The rc178 branch continued after #88 was squash-merged; this is its content fromb9ada7914(the tree #88 squashed) to094eee31a, as one change on main. The individual commits stay on the rc178 branch: - still battery: --cold evicts each set's input from the page cache; Alvra pixel masks; manifest fixes - AGIPD: converter to one rigid panel per module, int16 photons, mask folded in; still battery reads the converted sets - DetectorModules: panel look-up by id, plane -> panel, plane bounds and a per-pixel walk; mask size checked - tests: [PanelLayout] equivalence harness, stacked vs assembled panel layout - Dense per-pixel maps through the panel table (panel layout stage 1) - Panel id on spots and the panel table in the start message - Viewer and preview show a panel detector as it lies on the detector plane - Panel layout stage 3: per-panel spot finding (CPU+GPU, CCL) and raster algorithms on the plane raster - Panel layout stage 2: prediction and Bragg integration through the panel table - XTC reader: frames handed up as stored, streams indexed in parallel - XFEL reader: integer frames stay integer, one gain, placement by panel - EXTERNAL_TEST_DATA_STILLS.md: images used vs the entry for every set; drop "Not in the battery" - still battery: EuXFEL sets read the depositors' Cheetah CXI files directly; AGIPD converter removed - float32_to_int16.py: a non-finite pixel becomes -32768, the int16 error marker, not a zero count - CrystFEL geometry: read the pixel masks and bad regions instead of ignoring them - Panel layout stage 5: the XFEL reader hands up the stored frame and its panel table - Panel table persisted in NXmx; modulation grid and pre-scan memo key on the plane - still battery: Alvra sets take their pixel mask from the CrystFEL geometry, not --mask-good - still battery: take the deposited model as mmCIF where the RCSB has no PDB-format file - still battery: dimple gets PDB-format coordinates converted from an mmCIF-only deposition - stills fixed cost: geometry refinement and pre-scan do the same work in less wall time - stills geometry sample and trial spot finding run as many workers as the image pass - Stills integration: background ring reach measured on empty apertures, radial curvature from the whole frame - StillsPartialityRefine: the partiality width is the run's, measured on the crystals, not the prediction window's - MergeOnTheFly: capture term and multiplicative outlier band for the stills merge (both opt-in) - Stills given a cell: the written cell is the mean over the frames that are merged - Stills: the radial curvature correction decided per run on the same empty apertures - StillsPartialityRefine: measure the run width only on shells with signal - Stills pre-scan: report the paired z of the radial-correction comparison - module placement: the five concurrent fits each keep every thread - still battery: score R-free against the deposited data through the same dimple protocol - still battery: the R-free target is the lower of the deposition's dimple and published values - Stills: background clip follows the radial curve; signal disk from the lattice spacing - Stills keep an overloaded observation as a lower bound instead of dropping it - Stills: drop the lattice-spacing signal disk; the correction decision back on the plain clip - battery: R-free against the deposition without refinement only, one protocol for rotation and stills - still battery: EuXFEL sets run on a 2,000-image subset for now - stills geometry refinement: fit the detector distance and the cell together - stills geometry refinement: a distance given with --detector-distance is held in the joint fit - Metal integration engine: back to its panel-s5 kernels; Mac stills keep the old clip, no saturation count - Metal integration test: the CPU comparison runs on a rotation experiment - Stills: kept overloads go back to the drop where they are not concentrated at low resolution - stills distance search: an absolute 30-3000 mm scan, a sample found without d-limits, the fit iterated - battery results: XFEL still battery 20261022-1358 on rc1780cf62452c- 12 sets, cold, R_free unrefined - battery results: still summary gains the resolution of our merge and of the deposition - Pre-scan masks a pixel at the saturation limit on most frames, as one holding the error value - Stills keep an overload as a lower bound only where it has pixels at the limit; run-level gate removed - XFEL reader: a per-frame mask is read the way the frames are, its chunk inflated outside the HDF5 lock - stills distance search: every centre scanned with a wider acceptance, a larger sample where nothing indexes - rugnux usage: --beam-center-check describes the absolute 30-3000 mm stills distance scan, not the old 60-160 % grid - stills: detector tilt refined in the geometry pre-pass, kept where held-out frames agree - CLAUDE.md: the changelog is written once, just before the merge into main - condensed one-liners of what users get - broker: serve the placed model and its maps of the last rugnux live run (/rugnux/model.cif, /rugnux/map.ccp4) - frontend: Mol* viewer of the placed model and its density on the Rugnux live page - writer: _model.cif from rugnux live keeps the input model's metadata, as the served model.cif does - rugnux live maps: one unit cell centred on the model; the viewer opens on all of it - Anomalous difference map: ANOM/PHANOM in _maps.mtz, /rugnux/map.ccp4?type=anom, a magenta mesh in the viewer - Mol* viewer: open with the maps drawn within 10 A of the centre of view - Mol* viewer: aaredb's structure-viewer setup, on a black stage - rugnux: the gain of a stills file that states none is read off its single-photon peak where the background resolves photons - Mol* viewer: in line with AareDB's StructureView at its current head (8ece2c2) - ACKNOWLEDGEMENT: the web frontend's Mol* viewer follows AareDB's setup (G. Gotthard, PSI) - stills tilt decision: the modules stay where the run placed them - still battery: no distance pins and no per-set tuning flags; gain from the data except where a file's baseline hides it - battery results: rc178 6f6f69 - full still battery and full rotation battery with REFMAC - Bragg integration: a CCD rotation sweep's sigmas at the measured gain, intensities in photons - BackgroundGain: the gain of a frame that resolves photons is the spacing of its photon peaks, so a baseline left in the frame no longer hides it - ShadowFinder: measure the background's azimuthal modulation instead of predicting it from the polarization - BackgroundGain: one gain estimate for rotation and stills; the still battery no longer gives EuXFEL 