From b8091b99204cabedc9bbe345bb6aaa3feb94993c Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Fri, 22 Jun 2018 11:24:25 +0200
Subject: [PATCH] find MSrun on absolute file path if possible or on sample
name only
---
src/utils/msrunstore.cpp | 127 +++++++++++++++++++++++++--------------
1 file changed, 81 insertions(+), 46 deletions(-)
diff --git a/src/utils/msrunstore.cpp b/src/utils/msrunstore.cpp
index 677efe12..f867fb0b 100644
--- a/src/utils/msrunstore.cpp
+++ b/src/utils/msrunstore.cpp
@@ -7,72 +7,107 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "msrunstore.h"
#include <pappsomspp/exception/exceptionnotfound.h>
#include <pappsomspp/utils.h>
+#include <QFileInfo>
MsRunStore::MsRunStore()
{
-
}
MsRunStore::~MsRunStore()
{
-
}
-MsRunSp MsRunStore::getInstance(const MsRun * p_msrun) {
- auto it = std::find_if(_map_msrun.begin(), _map_msrun.end(), [p_msrun] (const MsRunSp & msrun_sp) {return msrun_sp.get()== p_msrun;});
- if (it != _map_msrun.end()) {
- return (*it);
+MsRunSp
+MsRunStore::getInstance(const MsRun *p_msrun)
+{
+ auto it = std::find_if(
+ _map_msrun.begin(), _map_msrun.end(),
+ [p_msrun](const MsRunSp &msrun_sp) { return msrun_sp.get() == p_msrun; });
+ if(it != _map_msrun.end())
+ {
+ return (*it);
}
- MsRunSp p_xtfile;
- return p_xtfile;
+ MsRunSp p_xtfile;
+ return p_xtfile;
}
-MsRunSp MsRunStore::getInstance(const QString & location) {
+MsRunSp
+MsRunStore::getInstance(const QString &location)
+{
- auto it = std::find_if(_map_msrun.begin(), _map_msrun.end(), [location] (const MsRunSp & msrun_sp) {return msrun_sp.get()->getFilename()==location;});
- if (it != _map_msrun.end()) {
- return *it;
+ QFileInfo file_ondisk(location);
+ auto it = _map_msrun.end();
+ if(file_ondisk.baseName() == location)
+ {
+ // look only for the same sample name
+ it = std::find_if(_map_msrun.begin(), _map_msrun.end(),
+ [location](const MsRunSp &msrun_sp) {
+ return msrun_sp.get()->getSampleName() == location;
+ });
}
- else {
- MsRunSp p_xtfile = std::make_shared<MsRun>(location);
- p_xtfile.get()->setXmlId(QString("msrun%1").arg(pappso::Utils::getLexicalOrderedString(_map_msrun.size()+1)));
- p_xtfile.get()->setFilename(location);
- _map_msrun.push_back( p_xtfile);
- return p_xtfile;
-
+ else
+ {
+ // look for an absolute file path
+ it = std::find_if(_map_msrun.begin(), _map_msrun.end(),
+ [location](const MsRunSp &msrun_sp) {
+ if(msrun_sp.get()->getSampleName() ==
+ msrun_sp.get()->getFilename())
+ {
+ return msrun_sp.get()->getSampleName() ==
+ QFileInfo(location).baseName();
+ }
+ return msrun_sp.get()->getFilename() == location;
+ });
+ }
+ if(it != _map_msrun.end())
+ {
+ return *it;
}
- throw pappso::ExceptionNotFound(QObject::tr("Ms resource %1 not found").arg(location));
+ else
+ {
+ MsRunSp p_xtfile = std::make_shared<MsRun>(location);
+ p_xtfile.get()->setXmlId(QString("msrun%1").arg(
+ pappso::Utils::getLexicalOrderedString(_map_msrun.size() + 1)));
+ p_xtfile.get()->setFilename(location);
+ _map_msrun.push_back(p_xtfile);
+ return p_xtfile;
+ }
+ throw pappso::ExceptionNotFound(
+ QObject::tr("Ms resource %1 not found").arg(location));
}
-const std::vector<MsRunSp> & MsRunStore::getMsRunList() const {
- //std::vector<MsRunSp> msrun_list;
- // for (auto & msrun_pair :_map_msrun) {
- // msrun_list.push_back(msrun_pair.second);
- // }
- return _map_msrun;
+const std::vector<MsRunSp> &
+MsRunStore::getMsRunList() const
+{
+ // std::vector<MsRunSp> msrun_list;
+ // for (auto & msrun_pair :_map_msrun) {
+ // msrun_list.push_back(msrun_pair.second);
+ // }
+ return _map_msrun;
}
--
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