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

parent 6efb4d31
Showing with 85 additions and 19 deletions
CMakeLists.txt
...@@ -109,6 +109,7 @@ if(NOT PDB_REDO_META) ...@@ -109,6 +109,7 @@ if(NOT PDB_REDO_META)
if(BUILD_WEBSERVER) if(BUILD_WEBSERVER)
find_package(zeep REQUIRED) find_package(zeep REQUIRED)
find_package(gxrio REQUIRED)
endif() endif()
endif() endif()
...@@ -145,7 +146,7 @@ if(BUILD_WEBSERVER) ...@@ -145,7 +146,7 @@ if(BUILD_WEBSERVER)
${PROJECT_SOURCE_DIR}/src/dssp-io.cpp ${PROJECT_SOURCE_DIR}/src/dssp-io.cpp
${PROJECT_SOURCE_DIR}/src/dssp-server.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 # yarn rules for javascripts
set(webpack_input set(webpack_input
......
docroot/index.html
<!DOCTYPE html SYSTEM "about:legacy-compat" [ <!DOCTYPE html SYSTEM "about:legacy-compat" [ <!ENTITY nbsp "&#160;">
<!ENTITY nbsp "&#160;">
]> ]>
<html xmlns="http://www.w3.org/1999/xhtml" xmlns:z2="http://www.hekkelman.com/libzeep/m2" lang="nl"> <html xmlns="http://www.w3.org/1999/xhtml" xmlns:z2="http://www.hekkelman.com/libzeep/m2" lang="nl">
...@@ -26,7 +25,24 @@ ...@@ -26,7 +25,24 @@
<article> <article>
<h2>Submit your structure</h2> <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> </article>
...@@ -35,4 +51,4 @@ ...@@ -35,4 +51,4 @@
<footer z2:replace="~{footer::content}"></footer> <footer z2:replace="~{footer::content}"></footer>
</body> </body>
</html> </html>
\ No newline at end of file
src/dssp-io.hpp
...@@ -31,3 +31,6 @@ ...@@ -31,3 +31,6 @@
void writeDSSP(const dssp& dssp, std::ostream& os); void writeDSSP(const dssp& dssp, std::ostream& os);
void annotateDSSP(cif::datablock &db, const dssp& dssp, bool writeOther, bool writeExperimental, 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 @@ ...@@ -28,15 +28,18 @@
#include "revision.hpp" #include "revision.hpp"
#include <cif++.hpp>
#include <gxrio.hpp>
#include <mcfp.hpp> #include <mcfp.hpp>
#include <zeep/http/daemon.hpp>
#include <zeep/http/html-controller.hpp> #include <zeep/http/html-controller.hpp>
#include <zeep/http/rest-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 class dssp_html_controller : public zeep::http::html_controller
{ {
public: public:
...@@ -48,7 +51,7 @@ class dssp_html_controller : public zeep::http::html_controller ...@@ -48,7 +51,7 @@ class dssp_html_controller : public zeep::http::html_controller
mount("", &dssp_html_controller::index); 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); get_template_processor().create_reply_from_template("index", scope, reply);
} }
...@@ -59,13 +62,55 @@ class dssp_html_controller : public zeep::http::html_controller ...@@ -59,13 +62,55 @@ class dssp_html_controller : public zeep::http::html_controller
class dssp_rest_controller : public zeep::http::rest_controller class dssp_rest_controller : public zeep::http::rest_controller
{ {
public: public:
dssp_rest_controller() dssp_rest_controller(const std::string &prefix)
: zeep::http::rest_controller("") : 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[]) int main(int argc, char *argv[])
...@@ -90,7 +135,7 @@ int main(int argc, char *argv[]) ...@@ -90,7 +135,7 @@ int main(int argc, char *argv[])
mcfp::make_option<std::string>("context", "", "Root context for web server"), mcfp::make_option<std::string>("context", "", "Root context for web server"),
mcfp::make_option("no-daemon,F", "Do not fork into background"), mcfp::make_option("no-daemon,F", "Do not fork into background"),
mcfp::make_option<std::string>("config", "Config file to use")); mcfp::make_option<std::string>("config", "Config file to use"));
std::error_code ec; std::error_code ec;
...@@ -124,7 +169,7 @@ int main(int argc, char *argv[]) ...@@ -124,7 +169,7 @@ int main(int argc, char *argv[])
std::cout << config << std::endl; std::cout << config << std::endl;
exit(0); exit(0);
} }
if (config.operands().empty()) if (config.operands().empty())
{ {
std::cerr << "Missing command, should be one of start, stop, status or reload" << std::endl; std::cerr << "Missing command, should be one of start, stop, status or reload" << std::endl;
...@@ -137,8 +182,8 @@ int main(int argc, char *argv[]) ...@@ -137,8 +182,8 @@ int main(int argc, char *argv[])
std::string address = config.get<std::string>("address"); std::string address = config.get<std::string>("address");
uint16_t port = config.get<uint16_t>("port"); 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(); auto s = new zeep::http::server();
#ifndef NDEBUG #ifndef NDEBUG
...@@ -146,10 +191,10 @@ int main(int argc, char *argv[]) ...@@ -146,10 +191,10 @@ int main(int argc, char *argv[])
#else #else
s->set_template_processor(new zeep::http::rsrc_based_html_template_processor()); s->set_template_processor(new zeep::http::rsrc_based_html_template_processor());
#endif #endif
s->add_controller(new dssp_rest_controller()); s->add_controller(new dssp_rest_controller(context));
s->add_controller(new dssp_html_controller(config.get("context"))); s->add_controller(new dssp_html_controller(context));
return s; return s; },
}, kProjectName ); kProjectName);
std::string command = config.operands().front(); std::string command = config.operands().front();
......
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