152 its gain - ShadowFinder: measure the modulation robustly under a wide one-sided shadow - ShadowFinderTest: a one-sided shadow is not fitted as part of the background's modulation - ShadowFinder: back to the predicted polarization factor, in the plane the background shows - MXAnalysisAfterFPGA: the Bragg engine's edge mask in the image's layout, so raw / untransformed FPGA runs start again - battery results: still battery on rc178 e54f55 replaces the earlier rc178 still tables - XFELReader: per-frame mask and photon conversion without a library call or a branch per pixel - stills geometry trial: the hypotheses a search asks are indexed side by side - stills tilt decision: the fits start beside the pre-scan and the geometry trial - XFELReader: a deflated frame is inflated and converted a piece at a time, while it is in the cache - XFELReader: a byte-shuffled frame is unshuffled a piece at a time, a whole pixel per step - GeometryRefiner: residuals carry only the blocks a fit moves; beam and distance one block - GeometryRefiner: a spot's residual differentiates its observed and predicted halves apart - docs: EXTERNAL_TEST_DATA lists every open-arm battery set, with corrected values and counts - battery: doc_check.py cross-checks the manifests against the dataset pages - stills module placement: the placement fit gets half the threads, each held-out fit an eighth - still battery: the EuXFEL sets run on all their frames, as the published still runs did - battery results: still battery on rc178 a0ce6c, cold on a quiet machine, replaces the earlier rc178 table - macOS build: explicit size_t in the XFEL reader's row bounds; parentheses in the CPU preprocessor's select Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
162 lines
8.2 KiB
C++
162 lines
8.2 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 <httplib.h>
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#include <nlohmann/json.hpp>
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#include <chrono>
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#include <thread>
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#include "../broker/JFJochBrokerHttp.h"
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// The tokens given to /start guard the endpoints that expose the dataset, and nothing else, for as
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// long as that dataset is the current one. Runs the real HTTP layer against a broker with no
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// receiver: /start is then accepted and finishes at once with nothing to acquire.
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TEST_CASE("JFJochBrokerHttp_BearerTokens", "[broker]") {
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DiffractionExperiment experiment;
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SpotFindingSettings spot_finding;
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JFJochBrokerHttp broker(experiment, spot_finding);
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broker.AddDetectorSetup(DetJF4M());
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httplib::Server server;
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broker.attach(server);
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const int port = server.bind_to_any_port("127.0.0.1");
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REQUIRE(port > 0);
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// Stopped and joined however the test ends, so a failed REQUIRE does not abort on a joinable thread.
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struct ServerThread {
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httplib::Server &server;
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std::thread thread;
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explicit ServerThread(httplib::Server &s) : server(s), thread([&s] { s.listen_after_bind(); }) {}
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~ServerThread() { server.stop(); thread.join(); }
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} server_thread(server);
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server.wait_until_ready();
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httplib::Client client("127.0.0.1", port);
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const httplib::Headers good{{"Authorization", "Bearer secret-1"}};
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const httplib::Headers other{{"Authorization", "Bearer secret-2"}};
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const httplib::Headers wrong{{"Authorization", "Bearer nope"}};
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auto start = [&](const nlohmann::json &extra) {
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nlohmann::json body = {{"beam_x_pxl", 1000}, {"beam_y_pxl", 1000},
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{"detector_distance_mm", 100}, {"incident_energy_keV", 12.4},
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{"images_per_trigger", 1}, {"ntrigger", 1},
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{"file_prefix", "protected_run"}};
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body.update(extra);
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auto res = client.Post("/start", body.dump(), "application/json");
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REQUIRE(res);
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REQUIRE(res->status == 200);
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// With no receiver the measurement thread idles for 30 s before the run ends; wait it out.
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for (int i = 0; i < 120; i++) {
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auto status = client.Get("/status");
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REQUIRE(status);
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if (nlohmann::json::parse(status->body).at("state") == "Idle")
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return;
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std::this_thread::sleep_for(std::chrono::milliseconds(500));
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}
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FAIL("broker did not return to Idle after the start");
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};
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REQUIRE(client.Post("/initialize")->status == 200);
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// Nothing started yet: open, whatever the header says.
