From 4c5a2e05c1501725c4c35fd329de93e759ad02d4 Mon Sep 17 00:00:00 2001
From: Fabien Castan <fabcastan@gmail.com>
Date: Tue, 13 Aug 2019 12:25:07 +0200
Subject: [PATCH 1/4] bug fix: decomposeFilename max digit

Time is ssize_t and not size_t, so the max number of digit is not the
same. This could generate an exception from boost::lexical_cast in
FileNumbers::push_back.
---
 src/sequenceParser/detail/analyze.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/sequenceParser/detail/analyze.cpp b/src/sequenceParser/detail/analyze.cpp
index 74e0aa3..d73b8fb 100644
--- a/src/sequenceParser/detail/analyze.cpp
+++ b/src/sequenceParser/detail/analyze.cpp
@@ -378,7 +378,7 @@ std::vector<Sequence> buildSequences( const boost::filesystem::path& directory,
 
 std::size_t decomposeFilename( const std::string& filename, FileStrings& stringParts, FileNumbers& numberParts, const EDetection& options )
 {
-	static const std::size_t max = std::numeric_limits<std::size_t>::digits10;
+	static const std::size_t max = std::numeric_limits<Time>::digits10;
 	std::string regex;
 	if( options & eDetectionNegative )
 	{

From f30a134cff925e9e372062cb990802cd19feb54a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Micha=C3=ABl=20Guiral?= <michael.guiral@mikrosimage.com>
Date: Mon, 19 Aug 2019 16:50:15 +0200
Subject: [PATCH 2/4] Centos7 build

---
 tools/docker/centos6/Dockerfile             | 28 --------------------
 tools/docker/centos6/build.sh               |  6 -----
 tools/docker/centos7/Dockerfile             | 29 +++++++++++++++++++++
 tools/docker/{centos6 => centos7}/README.md |  4 +--
 tools/docker/centos7/build.sh               |  6 +++++
 5 files changed, 37 insertions(+), 36 deletions(-)
 delete mode 100644 tools/docker/centos6/Dockerfile
 delete mode 100755 tools/docker/centos6/build.sh
 create mode 100644 tools/docker/centos7/Dockerfile
 rename tools/docker/{centos6 => centos7}/README.md (65%)
 create mode 100755 tools/docker/centos7/build.sh

