leonarski_f
ac58921445
tf_z, rf_z, mr_d_min, the placed model's R-factors, CC, map and anomalous sigmas, the rigid body's move, the refinement's R-factors and rmsds, and the headline d_min are set only where finite (llg_z and null_sigma already were). nlohmann writes NaN/inf as null, which the page's "!== undefined" checks let through to .toFixed(), and which the zod schema rejects for the required blob distance - a blob with no atom within 12 A has an infinite one. That distance is now optional (jfjoch_api.yaml; C++ model and frontend client regenerated), absent then. The model cards test for != null, so a null that arrives anyway does not take the page down. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit 62ff026aa507e5bda1daa5aa079f32fb5c21f16e)
324 lines
11 KiB
C++
324 lines
11 KiB
C++
// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#include <catch2/catch_all.hpp>
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#include <cmath>
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#include "../receiver/RugnuxLiveStatus.h"
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#include "../receiver/JFJochReceiverRugnux.h"
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#include "../broker/OpenAPIConvert.h"
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#include "../image_puller/TestImagePuller.h"
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using namespace std::chrono_literals;
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TEST_CASE("RugnuxLiveStatus_TimesFromFirstImage", "[RugnuxLive]") {
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// 11 images at 100 Hz, the first 3 s after START, reported out of order as several forward threads do
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const auto start = std::chrono::steady_clock::now() - 10s;
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const auto first = start + 3s;
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RugnuxLiveStatus status;
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status.Start(11, 0.11, start);
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for (int i: {1, 0, 2, 3, 4, 5, 6, 7, 8, 10, 9})
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status.ImageReceived(first + i * 10ms);
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auto s = status.Get();
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CHECK(s.expected_collection_s.value() == Catch::Approx(0.11));
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REQUIRE(s.images_received == 11);
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REQUIRE(s.start_to_first_image_s.value() == Catch::Approx(3.0));
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CHECK(!s.last_image_s);
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// "now" is 10 s after START, 7 s after the first image
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CHECK(s.elapsed_s == Catch::Approx(7.0).margin(0.5));
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REQUIRE(status.LastImage() == first + 100ms);
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s = status.Get();
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REQUIRE(s.last_image_s.value() == Catch::Approx(0.1));
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CHECK((s.images_received - 1) / s.last_image_s.value() == Catch::Approx(100.0));
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}
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TEST_CASE("RugnuxLiveStatus_BeforeFirstImage", "[RugnuxLive]") {
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RugnuxLiveStatus status;
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status.Start(10, std::nullopt, std::chrono::steady_clock::now() - 2s);
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status.Step("waiting");
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const auto s = status.Get();
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CHECK(!s.start_to_first_image_s);
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CHECK(!s.expected_collection_s);
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CHECK(s.elapsed_s == 0.0);
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REQUIRE(s.steps.size() == 1);
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CHECK(s.steps[0].started_s <= 0.0);
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CHECK(!status.LastImage());
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}
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TEST_CASE("RugnuxLiveStatus_Clear", "[RugnuxLive]") {
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RugnuxLiveStatus status;
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status.Start(10, 1.0, std::chrono::steady_clock::now() - 2s);
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status.ImageReceived(std::chrono::steady_clock::now() - 1s);
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status.Step("indexing");
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status.Probe("lattice found");
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status.Result("OK", "fine", {{"Space group", "P 1"}}, {"a warning"});
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status.Finish(RugnuxLiveState::Done);
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REQUIRE(status.LastImage());
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status.Clear();
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const auto s = status.Get();
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CHECK(s.state == RugnuxLiveState::Idle);
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CHECK(s.images_expected == 0);
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CHECK(s.images_received == 0);
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CHECK(s.steps.empty());
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CHECK(s.probe.empty());
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CHECK(s.verdict.empty());
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CHECK(s.summary.empty());
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CHECK(s.warnings.empty());
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CHECK(!s.start_to_first_image_s);
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CHECK(!s.last_image_s);
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CHECK(s.elapsed_s == 0.0);
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CHECK(!status.LastImage());
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}
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TEST_CASE("TestImagePuller_SetsReceiveTime", "[RugnuxLive]") {
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TestImagePuller puller;
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const auto before = std::chrono::steady_clock::now();
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puller.Put(ImagePullerOutput{});
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const auto given = before - 5s;
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puller.Put(ImagePullerOutput{.received = given});
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auto out = puller.PollImage();
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REQUIRE(out);
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CHECK(out->received >= before);
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out = puller.PollImage();
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REQUIRE(out);
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CHECK(out->received == given);
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}
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TEST_CASE("RugnuxLiveModel_MolecularReplacement", "[RugnuxLive]") {
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ProcessResult r;
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CHECK(!LiveModel(r));
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MolecularReplacementResult mr;
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mr.ok = true;
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mr.model_name = "model.cif";
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mr.predicted_model = true;
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mr.decision = "AGREES";
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mr.d_min_search = 2.5;
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MRCandidate c;
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c.space_group = *gemmi::find_spacegroup_by_name("P 1 21 1");
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c.copies = 2;
