1.1 --- a/.hgignore	Wed Nov 28 00:35:35 2012 +0400
     1.2 +++ b/.hgignore	Wed Nov 28 14:42:15 2012 +0400
     1.3 @@ -34,7 +34,7 @@
     1.4  pair_cores/web/wc
     1.5  pair_cores/web/*.o
     1.6  pair_cores/web/*root
     1.7 -pair_cores/web/pair-cores.wt
     1.8 +pair_cores/web/*.wt
     1.9  *.zip
    1.10  
    1.11  # Temporary files from sphinx

     2.1 --- a/pair_cores/web/Makefile	Wed Nov 28 00:35:35 2012 +0400
     2.2 +++ b/pair_cores/web/Makefile	Wed Nov 28 14:42:15 2012 +0400
     2.3 @@ -2,7 +2,7 @@
     2.4  all: build environment
     2.5  
     2.6  .PHONY: build
     2.7 -build: pair-cores.wt
     2.8 +build: pair-cores.wt compare-aln-3d.wt
     2.9  
    2.10  .PHONY: environment
    2.11  environment: wc
    2.12 @@ -23,7 +23,7 @@
    2.13  
    2.14  wc_hpp = $(wc_cpp:.cpp=.hpp) wc/src/global.hpp
    2.15  
    2.16 -sources = $(wc_cpp) pair-cores.cpp
    2.17 +sources = $(wc_cpp)
    2.18  objects = $(sources:.cpp=.o)
    2.19  headers = $(wc_hpp)
    2.20  
    2.21 @@ -39,8 +39,11 @@
    2.22  
    2.23  $(wc_cpp) $(wc_hpp): wc
    2.24  
    2.25 -pair-cores.wt: $$(objects)
    2.26 -	$(LINK) $(LFLAGS) $(objects) $(LIBS) -o $@
    2.27 +pair-cores.wt: $$(objects) pair-cores.o
    2.28 +	$(LINK) $(LFLAGS) $^ $(LIBS) -o $@
    2.29 +
    2.30 +compare-aln-3d.wt: $$(objects) compare-aln-3d.o
    2.31 +	$(LINK) $(LFLAGS) $^ $(LIBS) -o $@
    2.32  
    2.33  wc:
    2.34  	wget https://bitbucket.org/starius/wt-classes/get/1.4.0.tar.gz -O - | \

     3.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     3.2 +++ b/pair_cores/web/compare-aln-3d.cpp	Wed Nov 28 14:42:15 2012 +0400
     3.3 @@ -0,0 +1,171 @@
     3.4 +#include <boost/bind.hpp>
     3.5 +
     3.6 +#include <Wt/WApplication>
     3.7 +#include <Wt/WEnvironment>
     3.8 +#include <Wt/WIntValidator>
     3.9 +#include <Wt/WDoubleValidator>
    3.10 +#include <Wt/WLineEdit>
    3.11 +#include <Wt/WTextArea>
    3.12 +#include <Wt/WCheckBox>
    3.13 +#include <Wt/WTemplate>
    3.14 +#include <Wt/WFileUpload>
    3.15 +#include <Wt/WPushButton>
    3.16 +
    3.17 +#include "wc/src/Wbi.hpp"
    3.18 +#include "wc/src/util.hpp"
    3.19 +
    3.20 +using namespace Wt;
    3.21 +using namespace Wt::Wc;
    3.22 +
    3.23 +TaskNumberQueue queue(100);
    3.24 +
    3.25 +std::string name_gen(TextFileInput* input_aln,
    3.26 +                     std::string extension) {
    3.27 +    TextFileInput* input = input_aln;
    3.28 +    std::string file = input->file_upload()->clientFileName().toUTF8();
    3.29 +    std::string without_extension = file.substr(0, file.find_last_of("."));
    3.30 +    if (without_extension.empty()) {
    3.31 +        without_extension = "pair-cores";
    3.32 +    }
    3.33 +    return without_extension + "." + extension;
    3.34 +}
    3.35 +
    3.36 +class PairCoresApp : public WApplication {
    3.37 +public:
    3.38 +    PairCoresApp(const WEnvironment& env);
    3.39 +
    3.40 +private:
    3.41 +    void reset_contents();
    3.42 +
    3.43 +    void do_nothing()
    3.44 +    { }
    3.45 +
    3.46 +    static Wt::WString tr(const char* key) {
    3.47 +        return Wt::WString::tr(key);
    3.48 +    }
    3.49 +};