diff --git a/tools/docker/centos6/Dockerfile b/tools/docker/centos6/Dockerfile
deleted file mode 100644
index 1750759..0000000
--- a/tools/docker/centos6/Dockerfile
+++ /dev/null
@@ -1,28 +0,0 @@
-FROM centos:6
-
-#Install dependencies
-RUN yum install -y wget cmake tar gcc gcc-c++ pcre-devel python-devel
-
-#Install boost
-RUN wget http://repo.enetres.net/enetres.repo -O /etc/yum.repos.d/enetres.repo && \
-    yum install -y boost-devel-1.55.0
-
-#Install JAVA
-RUN cd /opt/ && \
-    wget -nv --no-cookies --no-check-certificate --header "Cookie: gpw_e24=http%3A%2F%2Fwww.oracle.com%2F; oraclelicense=accept-securebackup-cookie" http://download.oracle.com/otn-pub/java/jdk/8u111-b14/jdk-8u111-linux-x64.rpm && \
-    rpm -i jdk-8u111-linux-x64.rpm && \
-    rm -rf jdk-8u111-linux-x64.rpm
-
-#Install Swig 2.0.11
-RUN cd /opt/ && \
-    wget -O swig-2.0.11.tar.gz https://sourceforge.net/projects/swig/files/swig/swig-2.0.11/swig-2.0.11.tar.gz/download && \
-    tar xzf swig-2.0.11.tar.gz && \
-    cd swig-2.0.11 && \
-    ./configure && \
-    make && make install && \
-    cd /opt/ && rm -rf swig-2.0.11*
-
-ENV JAVA_HOME /usr/java/latest
-ENV JDK_HOME /usr/java/latest
-
-
diff --git a/tools/docker/centos6/build.sh b/tools/docker/centos6/build.sh
deleted file mode 100755
index f709ad1..0000000
--- a/tools/docker/centos6/build.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-
-cd /opt/sequenceparser
-cmake . -DCMAKE_INSTALL_PREFIX=/opt/sequenceparser/centos6 -DBOOST_ROOT=/usr/include/boost/
-make
-make install
diff --git a/tools/docker/centos7/Dockerfile b/tools/docker/centos7/Dockerfile
new file mode 100644
index 0000000..ac02e69
--- /dev/null
+++ b/tools/docker/centos7/Dockerfile
@@ -0,0 +1,29 @@
+FROM centos:7
+
+#Install dependencies
+RUN yum install -y wget cmake tar gcc gcc-c++ pcre-devel python-devel make zlib-devel bzip2-devel
+
+#Install boost
+RUN cd /opt/ && \ 
+    wget https://sourceforge.net/projects/boost/files/boost/1.55.0/boost_1_55_0.tar.gz && \
+    tar xzf boost_1_55_0.tar.gz && \
+    cd boost_1_55_0 && \
+    ./bootstrap.sh && \
+    ./b2 install --with=all && \
+    rm -rf boost_1_55_0.tar.gz && \
+    rm -rf boost_1_55_0.tar
+     
+
+
+#Install JAVA
+RUN yum install -y java-1.8.0-openjdk java-1.8.0-openjdk-devel
+
+#Install Swig 2.0.11
+
+RUN cd /opt/ && \
+    wget -O swig-2.0.11.tar.gz https://sourceforge.net/projects/swig/files/swig/swig-2.0.11/swig-2.0.11.tar.gz/download && \
+    tar xzf swig-2.0.11.tar.gz && \
+    cd swig-2.0.11 && \
+    ./configure && \
+    make && make install && \
+    cd /opt/ && rm -rf swig-2.0.11*
diff --git a/tools/docker/centos6/README.md b/tools/docker/centos7/README.md
similarity index 65%
rename from tools/docker/centos6/README.md
rename to tools/docker/centos7/README.md
index ffc51a6..98b4c8b 100644
--- a/tools/docker/centos6/README.md
+++ b/tools/docker/centos7/README.md
@@ -1,6 +1,6 @@
 ### How to compile with docker
 ```Shell
-docker build -t sequenceparser:centos6 .
-docker run -v <path to sequenceparser>:/opt/sequenceparser sequenceparser:centos6 /opt/sequenceparser/docker/centos6/build.sh
+docker build -t sequenceparser:centos7 .
+docker run -v <path to sequenceparser>:/opt/sequenceparser sequenceparser:centos7 /opt/sequenceparser/tools/docker/centos7/build.sh
 ```
 The compiled libraries is installed into centos6 folder at root folder of sequenceparser repository
diff --git a/tools/docker/centos7/build.sh b/tools/docker/centos7/build.sh
new file mode 100755
index 0000000..914ca1a
--- /dev/null
+++ b/tools/docker/centos7/build.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+cd /opt/sequenceparser
+cmake . -DCMAKE_INSTALL_PREFIX=/opt/sequenceparser/install -DBOOST_ROOT=/usr/local/include/boost/
+make
+make install

From 88208676ae5b9a23f09a0499af0fc1cf8386adbf Mon Sep 17 00:00:00 2001
From: Fabien Castan <fabcastan@gmail.com>
Date: Tue, 20 Aug 2019 10:25:34 +0200
Subject: [PATCH 3/4] [sequenceParser] ItemStat: avoid conflicts with get/set
 function generated for java

Now getUserName and getGroupName are available in the java binding
---
 src/sequenceParser/ItemStat.cpp | 20 ++++++++++----------
 src/sequenceParser/ItemStat.hpp |  6 ++++--
 2 files changed, 14 insertions(+), 12 deletions(-)

diff --git a/src/sequenceParser/ItemStat.cpp b/src/sequenceParser/ItemStat.cpp
index 19f057d..d0db961 100644
--- a/src/sequenceParser/ItemStat.cpp
+++ b/src/sequenceParser/ItemStat.cpp
@@ -82,14 +82,14 @@ void ItemStat::setPermissions( const mode_t& protection )
 	otherCanExecute = protection & S_IXOTH;
 }
 