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c.tf_z = 12.5;
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c.rf_z = 6.0;
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c.null_sigma = 20.0;
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mr.candidates = {MRCandidate{}, c};
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mr.chosen = 1;
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r.model_prior = mr;
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ModelValidationResult v;
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v.ok = true;
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v.r_work = 0.38;
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v.r_free = 0.40;
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v.cc_model_overall = 0.71;
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v.mean_atom_density_sigma = 1.6;
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v.anomalous_sites = {{"SD MET A1", 5.5}};
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r.model_validation = v;
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r.model_placement = "MR";
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const auto m = LiveModel(r);
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REQUIRE(m);
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CHECK(m->placement == "MR");
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CHECK(m->predicted);
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CHECK(m->mr_space_group == "P 1 21 1");
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CHECK(m->copies.value() == 2);
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CHECK(m->tf_z.value() == Catch::Approx(12.5));
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CHECK(!m->llg_z);
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CHECK(m->fit_sigma.value() == Catch::Approx(20.0)); // MR's null: the rigid body's was not tested
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CHECK(m->r_free.value() == Catch::Approx(0.40));
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CHECK(m->cc_model.value() == Catch::Approx(0.71));
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CHECK(!m->rigid_body_shift_A);
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CHECK(m->anomalous_site == "SD MET A1");
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RugnuxLiveStatus status;
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status.Start(10, 1.0, std::chrono::steady_clock::now());
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status.Result("OK", "fine", {}, {}, true);
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status.Model(*m);
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nlohmann::json j = Convert(status.Get());
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CHECK(j["anomalous_signal"] == true);
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CHECK(j["model"]["placement"] == "MR");
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CHECK(j["model"]["copies"] == 2);
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CHECK(j["model"]["r_free"].get<double>() == Catch::Approx(0.40));
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CHECK(!j["model"].contains("llg_z"));
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CHECK(!j["model"].contains("rigid_body_angle_deg"));
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status.Clear();
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CHECK(!status.Get().model);
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CHECK(!status.Get().anomalous_signal);
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}
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TEST_CASE("RugnuxLiveStatus_Headline", "[RugnuxLive]") {
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RugnuxLiveStatus status;
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status.Start(10, 1.0, std::chrono::steady_clock::now());
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nlohmann::json j = Convert(status.Get());
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CHECK(!j.contains("space_group"));
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CHECK(!j.contains("d_min"));
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CHECK(!j.contains("isa"));
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status.Headline("P 1 21 1", 1.25, 24.2);
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j = Convert(status.Get());
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CHECK(j["space_group"] == "P 1 21 1");
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CHECK(j["d_min"].get<double>() == Catch::Approx(1.25));
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CHECK(j["isa"].get<double>() == Catch::Approx(24.2));
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// ISa undetermined
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status.Headline("P 1 21 1", 1.25, std::nullopt);
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j = Convert(status.Get());
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CHECK(!j.contains("isa"));
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status.Clear();
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CHECK(status.Get().space_group.empty());
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CHECK(!status.Get().d_min);
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}
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TEST_CASE("RugnuxLiveModel_Refinement", "[RugnuxLive]") {
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ProcessResult r;
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ModelValidationResult v;
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v.ok = true;
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v.r_work = 0.38;
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v.r_free = 0.40;
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r.model_validation = v;
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r.model_placement = "RIGID_BODY";
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CHECK(!LiveModel(r)->refinement);
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RefinementResult rf;
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rf.ok = true;
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rf.on_gpu = true;
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rf.seconds = 3.5;
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rf.r_work_placement = 0.30;
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rf.r_free_placement = 0.33;
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rf.restrained = true;
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rf.r_work = 0.19;
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rf.r_free = 0.23;
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rf.geometry.rmsd_bonds = 0.011;
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rf.geometry.rmsd_angles = 1.6;
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DensityBlob b;
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b.kind = DensityBlob::Kind::Ligand;
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b.centroid = gemmi::Position(1.0, 2.0, 3.0);
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b.peak_sigma = 7.5;
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b.volume = 40.0;
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b.nearest_atom = "OG1 THR A42";
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b.nearest_atom_distance = 3.1;
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rf.blobs.assign(RugnuxLiveRefinement::MAX_BLOBS + 5, b);
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r.refinement = rf;
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const auto m = LiveModel(r);
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REQUIRE(m->refinement);
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const RugnuxLiveRefinement &lr = *m->refinement;
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CHECK(lr.performed);
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CHECK(lr.r_free.value() == Catch::Approx(0.23));
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CHECK(lr.rmsd_bonds_A.value() == Catch::Approx(0.011));
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CHECK(lr.blob_count == static_cast<int64_t>(RugnuxLiveRefinement::MAX_BLOBS + 5));
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CHECK(lr.blobs.size() == RugnuxLiveRefinement::MAX_BLOBS);
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// the placed model's R-factors are untouched
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CHECK(m->r_free.value() == Catch::Approx(0.40));