    3.50 +
    3.51 +PairCoresApp::PairCoresApp(const WEnvironment& env):
    3.52 +    WApplication(env) {
    3.53 +    enableUpdates(true);
    3.54 +    std::string approot = config_value("approot", "");
    3.55 +    messageResourceBundle().use(approot + "wc-locales/wtclasses");
    3.56 +    messageResourceBundle().use(approot + "locales/pair-cores-web");
    3.57 +    useStyleSheet("css/pair-cores.css");
    3.58 +    reset_contents();
    3.59 +}
    3.60 +
    3.61 +void PairCoresApp::reset_contents() {
    3.62 +    root()->clear();
    3.63 +    //
    3.64 +    new Wt::WTemplate(tr("pair.main.Header"), root());
    3.65 +    if (!environment().ajax()) {
    3.66 +        WPushButton* refresh = new WPushButton(tr("pair.main.Refresh"), root());
    3.67 +        refresh->clicked().connect(this, &PairCoresApp::do_nothing);
    3.68 +    }
    3.69 +    WPushButton* reset = new WPushButton(tr("pair.main.Reset"), root());
    3.70 +    reset->clicked().connect(this, &PairCoresApp::reset_contents);
    3.71 +    //
    3.72 +    TableTask* task = new TableTask(root());
    3.73 +    //
    3.74 +    TextFileInput* input_aln = new TextFileInput("-i");
    3.75 +    input_aln->text_area()->setColumns(60);
    3.76 +    input_aln->text_area()->setRows(12);
    3.77 +    task->add_input(input_aln, tr("pair.in.Alignment"));
    3.78 +    //
    3.79 +    WLineEdit* delta_edit = new WLineEdit("2.0");
    3.80 +    delta_edit->setValidator(new WDoubleValidator(0, 10));
    3.81 +    delta_edit->validator()->setMandatory(true);
    3.82 +    LineEditInput* delta = new LineEditInput(delta_edit, "-d");
    3.83 +    task->add_input(delta, tr("pair.in.Delta"));
    3.84 +    //
    3.85 +    WLineEdit* width_edit = new WLineEdit("3");
    3.86 +    width_edit->setValidator(new WIntValidator(3, 9999));
    3.87 +    width_edit->validator()->setMandatory(true);
    3.88 +    LineEditInput* width = new LineEditInput(width_edit, "-w");
    3.89 +    task->add_input(width, tr("pair.in.Width"));
    3.90 +    //
    3.91 +    BoolInput* blocks3d = new BoolInput(new WCheckBox(), "--blocks3d");
    3.92 +    task->add_input(blocks3d, tr("pair.in.Blocks3D"));
    3.93 +    //
    3.94 +    BoolInput* ioss = new BoolInput(new WCheckBox(), "-e");
    3.95 +    ioss->set_value_if_true("True");
    3.96 +    task->add_input(ioss, tr("pair.in.SS"));
    3.97 +    //
    3.98 +    WLineEdit* pair_timeout_edit = new WLineEdit("10");
    3.99 +    pair_timeout_edit->setValidator(new WIntValidator(-1, 30 * 24 * 3600));
   3.100 +    pair_timeout_edit->validator()->setMandatory(true);
   3.101 +    LineEditInput* pair_timeout = new LineEditInput(pair_timeout_edit,
   3.102 +            "--pair-timeout");
   3.103 +    task->add_input(pair_timeout, tr("pair.in.Pair_timeout"));
   3.104 +    //
   3.105 +    WLineEdit* blocks3d_timeout_edit = new WLineEdit("-1");
   3.106 +    blocks3d_timeout_edit->setValidator(new WIntValidator(-1, 30 * 24 * 3600));
   3.107 +    blocks3d_timeout_edit->validator()->setMandatory(true);
   3.108 +    LineEditInput* blocks3d_timeout = new LineEditInput(blocks3d_timeout_edit,
   3.109 +            "--blocks3d-timeout");
