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dssp
Commit 9f3a5528 by Maarten L. Hekkelman
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Working web server

parent 6efb4d31
Showing with 79 additions and 14 deletions
CMakeLists.txt
......@@ -109,6 +109,7 @@ if(NOT PDB_REDO_META)
if(BUILD_WEBSERVER)
find_package(zeep REQUIRED)
find_package(gxrio REQUIRED)
endif()
endif()
......@@ -145,7 +146,7 @@ if(BUILD_WEBSERVER)
${PROJECT_SOURCE_DIR}/src/dssp-io.cpp
${PROJECT_SOURCE_DIR}/src/dssp-server.cpp)
target_link_libraries(dsspd PRIVATE dssp cifpp::cifpp libmcfp::libmcfp dssp::dssp zeep::zeep)
target_link_libraries(dsspd PRIVATE dssp cifpp::cifpp libmcfp::libmcfp dssp::dssp zeep::zeep gxrio::gxrio)
# yarn rules for javascripts
set(webpack_input
......
docroot/index.html
<!DOCTYPE html SYSTEM "about:legacy-compat" [
<!ENTITY nbsp "&#160;">
<!DOCTYPE html SYSTEM "about:legacy-compat" [ <!ENTITY nbsp "&#160;">
]>
<html xmlns="http://www.w3.org/1999/xhtml" xmlns:z2="http://www.hekkelman.com/libzeep/m2" lang="nl">
......@@ -26,7 +25,24 @@
<article>
<h2>Submit your structure</h2>
<form z2:fragment="submit-form" name="job-form" method="post" enctype="multipart/form-data"
z2:action="@{/do}">
<div class="input-group mb-3">
<label class="input-group-text" for="input-group-pdb-file">Coordinates</label>
<input type="file" class="form-control" id="input-group-pdb-file" name="data" required="required" />
</div>
<div class="input-group mb-3">
<label class="input-group-text" for="format-select">Format</label>
<select class="form-select" id="format-select" name="format">
<option value="mmcif">Annotated mmCIF</option>
<option value="dssp">Historic DSSP format, may fail on larger structures</option>
</select>
</div>
<button type="submit" class="btn btn-sm btn-primary mt-3">Submit</button>
</form>
</article>
......
src/dssp-io.hpp
......@@ -31,3 +31,6 @@
void writeDSSP(const dssp& dssp, std::ostream& os);
void annotateDSSP(cif::datablock &db, const dssp& dssp, bool writeOther, bool writeExperimental, std::ostream& os);
void writeDSSP(std::istream &is, std::ostream& os);
void annotateDSSP(cif::datablock &db, const dssp& dssp, bool writeOther, bool writeExperimental, std::ostream& os);
src/dssp-server.cpp
......@@ -28,15 +28,18 @@
#include "revision.hpp"
#include <cif++.hpp>
#include <gxrio.hpp>
#include <mcfp.hpp>
#include <zeep/http/daemon.hpp>
#include <zeep/http/html-controller.hpp>
#include <zeep/http/rest-controller.hpp>
#include <zeep/http/daemon.hpp>
#include <zeep/streambuf.hpp>
// --------------------------------------------------------------------
class dssp_html_controller : public zeep::http::html_controller
{
public:
......@@ -48,7 +51,7 @@ class dssp_html_controller : public zeep::http::html_controller
mount("", &dssp_html_controller::index);
}
void index(const zeep::http::request& request, const zeep::http::scope& scope, zeep::http::reply& reply)
void index(const zeep::http::request &request, const zeep::http::scope &scope, zeep::http::reply &reply)
{
get_template_processor().create_reply_from_template("index", scope, reply);
}
......@@ -59,13 +62,55 @@ class dssp_html_controller : public zeep::http::html_controller
class dssp_rest_controller : public zeep::http::rest_controller
{
public:
dssp_rest_controller()
: zeep::http::rest_controller("")
dssp_rest_controller(const std::string &prefix)
: zeep::http::rest_controller(prefix)
{
// map_post_request("dssp", &dssp_rest_controller::calculate, "data");
map_post_request("do", &dssp_rest_controller::work, "data", "format");
}
zeep::http::reply work(const zeep::http::file_param &coordinates, std::optional<std::string> format);
};
zeep::http::reply dssp_rest_controller::work(const zeep::http::file_param &coordinates, std::optional<std::string> format)
{
zeep::char_streambuf sb(coordinates.data, coordinates.length);
gxrio::istream in(&sb);
cif::file f = cif::pdb::read(in);
if (f.empty())
throw std::runtime_error("Invalid input file, is it empty?");
// --------------------------------------------------------------------
short pp_stretch = 3; //minPPStretch.value_or(3);
std::string fmt = format.value_or("mmcif");
dssp dssp(f.front(), 1, pp_stretch, true);
std::ostringstream os;
if (fmt == "dssp")
writeDSSP(dssp, os);
else
annotateDSSP(f.front(), dssp, true, true, os);
// --------------------------------------------------------------------
std::string name = f.front().name();
if (fmt == "dssp")
name += ".dssp";
else
name += ".cif";
zeep::http::reply rep{ zeep::http::ok };
rep.set_content(os.str(), "text/plain");
rep.set_header("content-disposition", "attachement; filename = \"" + name + '"');
return rep;
}
// --------------------------------------------------------------------
int main(int argc, char *argv[])
......@@ -137,7 +182,7 @@ int main(int argc, char *argv[])
std::string address = config.get<std::string>("address");
uint16_t port = config.get<uint16_t>("port");
zh::daemon server([&]()
zeep::http::daemon server([&, context = config.get("context")]()
{
auto s = new zeep::http::server();
......@@ -146,10 +191,10 @@ int main(int argc, char *argv[])
#else
s->set_template_processor(new zeep::http::rsrc_based_html_template_processor());
#endif
s->add_controller(new dssp_rest_controller());
s->add_controller(new dssp_html_controller(config.get("context")));
return s;
}, kProjectName );
s->add_controller(new dssp_rest_controller(context));
s->add_controller(new dssp_html_controller(context));
return s; },
kProjectName);
std::string command = config.operands().front();
......
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