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RugnuxLiveStatus status;
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status.Start(10, 1.0, std::chrono::steady_clock::now());
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status.Model(*m);
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nlohmann::json j = Convert(status.Get());
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CHECK(j["refined_model"] == false);
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CHECK(j["model"]["r_free"].get<double>() == Catch::Approx(0.40));
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CHECK(j["model"]["refinement"]["r_free"].get<double>() == Catch::Approx(0.23));
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CHECK(j["model"]["refinement"]["on_gpu"] == true);
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CHECK(j["model"]["refinement"]["blob_count"] == RugnuxLiveRefinement::MAX_BLOBS + 5);
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CHECK(j["model"]["refinement"]["blobs"].size() == RugnuxLiveRefinement::MAX_BLOBS);
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CHECK(j["model"]["refinement"]["blobs"][0]["kind"] == "LIGAND");
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CHECK(j["model"]["refinement"]["blobs"][0]["z"].get<double>() == Catch::Approx(3.0));
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// Only the placement stage ran: its R-factors, no geometry
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rf.restrained = false;
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r.refinement = rf;
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const auto p = LiveModel(r);
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CHECK(p->refinement->r_free.value() == Catch::Approx(0.33));
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CHECK(!p->refinement->rmsd_bonds_A);
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// Failed
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RefinementResult failed;
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failed.failure_reason = "no dictionary";
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r.refinement = failed;
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status.Model(*LiveModel(r));
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j = Convert(status.Get());
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CHECK(j["model"]["refinement"]["performed"] == false);
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CHECK(j["model"]["refinement"]["reason"] == "no dictionary");
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CHECK(!j["model"]["refinement"].contains("r_free"));
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}
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TEST_CASE("RugnuxLiveModel_RefinementCancelled", "[RugnuxLive]") {
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ProcessResult r;
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ModelValidationResult v;
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v.ok = true;
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r.model_validation = v;
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r.model_placement = "MR";
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RefinementResult rf;
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rf.ok = true;
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rf.cancelled = true;
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r.refinement = rf;
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const auto m = LiveModel(r);
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CHECK(m->refinement->cancelled);
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RugnuxLiveStatus status;
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status.Start(10, 1.0, std::chrono::steady_clock::now());
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status.Model(*m);
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const nlohmann::json j = Convert(status.Get());
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CHECK(j["model"]["refinement"]["cancelled"] == true);
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}
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// A score that is not a number is left out, not written as null: the page reads every present one as a number.
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TEST_CASE("RugnuxLiveModel_NonFiniteScores", "[RugnuxLive]") {
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ProcessResult r;
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MolecularReplacementResult mr;
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mr.ok = true;
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mr.d_min_search = NAN;
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MRCandidate c;
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c.space_group = *gemmi::find_spacegroup_by_name("P 1 21 1");
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c.tf_z = NAN;
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c.rf_z = INFINITY;
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mr.candidates = {c};
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mr.chosen = 0;
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r.model_prior = mr;
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ModelValidationResult v;
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v.ok = true;
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v.r_work = NAN;
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v.r_free = NAN;
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v.mean_atom_density_sigma = NAN;
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r.model_validation = v;
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r.model_placement = "MR";
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RefinementResult rf;
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rf.ok = true;
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rf.restrained = true;
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rf.r_work = NAN;
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rf.r_free = 0.25;
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rf.geometry.rmsd_bonds = NAN;
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DensityBlob b;
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b.nearest_atom_distance = INFINITY;
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rf.blobs = {b};
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r.refinement = rf;
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const auto m = LiveModel(r);
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REQUIRE(m);
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CHECK(!m->tf_z);
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CHECK(!m->rf_z);
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CHECK(!m->mr_d_min);
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CHECK(!m->r_free);
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CHECK(!m->map_atom_sigma);
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CHECK(!m->refinement->r_work);
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CHECK(m->refinement->r_free.value() == Catch::Approx(0.25));
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CHECK(!m->refinement->rmsd_bonds_A);
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CHECK(!m->refinement->blobs.at(0).nearest_atom_distance_A);
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RugnuxLiveStatus status;
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status.Start(10, 1.0, std::chrono::steady_clock::now());
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status.Model(*m);
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const nlohmann::json j = Convert(status.Get());
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CHECK(!j["model"].contains("tf_z"));
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CHECK(!j["model"].contains("rf_z"));
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CHECK(!j["model"].contains("r_free"));
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CHECK(!j["model"]["refinement"].contains("r_work"));
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CHECK(!j["model"]["refinement"]["blobs"][0].contains("nearest_atom_distance_A"));
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CHECK(j.dump().find("null") == std::string::npos);
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}
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