Merge pull request #149 from ehb54/master

bring branch alexey-dev-issue367 (data-from-disk integration) to the latest master state
ehb54 · Oct 31, 2024 · 5ae0913 · 5ae0913
2 parents 840dabf + 6e2a7f7
commit 5ae0913
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diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
@@ -45,6 +45,9 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
+      - name: Install libarchive
+        run: |
+          apt-get install -y libarchive-dev
       - name: Initialize CodeQL
         uses: github/codeql-action/init@v3
         with:
@@ -83,6 +86,9 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
+      - name: Install libarchive
+        run: |
+          apt-get install -y libarchive-dev
       - name: Initialize CodeQL
         uses: github/codeql-action/init@v3
         with:

diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,8 +1,7 @@
 UltraScan is licensed under the LGPL v3 license.
 
 Copyright ©  Borries Demeler, Ph.D.
-The University of Texas
-****************************************************************************************
+***************************************************************************************
 
 GNU LESSER GENERAL PUBLIC LICENSE
 

diff --git a/admin/codeql/docker/docker/Dockerfile b/admin/codeql/docker/docker/Dockerfile
@@ -23,6 +23,7 @@ RUN apt-get install -y xorg
 RUN apt-get install -y x11-apps
 RUN apt-get install -y telnet
 RUN apt-get install -y cmake
+RUN apt-get install -y libarchive-dev
 
 # qt
 RUN apt-get install -y qtbase5-dev

diff --git a/admin/codeql/docker/dockerdev/Dockerfile b/admin/codeql/docker/dockerdev/Dockerfile
@@ -23,6 +23,7 @@ RUN apt-get install -y xorg
 RUN apt-get install -y x11-apps
 RUN apt-get install -y telnet
 RUN apt-get install -y cmake
+RUN apt-get install -y libarchive-dev
 
 # qt
 RUN apt-get install -y qtbase5-dev

diff --git a/admin/release/centos7/Dockerfile b/admin/release/centos7/Dockerfile
@@ -49,6 +49,7 @@ RUN yum install -y telnet
 RUN yum install -y $apt_python_version
 RUN yum install -y rsync
 RUN yum install -y glib2-devel postgresql-devel at-spi2-core-devel libjpeg-devel fontconfig-devel 
+RUN yum install -y libarchive-devel
 
 # bits to ease development/testing
 

diff --git a/admin/release/redhat/Dockerfile b/admin/release/redhat/Dockerfile
@@ -49,6 +49,7 @@ RUN dnf install -y telnet
 RUN dnf install -y $apt_python_version
 RUN dnf install -y rsync
 RUN dnf install -y glib2-devel postgresql-devel at-spi2-core-devel libjpeg-devel fontconfig-devel 
+RUN dnf install -y libarchive-devel
 
 # bits to ease development/testing
 

diff --git a/admin/release/ubuntu/Dockerfile b/admin/release/ubuntu/Dockerfile
@@ -49,6 +49,7 @@ RUN apt-get install -y x11-apps
 RUN apt-get install -y telnet
 RUN apt-get install -y $apt_python_version
 RUN apt-get install -y rsync
+RUN apt-get install -y libarchive-dev
 
 # bits to ease development/testing
 

diff --git a/alpha/us.cpp b/alpha/us.cpp
@@ -627,11 +627,11 @@ void US_Win::help( int index )
 
             " * Nikolay Dokholyan\n"
             " * Jose Garcia de la Torre\n"
-				" * Haram Kim\n"
-				" * Minji Kim\n"
+			" * Haram Kim\n"
+			" * Minji Kim\n"
             " * Brad Langford\n"
             " * Thomas Laue\n"
-				" * Konrad Löhr\n"
+			" * Konrad Löhr\n"
             " * Luitgard Nagel-Steger\n"
             " * Zach Ozer\n"
             " * Karel Planken\n"
@@ -652,18 +652,12 @@ void US_Win::help( int index )
         tr( "About UltraScan..." ),
         tr( "UltraScan III version %1  (DEVELOPMENT)\n"
             "%2\n"
-            "Copyright 1989 - 2018\n"
-            "Borries Demeler and the University of Texas System\n\n"
+            "Copyright 1989 - 2024\n"
+            "Borries Demeler\n\n"
             "For more information, please visit:\n"
-            "http://www.ultrascan.uthscsa.edu/\n\n"
+            "http://www.ultrascan.aucsolutions.com/\n\n"
             "The author can be reached at:\n"
-            "The University of Texas Health Science Center\n"
-            "Department of Biochemistry\n"
-            "7703 Floyd Curl Drive\n"
-            "San Antonio, Texas 78229-3900\n"
-            "voice: (210) 767-3332\n"
-            "Fax:   (210) 567-6595\n"
-            "E-mail: [email protected]" ).arg( US_Version ).arg( REVISION ) );
+            "E-mail: [email protected]" ).arg( US_Version ).arg( REVISION ) );
 
