ").each() { wrd ->
|
|
if ((oline.size() + wrd.size()) <= dec_linewidth) {
|
|
oline += wrd + " "
|
|
} else {
|
|
olines += oline
|
|
oline = wrd + " "
|
|
}
|
|
}
|
|
olines += oline
|
|
description_default = olines.join("\n" + " " * desc_indent)
|
|
}
|
|
group_output += " --" + param.padRight(max_chars) + colors.dim + type.padRight(10) + colors.reset + description_default + '\n'
|
|
num_params += 1
|
|
}
|
|
group_output += '\n'
|
|
if (num_params > 0){
|
|
output += group_output
|
|
}
|
|
}
|
|
if (num_hidden > 0){
|
|
output += colors.dim + "!! Hiding $num_hidden params, use --show_hidden_params to show them !!\n" + colors.reset
|
|
}
|
|
output += NfcoreTemplate.dashedLine(params.monochrome_logs)
|
|
return output
|
|
}
|
|
|
|
//
|
|
// Groovy Map summarising parameters/workflow options used by the pipeline
|
|
//
|
|
public static LinkedHashMap paramsSummaryMap(workflow, params, schema_filename='nextflow_schema.json') {
|
|
// Get a selection of core Nextflow workflow options
|
|
def Map workflow_summary = [:]
|
|
if (workflow.revision) {
|
|
workflow_summary['revision'] = workflow.revision
|
|
}
|
|
workflow_summary['runName'] = workflow.runName
|
|
if (workflow.containerEngine) {
|
|
workflow_summary['containerEngine'] = workflow.containerEngine
|
|
}
|
|
if (workflow.container) {
|
|
workflow_summary['container'] = workflow.container
|
|
}
|
|
workflow_summary['launchDir'] = workflow.launchDir
|
|
workflow_summary['workDir'] = workflow.workDir
|
|
workflow_summary['projectDir'] = workflow.projectDir
|
|
workflow_summary['userName'] = workflow.userName
|
|
workflow_summary['profile'] = workflow.profile
|
|
workflow_summary['configFiles'] = workflow.configFiles.join(', ')
|
|
|
|
// Get pipeline parameters defined in JSON Schema
|
|
def Map params_summary = [:]
|
|
def params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename))
|
|
for (group in params_map.keySet()) {
|
|
def sub_params = new LinkedHashMap()
|
|
def group_params = params_map.get(group) // This gets the parameters of that particular group
|
|
for (param in group_params.keySet()) {
|
|
if (params.containsKey(param)) {
|
|
def params_value = params.get(param)
|
|
def schema_value = group_params.get(param).default
|
|
def param_type = group_params.get(param).type
|
|
if (schema_value != null) {
|
|
if (param_type == 'string') {
|
|
if (schema_value.contains('$projectDir') || schema_value.contains('${projectDir}')) {
|
|
def sub_string = schema_value.replace('\$projectDir', '')
|
|
sub_string = sub_string.replace('\${projectDir}', '')
|
|
if (params_value.contains(sub_string)) {
|
|
schema_value = params_value
|
|
}
|
|
}
|
|
if (schema_value.contains('$params.outdir') || schema_value.contains('${params.outdir}')) {
|
|
def sub_string = schema_value.replace('\$params.outdir', '')
|
|
sub_string = sub_string.replace('\${params.outdir}', '')
|
|
if ("${params.outdir}${sub_string}" == params_value) {
|
|
schema_value = params_value
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
// We have a default in the schema, and this isn't it
|
|
if (schema_value != null && params_value != schema_value) {
|
|
sub_params.put(param, params_value)
|
|
}
|
|
// No default in the schema, and this isn't empty
|
|
else if (schema_value == null && params_value != "" && params_value != null && params_value != false) {
|
|
sub_params.put(param, params_value)
|
|
}
|
|
}
|
|
}
|
|
params_summary.put(group, sub_params)
|
|
}
|
|
return [ 'Core Nextflow options' : workflow_summary ] << params_summary
|
|
}
|
|
|
|
//
|
|
// Beautify parameters for summary and return as string
