Merge pull request #70 from nextflow-io/fix-more-race-conditions

Fix race conditions
nextflow-io · Oct 29, 2024 · 0800dbb · 0800dbb
2 parents 4c4cd85 + 5053f62
commit 0800dbb
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Showing 3 changed files with 24 additions and 24 deletions.
diff --git a/plugins/nf-schema/src/main/nextflow/validation/JsonSchemaValidator.groovy b/plugins/nf-schema/src/main/nextflow/validation/JsonSchemaValidator.groovy
@@ -22,9 +22,9 @@ import java.util.regex.Matcher
 @CompileStatic
 public class JsonSchemaValidator {
 
-    private static ValidatorFactory validator
-    private static Pattern uriPattern = Pattern.compile('^#/(\\d*)?/?(.*)$')
-    private static ValidationConfig config
+    private ValidatorFactory validator
+    private Pattern uriPattern = Pattern.compile('^#/(\\d*)?/?(.*)$')
+    private ValidationConfig config
 
     JsonSchemaValidator(ValidationConfig config) {
         this.validator = new ValidatorFactory()
@@ -34,7 +34,7 @@ public class JsonSchemaValidator {
         this.config = config
     }
 
-    private static List<String> validateObject(JsonNode input, String validationType, Object rawJson, String schemaString) {
+    private List<String> validateObject(JsonNode input, String validationType, Object rawJson, String schemaString) {
         def JSONObject schema = new JSONObject(schemaString)
         def String draft = Utils.getValueFromJson("#/\$schema", schema)
         if(draft != "https://json-schema.org/draft/2020-12/schema") {
@@ -104,12 +104,12 @@ public class JsonSchemaValidator {
         return errors
     }
 
-    public static List<String> validate(JSONArray input, String schemaString) {
+    public List<String> validate(JSONArray input, String schemaString) {
         def JsonNode jsonInput = new OrgJsonNode.Factory().wrap(input)
         return this.validateObject(jsonInput, "field", input, schemaString)
     }
 
-    public static List<String> validate(JSONObject input, String schemaString) {
+    public List<String> validate(JSONObject input, String schemaString) {
         def JsonNode jsonInput = new OrgJsonNode.Factory().wrap(input)
         return this.validateObject(jsonInput, "parameter", input, schemaString)
     }

diff --git a/plugins/nf-schema/src/main/nextflow/validation/SamplesheetConverter.groovy b/plugins/nf-schema/src/main/nextflow/validation/SamplesheetConverter.groovy
@@ -19,38 +19,38 @@ import nextflow.Nextflow
 @CompileStatic
 class SamplesheetConverter {
 
-    private static ValidationConfig config
+    private ValidationConfig config
 
     SamplesheetConverter(ValidationConfig config) {
         this.config = config
     }
 
-    private static List<Map> rows = []
-    private static Map meta = [:]
+    private List<Map> rows = []
+    private Map meta = [:]
 
-    private static Map getMeta() {
+    private Map getMeta() {
         this.meta
     }
 
-    private static Map resetMeta() {
+    private Map resetMeta() {
         this.meta = [:]
     }
 
-    private static addMeta(Map newEntries) {
+    private addMeta(Map newEntries) {
         this.meta = this.meta + newEntries
     }
 
-    private static Boolean isMeta() {
+    private Boolean isMeta() {
         this.meta.size() > 0
     }
 
-    private static List unrecognisedHeaders = []
+    private List unrecognisedHeaders = []
 
-    private static addUnrecognisedHeader (String header) {
+    private addUnrecognisedHeader (String header) {
         this.unrecognisedHeaders.add(header)
     }
 
-    private static logUnrecognisedHeaders(String fileName) {
+    private logUnrecognisedHeaders(String fileName) {
         def Set unrecognisedHeaders = this.unrecognisedHeaders as Set
         if(unrecognisedHeaders.size() > 0) {
             def String processedHeaders = unrecognisedHeaders.collect { "\t- ${it}" }.join("\n")
@@ -66,7 +66,7 @@ class SamplesheetConverter {
     /*
     Convert the samplesheet to a list of entries based on a schema
     */
-    public static List validateAndConvertToList(
+    public List validateAndConvertToList(
         Path samplesheetFile,
         Path schemaFile,
         Map options
@@ -124,7 +124,7 @@ class SamplesheetConverter {
     This function processes an input value based on a schema. 
     The output will be created for addition to the output channel.
     */
-    private static Object formatEntry(Object input, LinkedHashMap schema, String headerPrefix = "") {
+    private Object formatEntry(Object input, LinkedHashMap schema, String headerPrefix = "") {
 
         // Add default values for missing entries
         input = input != null ? input : schema.containsKey("default") ? schema.default : []
@@ -172,15 +172,15 @@ class SamplesheetConverter {
 
     }
 
-    private static List validPathFormats = ["file-path", "path", "directory-path", "file-path-pattern"]
-    private static List schemaOptions = ["anyOf", "oneOf", "allOf"]
+    private List validPathFormats = ["file-path", "path", "directory-path", "file-path-pattern"]
+    private List schemaOptions = ["anyOf", "oneOf", "allOf"]
 
     /*
     This function processes a value that's not a map or list and casts it to a file type if necessary.
     When there is uncertainty if the value should be a path, some simple logic is applied that tries
     to guess if it should be a file type
     */
-    private static Object processValue(Object value, Map schemaEntry) {
+    private Object processValue(Object value, Map schemaEntry) {
         if(!(value instanceof String)) {
             return value
         }
@@ -234,7 +234,7 @@ class SamplesheetConverter {
     This function processes an input value based on a schema. 
     The output will be created for addition to the meta map.
     */
-    private static Object processMeta(Object input, LinkedHashMap schema, String headerPrefix) {
+    private Object processMeta(Object input, LinkedHashMap schema, String headerPrefix) {
         // Add default values for missing entries
         input = input != null ? input : schema.containsKey("default") ? schema.default : []
 

diff --git a/plugins/nf-schema/src/main/nextflow/validation/SchemaValidator.groovy b/plugins/nf-schema/src/main/nextflow/validation/SchemaValidator.groovy
@@ -40,7 +40,7 @@ import org.yaml.snakeyaml.Yaml
 @CompileStatic
 class SchemaValidator extends PluginExtensionPoint {
 
-    static final List<String> NF_OPTIONS = [
+    final List<String> NF_OPTIONS = [
             // Options for base `nextflow` command
             'bg',
             'c',
@@ -556,7 +556,7 @@ Please contact the pipeline maintainer(s) if you see this warning as a user.
     //
     // Clean and check parameters relative to Nextflow native classes
     //
-    private static Map cleanParameters(Map params) {
+    private Map cleanParameters(Map params) {
         def Map new_params = (Map) params.getClass().newInstance(params)
         for (p in params) {
             // remove anything evaluating to false