       statusBar()->showMessage( tr( "Ready" ) );
       break;
@@ -740,7 +734,7 @@ bool US_Win::notice_check()
    // Query notice table in the us3_notice database
    US_Passwd pw;
    US_DB2    db;
-   QString   host  ( "uslims3.uthscsa.edu" );
+   QString   host  ( "uslims3.aucsolutions.edu" );
    QString   dbname( "us3_notice" );
    QString   user  ( "us3_notice" );
    QString   passwd( "us3_notice" );

diff --git a/doc/manual/advanced_config.body b/doc/manual/advanced_config.body
@@ -9,7 +9,7 @@
     in an advanced mode. Certain applications can benefit from use of more
     than one thread. These variations are governed by the configuration values
     that are set in this panel. Actual values should be set only under the
-    guidance of UTHSCSA software developers, since meanings of settings vary
+    guidance of software developers, since meanings of settings vary
     considerably from application to application.</p>
 
     <p class='center'> <img src="images/advanced_config.png" alt='Advanced

diff --git a/doc/manual/convert.body b/doc/manual/convert.body
@@ -13,7 +13,7 @@
     channels us_convert would convert that into three binary AUC
     files, which can then be uploaded to an UltraScan III database
     and prepared for analysis. The AUC file format is described <a
-    href='http://wiki.bcf2.uthscsa.edu/ultrascan3/wiki/Us3Formats'>here</a>.
+    href='http://wiki.aucsolutions.com/ultrascan3/wiki/Us3Formats'>here</a>.
     </p>
 
     <p class='center'><img src="images/convert.png" 

diff --git a/doc/manual/ultrascan3.txt b/doc/manual/ultrascan3.txt
@@ -1,9 +1,8 @@
 UltraScan III
 
-Copyright 1989 - 2021
+Copyright 1989 - 2024
 
-Copyright � 1989?2021 Borries Demeler, Ph.D.
-Copyright � 1997?2021 The University of Texas Health Science Center at San Antonio
+Copyright � 1989?2021 Borries Demeler, Ph.D.
 All rights reserved.
 
 UltraScan is free software; you can redistribute it and/or modify it under the
@@ -12,14 +11,8 @@ Foundation; either version 3 of the License, or (at your option) any later
 version.
 
 For more information, please visit:
-http://www.ultrascan.uthscsa.edu/
+http://www.ultrascan.aucsolutions.com/
 
 The author can be reached at:
 
-The University of Texas Health Science Center
-Department of Biochemistry
-7703 Floyd Curl Drive
-San Antonio, Texas 78229-3900
-voice: (210) 567-6592
-Fax:   (210) 567-6595
-E-mail: [email protected]
+E-mail: [email protected]
diff --git a/gui/us_license.cpp b/gui/us_license.cpp
@@ -25,13 +25,13 @@ US_License::US_License( QWidget* parent, Qt::WindowFlags flags )
 
   // Banner
   QLabel* banner = us_banner( 
-     tr( "UltraScan III Registration\nPlease enter all fields" ) );
+     tr( "Please enter all fields" ) );
 
   banner->setGeometry( 
-      QRect( xpos, ypos, width, spacing + 2 * rowHeight ) );
+      QRect( xpos, ypos, width, spacing + rowHeight ) );
 
   // Row 1 - Name
-  ypos += rowHeight * 3 + spacing;
+  ypos += rowHeight + 2 * spacing;
 
   QLabel* firstname = us_label( tr( "Name (first, last):" ), 0, QFont::Bold );
   firstname->setGeometry( xpos, ypos, buttonw, rowHeight );
@@ -85,20 +85,6 @@ US_License::US_License( QWidget* parent, Qt::WindowFlags flags )
   connect( le_institution, SIGNAL( textChanged       ( const QString& ) ), 
                            SLOT  ( update_institution( const QString& ) ) );
 