|
|
//
|
|
public static String paramsSummaryLog(workflow, params) {
|
|
Map colors = NfcoreTemplate.logColours(params.monochrome_logs)
|
|
String output = ''
|
|
def params_map = paramsSummaryMap(workflow, params)
|
|
def max_chars = paramsMaxChars(params_map)
|
|
for (group in params_map.keySet()) {
|
|
def group_params = params_map.get(group) // This gets the parameters of that particular group
|
|
if (group_params) {
|
|
output += colors.bold + group + colors.reset + '\n'
|
|
for (param in group_params.keySet()) {
|
|
output += " " + colors.blue + param.padRight(max_chars) + ": " + colors.green + group_params.get(param) + colors.reset + '\n'
|
|
}
|
|
output += '\n'
|
|
}
|
|
}
|
|
output += "!! Only displaying parameters that differ from the pipeline defaults !!\n"
|
|
output += NfcoreTemplate.dashedLine(params.monochrome_logs)
|
|
return output
|
|
}
|
|
|
|
//
|
|
// Loop over nested exceptions and print the causingException
|
|
//
|
|
private static void printExceptions(ex_json, params_json, log, enums, limit=5) {
|
|
def causingExceptions = ex_json['causingExceptions']
|
|
if (causingExceptions.length() == 0) {
|
|
def m = ex_json['message'] =~ /required key \[([^\]]+)\] not found/
|
|
// Missing required param
|
|
if (m.matches()) {
|
|
log.error "* Missing required parameter: --${m[0][1]}"
|
|
}
|
|
// Other base-level error
|
|
else if (ex_json['pointerToViolation'] == '#') {
|
|
log.error "* ${ex_json['message']}"
|
|
}
|
|
// Error with specific param
|
|
else {
|
|
def param = ex_json['pointerToViolation'] - ~/^#\//
|
|
def param_val = params_json[param].toString()
|
|
if (enums.containsKey(param)) {
|
|
def error_msg = "* --${param}: '${param_val}' is not a valid choice (Available choices"
|
|
if (enums[param].size() > limit) {
|
|
log.error "${error_msg} (${limit} of ${enums[param].size()}): ${enums[param][0..limit-1].join(', ')}, ... )"
|
|
} else {
|
|
log.error "${error_msg}: ${enums[param].join(', ')})"
|
|
}
|
|
} else {
|
|
log.error "* --${param}: ${ex_json['message']} (${param_val})"
|
|
}
|
|
}
|
|
}
|
|
for (ex in causingExceptions) {
|
|
printExceptions(ex, params_json, log, enums)
|
|
}
|
|
}
|
|
|
|
//
|
|
// Remove an element from a JSONArray
|
|
//
|
|
private static JSONArray removeElement(json_array, element) {
|
|
def list = []
|
|
int len = json_array.length()
|
|
for (int i=0;i<len;i++){
|
|
list.add(json_array.get(i).toString())
|
|
}
|
|
list.remove(element)
|
|
JSONArray jsArray = new JSONArray(list)
|
|
return jsArray
|
|
}
|
|
|
|
//
|
|
// Remove ignored parameters
|
|
//
|
|
private static JSONObject removeIgnoredParams(raw_schema, params) {
|
|
// Remove anything that's in params.schema_ignore_params
|
|
params.schema_ignore_params.split(',').each{ ignore_param ->
|
|
if(raw_schema.keySet().contains('definitions')){
|
|
raw_schema.definitions.each { definition ->
|
|
for (key in definition.keySet()){
|
|
if (definition[key].get("properties").keySet().contains(ignore_param)){
|
|
// Remove the param to ignore
|
|
definition[key].get("properties").remove(ignore_param)
|
|
// If the param was required, change this
|
|
if (definition[key].has("required")) {
|
|
def cleaned_required = removeElement(definition[key].required, ignore_param)
|
|
definition[key].put("required", cleaned_required)
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
if(raw_schema.keySet().contains('properties') && raw_schema.get('properties').keySet().contains(ignore_param)) {
|
|
raw_schema.get("properties").remove(ignore_param)
|
|
}
|
|
if(raw_schema.keySet().contains('required') && raw_schema.required.contains(ignore_param)) {
