From 1fae29602bd09a886cb74184c837f26fedf2bf89 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?=
 <joaquintarraga@gmail.com>
Date: Wed, 11 Sep 2024 03:13:10 +0200
Subject: [PATCH] app: rename qc/data to qc/resources, #TASK-6772, #TASK-6766

---
 .../variant/qc/VariantQcAnalysis.java         | 29 ++++++++++++++-----
 .../karyotypic_sex_thresholds.json            |  0
 .../relatedness_thresholds.tsv                |  0
 3 files changed, 21 insertions(+), 8 deletions(-)
 rename opencga-app/app/analysis/qc/{data => resources}/karyotypic_sex_thresholds.json (100%)
 rename opencga-app/app/analysis/qc/{data => resources}/relatedness_thresholds.tsv (100%)

diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/qc/VariantQcAnalysis.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/qc/VariantQcAnalysis.java
index 1303304afb9..c5884e3cc51 100644
--- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/qc/VariantQcAnalysis.java
+++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/qc/VariantQcAnalysis.java
@@ -63,7 +63,8 @@ public class VariantQcAnalysis extends OpenCgaToolScopeStudy {
 
     // QC folders
     public static final String QC_FOLDER = "qc/";
-    public static final String QC_DATA_FOLDER = QC_FOLDER + "data/";
+    public static final String RESOURCES_FOLDER = "resources/";
+    public static final String QC_RESOURCES_FOLDER = QC_FOLDER + RESOURCES_FOLDER;
 
     // Data type
     public static final String FAMILY_QC_TYPE = "family";
@@ -292,17 +293,28 @@ protected static List<String> getNoSomaticSampleIds(Individual individual) {
     }
 
     protected Path getExternalFilePath(String analysisId, String resourceName) throws ToolException {
+        Path resourcesPath = getOutDir().resolve(RESOURCES_FOLDER);
+        if (!Files.exists(resourcesPath)) {
+            try {
+                Files.createDirectories(resourcesPath);
+                if (!Files.exists(resourcesPath)) {
+                    throw new ToolException("Something wrong happened when creating the resources folder at " + resourcesPath);
+                }
+            } catch (IOException e) {
+                throw new ToolException("Error creating the resources folder at " + resourcesPath, e);
+            }
+        }
         switch (resourceName) {
             case RELATEDNESS_THRESHOLDS_FILENAME:
             case INFERRED_SEX_THRESHOLDS_FILENAME:
-                return copyExternalFile(getOpencgaHome().resolve(ANALYSIS_FOLDER).resolve(QC_DATA_FOLDER).resolve(resourceName));
+                return copyExternalFile(getOpencgaHome().resolve(ANALYSIS_FOLDER).resolve(QC_RESOURCES_FOLDER).resolve(resourceName));
             default:
                 return downloadExternalFile(analysisId, resourceName);
         }
     }
 
     protected Path copyExternalFile(Path source) throws ToolException {
-        Path dest = getOutDir().resolve(source.getFileName());
+        Path dest = getOutDir().resolve(RESOURCES_FOLDER).resolve(source.getFileName());
         try {
             Files.copy(source, dest);
         } catch (IOException e) {
@@ -317,17 +329,18 @@ protected Path copyExternalFile(Path source) throws ToolException {
 
     protected Path downloadExternalFile(String analysisId, String resourceName) throws ToolException {
         URL url = null;
+        Path resourcesPath = getOutDir().resolve(RESOURCES_FOLDER);
         try {
             url = new URL(ResourceUtils.URL + ANALYSIS_FOLDER + analysisId + "/" + resourceName);
-            ResourceUtils.downloadThirdParty(url, getOutDir());
+            ResourceUtils.downloadThirdParty(url, resourcesPath);
         } catch (IOException e) {
-            throw new ToolException("Something wrong happened downloading the resource '" + resourceName + "' from '" + url + "'", e);
+            throw new ToolException("Something wrong happened when downloading the resource '" + resourceName + "' from '" + url + "'", e);
         }
 
-        if (!Files.exists(getOutDir().resolve(resourceName))) {
-            throw new ToolException("After downloading the resource '" + resourceName + "', it does not exist at " + getOutDir());
+        if (!Files.exists(resourcesPath.resolve(resourceName))) {
+            throw new ToolException("After downloading the resource '" + resourceName + "', it does not exist at " + resourcesPath);
         }
-        return getOutDir().resolve(resourceName);
+        return resourcesPath.resolve(resourceName);
     }
 
     protected Path downloadExternalFileAtResources(String analysisId, String resourceName) throws ToolException {
diff --git a/opencga-app/app/analysis/qc/data/karyotypic_sex_thresholds.json b/opencga-app/app/analysis/qc/resources/karyotypic_sex_thresholds.json
similarity index 100%
rename from opencga-app/app/analysis/qc/data/karyotypic_sex_thresholds.json
rename to opencga-app/app/analysis/qc/resources/karyotypic_sex_thresholds.json
diff --git a/opencga-app/app/analysis/qc/data/relatedness_thresholds.tsv b/opencga-app/app/analysis/qc/resources/relatedness_thresholds.tsv
similarity index 100%
rename from opencga-app/app/analysis/qc/data/relatedness_thresholds.tsv
rename to opencga-app/app/analysis/qc/resources/relatedness_thresholds.tsv