-  // Row 4 - Address
-  xpos = spacing;
-  ypos += rowHeight + spacing;
-
-  QLabel* address = us_label( tr( "Address:" ), 0, QFont::Bold );
-  address->setGeometry( xpos, ypos, buttonw, rowHeight );
-
-  xpos += buttonw + spacing;
-
-  le_address =  us_lineedit( "" );
-  le_address->setGeometry( xpos, ypos, full_buttonw, rowHeight );
-  connect( le_address, SIGNAL( textChanged   ( const QString& ) ), 
-                       SLOT  ( update_address( const QString& ) ) );
-
   // Row 5 - City/State/Zip
   xpos = spacing;
   ypos += rowHeight + spacing;
@@ -139,31 +125,12 @@ US_License::US_License( QWidget* parent, Qt::WindowFlags flags )
 
   xpos += mediumColumn + spacing + 10; // Adjust
 
-  QLabel* zip = us_label( tr( "Zip:" ), 0, QFont::Bold );
-  zip->setGeometry( xpos, ypos, smallColumn, rowHeight );
-
-  xpos += smallColumn + spacing;
-
-  le_zip = us_lineedit( "" );
-  le_zip->setGeometry( xpos, ypos, mediumColumn, rowHeight );
-  connect( le_zip, SIGNAL( textChanged( const QString& ) ), 
-                   SLOT  ( update_zip ( const QString& ) ) );
-
-  // Row 6 - Phone/License Type/Version
-  xpos  = spacing;
-  ypos += rowHeight + spacing;
+  //xpos  = spacing;
+ // ypos += rowHeight + spacing;
 
-  QLabel* phone = us_label( tr( "Phone Number:" ), 0, QFont::Bold );
-  phone->setGeometry( xpos, ypos, buttonw, rowHeight );
-
-  xpos += spacing + buttonw;
+ // xpos += spacing + buttonw;
 
-  le_phone = us_lineedit( "" );;
-  le_phone->setGeometry( xpos, ypos, buttonw, rowHeight );
-  connect( le_phone, SIGNAL( textChanged ( const QString& ) ), 
-                     SLOT  ( update_phone( const QString& ) ) );
-
-  xpos += buttonw + spacing;
+ // xpos += buttonw + spacing;
 
   QLabel* lb_licensetype = us_label( tr( "License:" ), 0, QFont::Bold );
   lb_licensetype->setGeometry( xpos, ypos, smallColumn, rowHeight );
@@ -179,13 +146,8 @@ US_License::US_License( QWidget* parent, Qt::WindowFlags flags )
   connect( cbb_licensetype, SIGNAL( currentIndexChanged( const QString& ) ), 
                             SLOT  ( update_licensetype ( const QString& ) ) );
 
-  xpos += mediumColumn + spacing + 10; // Adjust
-
-  lbl_version = us_label( tr( "Version:" ), 0, QFont::Bold );
-  lbl_version->setGeometry( xpos, ypos, smallColumn, rowHeight );
-
   xpos  = spacing;
-  ypos += 2 * rowHeight + spacing;
+  ypos += rowHeight + spacing;
 
   QLabel* status = us_banner( tr( "License Status" ) );
   status->setGeometry( QRect( xpos, ypos, width, spacing + rowHeight ) );
@@ -211,7 +173,7 @@ US_License::US_License( QWidget* parent, Qt::WindowFlags flags )
 
   // Row 8 - Expiration
   xpos  = spacing;
-  ypos += rowHeight + 2 * spacing;
+  ypos += rowHeight + spacing;
 
   lbl_expiration = us_label( "Expiration:", 0, QFont::Bold );
   lbl_expiration->setGeometry( xpos, ypos, buttonw, rowHeight );
@@ -225,7 +187,7 @@ US_License::US_License( QWidget* parent, Qt::WindowFlags flags )
 
   // Row 9 - Version
   xpos  = spacing;
-  ypos += rowHeight + 2 * spacing;
+  ypos += rowHeight + spacing;
 
   lbl_valid = us_label( "UltraScan III Version:", 0, QFont::Bold );
   lbl_valid->setGeometry( xpos, ypos, buttonw, rowHeight );
@@ -313,11 +275,11 @@ void US_License::load_current( void )
   lastname    = "";
   firstname   = "";
   institution = "";
-  address     = "";
+  address     = "n/a";
   city        = "";
   state       = "NON-US";
-  zip         = "";
-  phone       = "";
+  zip         = "n/a";
+  phone       = "n/a";
   email       = "";
   version     = US_Version;  // us_defines.h
   validation  = "";
@@ -349,6 +311,10 @@ void US_License::load_current( void )
     validation  = license [ 12 ];
     expiration  = license [ 13 ];
   }
+  // Force unused fields to "n/a"
+  address     = "n/a";
+  zip         = "n/a";
+  phone       = "n/a";
 
