Merge remote-tracking branch 'remotes/origin/master' into improve_NGS…

…DExportSV
imgag · Jan 15, 2025 · b03359d · b03359d
2 parents 4e4a6d7 + 38b6200
commit b03359d
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Showing 9 changed files with 64 additions and 4 deletions.
diff --git a/src/GSvarServer-TEST/Controller-Test.h b/src/GSvarServer-TEST/Controller-Test.h
@@ -410,6 +410,6 @@ private slots:
 
         // This test is intended to be changed when PathType changes, OTHER is always the last element,
         // it will always change when items are added or deleted
-        I_EQUAL(static_cast<int>(PathType::OTHER), 45);
+        I_EQUAL(static_cast<int>(PathType::OTHER), 47);
     }
 };
diff --git a/src/GSvarServer/ServerController.cpp b/src/GSvarServer/ServerController.cpp
@@ -443,9 +443,19 @@ HttpResponse ServerController::locateFileByType(const HttpRequest& request)
             case PathType::CFDNA_CANDIDATES:
                 file_list << file_locator->getSomaticCfdnaCandidateFile();
                 break;            
-            case PathType::GSVAR:
-                file_list << FileLocation(url_entity.file_id, PathType::GSVAR, found_file, true);
-                break;
+			case PathType::METHYLATION:
+				file_list << file_locator->getMethylationFile();
+				break;
+			case PathType::METHYLATION_IMAGE:
+				if (locus.isEmpty())
+				{
+					return HttpResponse(ResponseStatus::BAD_REQUEST, HttpUtils::detectErrorContentType(request.getHeaderByName("User-Agent")), EndpointManager::formatResponseMessage(request, "Locus value has not been provided"));
+				}
+				file_list << file_locator->getMethylationImage(locus);
+				break;
+			case PathType::GSVAR:
+				file_list << FileLocation(url_entity.file_id, PathType::GSVAR, found_file, true);
+				break;
             case PathType::SAMPLE_FOLDER:
             case PathType::FUSIONS_PIC_DIR:
             case PathType::FUSIONS:
@@ -467,8 +477,10 @@ HttpResponse ServerController::locateFileByType(const HttpRequest& request)
 		}
 	}
 
+
 	for (int i = 0; i < file_list.count(); ++i)
 	{
+		Log::info("file path: " + file_list.at(i).filename);
         QJsonObject cur_json_item;
         QJsonObject cur_json_item_without_token;
 		cur_json_item.insert("id", file_list[i].id);

diff --git a/src/cppNGSD/FileLocation.h b/src/cppNGSD/FileLocation.h
@@ -17,6 +17,7 @@ enum class PathType
 	BAM, //BAM file
 	VIRAL_BAM, //BAM file for a virus
     CRAM, //compressed version of BAM
+
 	//variant data
 	VCF, //small variants (VCF.GZ format)
 	GSVAR, //small variants (GSvar format)
@@ -60,6 +61,8 @@ enum class PathType
 	SIGNATURE_ID,	// Somatic: resut part from SigProfileExtractor for SNVs (CSV format)
 	SIGNATURE_DBS,	// Somatic: resut part from SigProfileExtractor for SNVs (CSV format)
 	SIGNATURE_CNV,	// Somatic: resut from SigProfileExtractor for CNVs (CSV format)
+	METHYLATION, // Methylation calls (TSV format)
+	METHYLATION_IMAGE, // image of a given methylation locus (PNG format)
 	OTHER // everything else
 };
 
@@ -212,6 +215,10 @@ struct FileLocation
 				return "SIGNATURE_DBS";
 			case PathType::SIGNATURE_CNV:
 				return "SIGNATURE_CNV";
+			case PathType::METHYLATION:
+				return "METHYLATION";
+			case PathType::METHYLATION_IMAGE:
+				return "METHYLATION_IMAGE";
 
 		}
 		THROW(ProgrammingException, "Unhandled path type '" + QString::number((int)pathtype) + "' in typeToString()!");
@@ -267,6 +274,8 @@ struct FileLocation
 		if (in_upper == "SIGNATURE_ID") return PathType::SIGNATURE_ID;
 		if (in_upper == "SIGNATURE_DBS") return PathType::SIGNATURE_DBS;
 		if (in_upper == "SIGNATURE_CNV") return PathType::SIGNATURE_CNV;
+		if (in_upper == "METHYLATION") return PathType::METHYLATION;
+		if (in_upper == "METHYLATION_IMAGE") return PathType::METHYLATION_IMAGE;
 		THROW(ProgrammingException, "Unhandled path type string '" + in_upper + "' in stringToType()!");
 	}
 