|
|
def cleaned_required = removeElement(raw_schema.required, ignore_param)
|
|
raw_schema.put("required", cleaned_required)
|
|
}
|
|
}
|
|
return raw_schema
|
|
}
|
|
|
|
//
|
|
// Clean and check parameters relative to Nextflow native classes
|
|
//
|
|
private static Map cleanParameters(params) {
|
|
def new_params = params.getClass().newInstance(params)
|
|
for (p in params) {
|
|
// remove anything evaluating to false
|
|
if (!p['value']) {
|
|
new_params.remove(p.key)
|
|
}
|
|
// Cast MemoryUnit to String
|
|
if (p['value'].getClass() == nextflow.util.MemoryUnit) {
|
|
new_params.replace(p.key, p['value'].toString())
|
|
}
|
|
// Cast Duration to String
|
|
if (p['value'].getClass() == nextflow.util.Duration) {
|
|
new_params.replace(p.key, p['value'].toString().replaceFirst(/d(?!\S)/, "day"))
|
|
}
|
|
// Cast LinkedHashMap to String
|
|
if (p['value'].getClass() == LinkedHashMap) {
|
|
new_params.replace(p.key, p['value'].toString())
|
|
}
|
|
}
|
|
return new_params
|
|
}
|
|
|
|
//
|
|
// This function tries to read a JSON params file
|
|
//
|
|
private static LinkedHashMap paramsLoad(String json_schema) {
|
|
def params_map = new LinkedHashMap()
|
|
try {
|
|
params_map = paramsRead(json_schema)
|
|
} catch (Exception e) {
|
|
println "Could not read parameters settings from JSON. $e"
|
|
params_map = new LinkedHashMap()
|
|
}
|
|
return params_map
|
|
}
|
|
|
|
//
|
|
// Method to actually read in JSON file using Groovy.
|
|
// Group (as Key), values are all parameters
|
|
// - Parameter1 as Key, Description as Value
|
|
// - Parameter2 as Key, Description as Value
|
|
// ....
|
|
// Group
|
|
// -
|
|
private static LinkedHashMap paramsRead(String json_schema) throws Exception {
|
|
def json = new File(json_schema).text
|
|
def Map schema_definitions = (Map) new JsonSlurper().parseText(json).get('definitions')
|
|
def Map schema_properties = (Map) new JsonSlurper().parseText(json).get('properties')
|
|
/* Tree looks like this in nf-core schema
|
|
* definitions <- this is what the first get('definitions') gets us
|
|
group 1
|
|
title
|
|
description
|
|
properties
|
|
parameter 1
|
|
type
|
|
description
|
|
parameter 2
|
|
type
|
|
description
|
|
group 2
|
|
title
|
|
description
|
|
properties
|
|
parameter 1
|
|
type
|
|
description
|
|
* properties <- parameters can also be ungrouped, outside of definitions
|
|
parameter 1
|
|
type
|
|
description
|
|
*/
|
|
|
|
// Grouped params
|
|
def params_map = new LinkedHashMap()
|
|
schema_definitions.each { key, val ->
|
|
def Map group = schema_definitions."$key".properties // Gets the property object of the group
|
|
def title = schema_definitions."$key".title
|
|
def sub_params = new LinkedHashMap()
|
|
group.each { innerkey, value ->
|
|
sub_params.put(innerkey, value)
|
|
}
|
|
params_map.put(title, sub_params)
|
|
}
|
|
|
|
// Ungrouped params
|
|
def ungrouped_params = new LinkedHashMap()
|
|
schema_properties.each { innerkey, value ->
|
|
ungrouped_params.put(innerkey, value)
|
|
}
|
|
params_map.put("Other parameters", ungrouped_params)
|
|
|
|
return params_map
|
|
}
|
|
|
|
//
|
|
// Get maximum number of characters across all parameter names
|
|
//
|
|
private static Integer paramsMaxChars(params_map) {
|
|
Integer max_chars = 0
|
|
for (group in params_map.keySet()) {
|
|
def group_params = params_map.get(group) // This gets the parameters of that particular group
|
|
for (param in group_params.keySet()) {
|
|
if (param.size() > max_chars) {
|
|
max_chars = param.size()
|
|
}
|
|
}
|
|
}
|
|
return max_chars
|
|
}
|
|
}
|