   update_screen();
 }
@@ -358,10 +324,7 @@ void US_License::update_screen( void )
   le_firstname   ->setText( firstname   );
   le_lastname    ->setText( lastname    );
   le_institution ->setText( institution );
-  le_address     ->setText( address     );
   le_city        ->setText( city        );
-  le_zip         ->setText( zip         );
-  le_phone       ->setText( phone       );
   le_email       ->setText( email       );
 
   le_platform    ->setText( platform + " / " + os );
@@ -431,10 +394,7 @@ void US_License::update( void )
   if ( firstname   == ""  ||
        lastname    == ""  ||
        institution == ""  ||
-       address     == ""  ||
        state       == ""  ||
-       zip         == ""  ||
-       phone       == ""  ||
        email       == ""  )
   {
     QMessageBox::information ( this, 
@@ -493,7 +453,7 @@ void US_License::update( void )
                   + "&licensetype=" + licensetype;
 //qDebug() << "requesting update";
   // Send request
-  QString url     = "https://ultrascan.aucsolutions.com/update-license.php";
+  QString url     = "https://ultrascan.aucsolutions.com/update-license-new.php";
   US_HttpPost* transmit = new US_HttpPost( url, req );
   connect( transmit, SIGNAL( US_Http_post_response( const QString& ) ),
            this,     SLOT  ( update_response      ( const QString& ) ) );

diff --git a/gui/us_license.h b/gui/us_license.h
@@ -72,10 +72,7 @@ class US_GUI_EXTERN US_License : public US_Widgets
     QLineEdit* le_firstname;
     QLineEdit* le_lastname;
     QLineEdit* le_institution;
-    QLineEdit* le_address;
     QLineEdit* le_city;
-    QLineEdit* le_zip;
-    QLineEdit* le_phone;
     QLineEdit* le_email;
     QLineEdit* le_platform;
     QLineEdit* le_expiration;
@@ -114,11 +111,8 @@ class US_GUI_EXTERN US_License : public US_Widgets
     void update_firstname  ( const QString& s ){ firstname   = trim( s ); };
     void update_lastname   ( const QString& s ){ lastname    = trim( s ); };
     void update_institution( const QString& s ){ institution = trim( s ); };
-    void update_address    ( const QString& s ){ address     = trim( s ); };
     void update_city       ( const QString& s ){ city        = trim( s ); };
     void update_state      ( const QString& s ){ state       = trim( s ); };
-    void update_zip        ( const QString& s ){ zip         = trim( s ); };
-    void update_phone      ( const QString& s ){ phone       = trim( s ); };
     void update_email      ( const QString& s ){ email       = trim( s ); };
     void update_licensetype( const QString& s ){ licensetype = trim( s ); };
 };

diff --git a/library.pri b/library.pri
@@ -26,6 +26,7 @@ unix {
     INCLUDEPATH  += $$MYSQLPATH
   }
   DEFINES      += INTEL LINUX
+  LIBS         += -larchive
 
 }
 
@@ -44,6 +45,7 @@ win32 {
   LIBS                   += $$MINGWDIR/lib/libws2_32.a $$MINGWDIR/lib/libadvapi32.a
   LIBS                   += $$MINGWDIR/lib/libgdi32.a $$MINGWDIR/lib/libuser32.a
   LIBS                   += $$MINGWDIR/lib/libkernel32.a $$MINGWDIR/lib/libpsapi.a
+  LIBS                   += -larchive
 
   #QMAKE_LFLAGS           += /IMPLIB:../lib/$${TARGET}.a /MACHINE:X86 /INCREMENTAL:NO 
   #QMAKE_CXXFLAGS_DEBUG   += /wd4996
@@ -58,5 +60,6 @@ macx {
   INCLUDEPATH  += ../gui ../utils $$QWTPATH/include ../mysql/include
   DEFINES      += MAC OSX
   LIBS         += $$QWTLIB
+  LIBS         += -larchive
 }
 
diff --git a/programs/us/us_de_DE.ts b/programs/us/us_de_DE.ts
@@ -333,16 +333,10 @@ Copyright 1989 - 2008
 Borries Demeler and the University of Texas System
 
 For more information, please visit:
-http://www.ultrascan.uthscsa.edu/
+http://www.ultrascan.aucsolutions.com/
 
 The author can be reached at:
-The University of Texas Health Science Center
-Department of Biochemistry
-7703 Floyd Curl Drive
-San Antonio, Texas 78229-3900
-voice: (210) 567-6592
-Fax:   (210) 567-6595
-E-mail: [email protected]</source>
+E-mail: [email protected]</source>
         <translation type="unfinished"></translation>
     </message>
 </context>