@@ -366,6 +375,10 @@ struct FileLocation
 				return "DBS signature";
 			case PathType::SIGNATURE_CNV:
 				return "CNV signature";
+			case PathType::METHYLATION:
+				return "methylation calls";
+			case PathType::METHYLATION_IMAGE:
+				return "image of a given methylation locus";
 		}
 		THROW(ProgrammingException, "Unhandled path type '" + QString::number((int)pathtype) + "' in typeToHumanReadableString()!");
 	}

diff --git a/src/cppNGSD/FileLocationProvider.h b/src/cppNGSD/FileLocationProvider.h
@@ -33,6 +33,10 @@ class CPPNGSDSHARED_EXPORT FileLocationProvider
 	virtual FileLocation getRepeatExpansionHistogram(QString locus) const = 0;
 	//Returns sample-specific qcML files.
 	virtual FileLocationList getQcFiles() const = 0;
+	//Returns the methylation TSV file of the current analysis
+	virtual FileLocation getMethylationFile() const = 0;
+	//Returns the methylation image of a given locus
+	virtual FileLocation getMethylationImage(QString locus) const = 0;
 
 	//############################## sample-specific files ##############################
 	//Returns sample-specific BAM files

diff --git a/src/cppNGSD/FileLocationProviderLocal.cpp b/src/cppNGSD/FileLocationProviderLocal.cpp
@@ -108,6 +108,22 @@ FileLocationList FileLocationProviderLocal::getQcFiles() const
 	return output;
 }
 
+FileLocation FileLocationProviderLocal::getMethylationFile() const
+{
+	QString name = QFileInfo(gsvar_file_).baseName();
+	QString file = gsvar_file_.left(gsvar_file_.length()-6) + "_var_methylation.tsv";
+
+	return FileLocation{name, PathType::METHYLATION, file, QFile::exists(file)};
+}
+
+FileLocation FileLocationProviderLocal::getMethylationImage(QString locus) const
+{
+	QString name = QFileInfo(gsvar_file_).baseName();
+	QString file = getAnalysisPath() + QDir::separator() + "methylartist" + QDir::separator() + name  + "_" + locus + ".png";
+
+	return FileLocation(name, PathType::METHYLATION_IMAGE, file, QFile::exists(file));
+}
+
 void FileLocationProviderLocal::addToList(const FileLocation& loc, FileLocationList& list, bool add_if_missing)
 {
 	bool exists = QFile::exists(loc.filename);

diff --git a/src/cppNGSD/FileLocationProviderLocal.h b/src/cppNGSD/FileLocationProviderLocal.h
@@ -22,6 +22,8 @@ class CPPNGSDSHARED_EXPORT FileLocationProviderLocal
 	FileLocation getRepeatExpansionImage(QString locus) const override;
 	FileLocation getRepeatExpansionHistogram(QString locus) const override;
 	FileLocationList getQcFiles() const override;
+	FileLocation getMethylationFile() const override;
+	FileLocation getMethylationImage(QString locus) const override;
 
 	FileLocationList getVcfFiles(bool return_if_missing) const override;
 	FileLocationList getBamFiles(bool return_if_missing) const override;

diff --git a/src/cppNGSD/FileLocationProviderRemote.cpp b/src/cppNGSD/FileLocationProviderRemote.cpp
@@ -52,6 +52,16 @@ FileLocationList FileLocationProviderRemote::getQcFiles() const
 	return getFileLocationsByType(PathType::QC, false);
 }
 
+FileLocation FileLocationProviderRemote::getMethylationFile() const
+{
+	return getOneFileLocationByType(PathType::METHYLATION, "");
+}
+
+FileLocation FileLocationProviderRemote::getMethylationImage(QString locus) const
+{
+	return getOneFileLocationByType(PathType::METHYLATION_IMAGE, locus);
+}
+
 FileLocationList FileLocationProviderRemote::getFileLocationsByType(PathType type, bool return_if_missing) const
 {
     FileLocationList output;

diff --git a/src/cppNGSD/FileLocationProviderRemote.h b/src/cppNGSD/FileLocationProviderRemote.h
@@ -25,6 +25,8 @@ class CPPNGSDSHARED_EXPORT FileLocationProviderRemote
 	FileLocation getRepeatExpansionImage(QString locus) const override;
 	FileLocation getRepeatExpansionHistogram(QString locus) const override;
 	FileLocationList getQcFiles() const override;
+	FileLocation getMethylationFile() const override;
+	FileLocation getMethylationImage(QString locus) const override;
 
 	FileLocationList getBamFiles(bool return_if_missing) const override;
 	FileLocationList getViralBamFiles(bool return_if_missing) const override;

diff --git a/src/cppNGSD/NGSD.cpp b/src/cppNGSD/NGSD.cpp
@@ -1364,6 +1364,7 @@ QString NGSD::processedSamplePath(const QString& processed_sample_id, PathType t
 			output += ps_name + "_repeats.vcf";
 		}
 	}
+	else if (type==PathType::METHYLATION) output += ps_name + "_var_methylation.tsv";
 	else if (type!=PathType::SAMPLE_FOLDER) THROW(ProgrammingException, "Unhandled PathType '" + FileLocation::typeToString(type) + "' in processedSamplePath!");
 
 	return QFileInfo(output).absoluteFilePath();