   3.110 +    task->add_input(blocks3d_timeout, tr("pair.in.Blocks3D_timeout"));
   3.111 +    //
   3.112 +    // outputs
   3.113 +    //
   3.114 +    boost::function<std::string(std::string)> name_gen2 = boost::bind(name_gen,
   3.115 +            input_aln, _1);
   3.116 +    //
   3.117 +    ViewFileOutput* homology = new ViewFileOutput("-y");
   3.118 +    homology->set_suggested_gen(boost::bind(name_gen2, "hom"));
   3.119 +    homology->set_selectable(false);
   3.120 +    task->add_output(homology, tr("pair.out.Homology"));
   3.121 +    //
   3.122 +    ViewFileOutput* pair_blocks = new ViewFileOutput("-b");
   3.123 +    pair_blocks->set_suggested_gen(boost::bind(name_gen2, "blocks"));
   3.124 +    task->add_output(pair_blocks, tr("pair.out.Pair_blocks"));
   3.125 +    //
   3.126 +    ViewFileOutput* pair_html = new ViewFileOutput("-H",
   3.127 +            &FileOutput::unique_name,
   3.128 +            "application/octet-stream",
   3.129 +            "text/html");
   3.130 +    pair_html->set_suggested_gen(boost::bind(name_gen2, "html"));
   3.131 +    task->add_output(pair_html, tr("pair.out.Pair_html"));
   3.132 +    //
   3.133 +    ViewFileOutput* pymol = new ViewFileOutput("-p");
   3.134 +    pymol->set_suggested_gen(boost::bind(name_gen2, "pml"));
   3.135 +    task->add_output(pymol, tr("pair.out.Pymol"));
   3.136 +    //
   3.137 +    ViewFileOutput* high_pymol = new ViewFileOutput("--high-blocks-pymol");
   3.138 +    high_pymol->set_suggested_gen(boost::bind(name_gen2, "pml"));
   3.139 +    task->add_output(high_pymol, tr("pair.out.High_pymol"));
   3.140 +    //
   3.141 +    ViewFileOutput* high_blocks = new ViewFileOutput("--high-blocks");
   3.142 +    high_blocks->set_suggested_gen(boost::bind(name_gen2, "blocks"));
   3.143 +    task->add_output(high_blocks, tr("pair.out.High_blocks"));
   3.144 +    //
   3.145 +    ViewFileOutput* high_html = new ViewFileOutput("--high-blocks-html",
   3.146 +            &FileOutput::unique_name,
   3.147 +            "application/octet-stream",
   3.148 +            "text/html");
   3.149 +    high_html->set_suggested_gen(boost::bind(name_gen2, "html"));
   3.150 +    task->add_output(high_html, tr("pair.out.High_html"));
   3.151 +    //
   3.152 +    PrintFileOutput* execution_log = new PrintFileOutput("&>");
   3.153 +    execution_log->set_suggested_gen(boost::bind(name_gen2, "log"));
   3.154 +    execution_log->set_selectable(false);
   3.155 +    task->add_output(execution_log, tr("pair.out.Log"));
   3.156 +    //
   3.157 +    task->set_runner(new ForkingRunner("pair-cores --no-read-local"));
   3.158 +    task->set_queue(&queue);
   3.159 +    new TaskCountup(task, root());
   3.160 +    //
   3.161 +    new WBreak(root());
   3.162 +    new Wt::WTemplate(tr("pair.main.Example"), root());
   3.163 +    new Wt::WTemplate(tr("pair.main.Example_fasta"), root());
   3.164 +    new Wt::WTemplate(tr("pair.main.Rfbr"), root());
   3.165 +}
   3.166 +
   3.167 +WApplication* createPairCoresApp(const WEnvironment& env) {
   3.168 +    return new PairCoresApp(env);
   3.169 +}
   3.170 +
   3.171 +int main(int argc, char** argv) {
   3.172 +    return WRun(argc, argv, &createPairCoresApp);
   3.173 +}
   3.174 +