-void ItemStat::setUserName()
+void ItemStat::updateUserName()
 {
     passwd* user = getpwuid(userId);
     if(user && user->pw_name)
         userName = std::string(user->pw_name);
 }
 
-void ItemStat::setGroupName()
+void ItemStat::updateGroupName()
 {
     group* group = getgrgid(groupId);
     if(group && group->gr_name)
@@ -126,8 +126,8 @@ void ItemStat::statLink( const boost::filesystem::path& path )
 	// size on hard-drive (takes hardlinks into account)
 	sizeOnDisk = (statInfos.st_blocks / nbHardLinks) * statInfos.st_blksize;
 	setPermissions(statInfos.st_mode);
-	setUserName();
-	setGroupName();
+	updateUserName();
+	updateGroupName();
 #else
 	fullNbHardLinks = nbHardLinks = 1;
 #endif
@@ -161,8 +161,8 @@ void ItemStat::statFolder( const boost::filesystem::path& path )
 	maxSize = size;
 	sizeOnDisk = statInfos.st_blocks * statInfos.st_blksize;
 	setPermissions(statInfos.st_mode);
-	setUserName();
-	setGroupName();
+	updateUserName();
+	updateGroupName();
 #endif
 
 	// size (takes hardlinks into account)
@@ -197,8 +197,8 @@ void ItemStat::statFile( const boost::filesystem::path& path )
 	// size on hard-drive (takes hardlinks into account)
 	sizeOnDisk = (statInfos.st_blocks / nbHardLinks) * statInfos.st_blksize;
 	setPermissions(statInfos.st_mode);
-	setUserName();
-	setGroupName();
+	updateUserName();
+	updateGroupName();
 #endif
 
 	// size (takes hardlinks into account)
@@ -219,8 +219,8 @@ void ItemStat::statSequence( const Item& item, const bool approximative )
 	groupId = statInfos.st_gid;
 	accessTime = statInfos.st_atime;
 	setPermissions(statInfos.st_mode);
-	setUserName();
-	setGroupName();
+	updateUserName();
+	updateGroupName();
 #endif
 
 	modificationTime = 0;
diff --git a/src/sequenceParser/ItemStat.hpp b/src/sequenceParser/ItemStat.hpp
index b5a8549..b64e856 100644
--- a/src/sequenceParser/ItemStat.hpp
+++ b/src/sequenceParser/ItemStat.hpp
@@ -24,8 +24,10 @@ class ItemStat
 	void statLink( const boost::filesystem::path& path );
 #ifdef __UNIX__
 	void setPermissions( const mode_t& protection );
-	void setUserName();
-	void setGroupName();
+    /// @brief Update user name from filesystem
+	void updateUserName();
+    /// @brief Update group name from filesystem
+	void updateGroupName();
 #endif
 
 public:

From 236490c09d407d0de721cbfd068aa9c6649bc0b4 Mon Sep 17 00:00:00 2001
From: Fabien Castan <fabcastan@gmail.com>
Date: Tue, 20 Aug 2019 10:25:58 +0200
Subject: [PATCH 4/4] [test] ItemStat: test access to getGroupName/getUserName

---
 test/java/StatLibraryTestMain.java | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/test/java/StatLibraryTestMain.java b/test/java/StatLibraryTestMain.java
index 2ed1d43..7c34e38 100644
--- a/test/java/StatLibraryTestMain.java
+++ b/test/java/StatLibraryTestMain.java
@@ -30,6 +30,8 @@ private static void displayFolderContent(ItemStat itemStat) {
         System.out.println("Full Hard links : " + itemStat.getFullNbHardLinks());
         System.out.println("Hardlinks : " + itemStat.getNbHardLinks());
         System.out.println("Device : " + itemStat.getDeviceId());
+        System.out.println("Group : " + itemStat.getGroupName());
+        System.out.println("User : " + itemStat.getUserName());
     }
 }