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REQUIRE(client.Get("/statistics/data_collection")->status == 200);
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REQUIRE(client.Get("/statistics/data_collection", wrong)->status == 200);
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REQUIRE(client.Get("/statistics")->status == 200);
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start({{"tokens", {"secret-1", "secret-2"}}});
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SECTION("protected endpoints refuse without a token and say nothing about the dataset") {
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for (const char *path: {"/statistics/data_collection", "/result/scan", "/image_buffer/start.cbor",
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"/image_buffer/image.cbor?id=0", "/image_buffer/image.tiff?id=0",
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"/image_buffer/image.jpeg?id=0", "/preview/plot?type=bkg_estimate",
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"/preview/plot.bin?type=bkg_estimate", "/live/events",
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"/rugnux/status", "/rugnux/model.cif", "/rugnux/map.ccp4?type=2fofc"}) {
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INFO(path);
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auto res = client.Get(path);
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REQUIRE(res);
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REQUIRE(res->status == 401);
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REQUIRE(res->get_header_value("WWW-Authenticate") == "Bearer");
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REQUIRE(res->body.find("protected_run") == std::string::npos);
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REQUIRE(client.Get(path, wrong)->status == 401);
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}
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// Live rugnux settings and its model prepare the next collection: open like the rest of the configuration.
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REQUIRE(client.Get("/config/rugnux")->status == 200);
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REQUIRE(client.Put("/config/rugnux", R"({"enable":false})", "application/json")->status == 200);
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REQUIRE(client.Put("/config/rugnux/model", "", "application/octet-stream")->status == 400);
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REQUIRE(client.Delete("/config/rugnux/model")->status == 200);
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}
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SECTION("either token opens them") {
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auto res = client.Get("/statistics/data_collection", good);
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REQUIRE(res->status == 200);
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REQUIRE(res->body.find("protected_run") != std::string::npos);
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REQUIRE(client.Get("/statistics/data_collection", other)->status == 200);
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REQUIRE(client.Get("/preview/plot?type=bkg_estimate", good)->status == 200);
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REQUIRE(client.Get("/rugnux/status", good)->status == 200);
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// No live run placed a model: nothing to serve, but the token is accepted.
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REQUIRE(client.Get("/rugnux/model.cif", good)->status == 404);
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REQUIRE(client.Get("/rugnux/map.ccp4", good)->status == 404);
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REQUIRE(client.Get("/rugnux/map.ccp4?type=fofc", good)->status == 404);
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REQUIRE(client.Get("/rugnux/map.ccp4?type=anom", good)->status == 404);
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REQUIRE(client.Get("/rugnux/map.ccp4?type=anomalous", good)->status == 400);
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}
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SECTION("the aggregate statistics drop the measurement block instead of refusing") {
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auto res = client.Get("/statistics");
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REQUIRE(res->status == 200);
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REQUIRE_FALSE(nlohmann::json::parse(res->body).contains("measurement"));
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REQUIRE(res->body.find("protected_run") == std::string::npos);
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auto with_token = client.Get("/statistics", good);
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REQUIRE(with_token->status == 200);
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REQUIRE(nlohmann::json::parse(with_token->body).contains("measurement"));
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}
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SECTION("with no receiver there is no collection to follow") {
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REQUIRE(client.Get("/live/events", good)->status == 409);
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}
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SECTION("initialize drops the tokens and everything they protected") {
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REQUIRE(client.Post("/initialize")->status == 200);
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for (int i = 0; i < 120 && nlohmann::json::parse(client.Get("/status")->body).at("state") != "Idle"; i++)
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std::this_thread::sleep_for(std::chrono::milliseconds(500));
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auto res = client.Get("/statistics/data_collection");
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REQUIRE(res->status == 200);
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REQUIRE(res->body.find("protected_run") == std::string::npos);
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auto stats = client.Get("/statistics");
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REQUIRE(stats->status == 200);
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REQUIRE(stats->body.find("protected_run") == std::string::npos);
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REQUIRE(client.Get("/rugnux/status")->status == 200);
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REQUIRE(client.Get("/result/scan")->status != 401);
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}
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SECTION("the control plane and the broker status stay open") {
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REQUIRE(client.Get("/status")->status == 200);
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REQUIRE(client.Get("/image_buffer/status")->status == 200);
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REQUIRE(client.Get("/config/detector")->status == 200);
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}
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SECTION("a refused start keeps the current tokens, an accepted one replaces them") {
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// Not idle: /start is refused, the dataset stays protected by its own tokens.
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REQUIRE(client.Post("/deactivate")->status == 200);
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nlohmann::json body = {{"beam_x_pxl", 1000}, {"beam_y_pxl", 1000},
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{"detector_distance_mm", 100}, {"incident_energy_keV", 12.4}};
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REQUIRE(client.Post("/start", body.dump(), "application/json")->status == 500);
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REQUIRE(client.Get("/statistics/data_collection")->status == 401);
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REQUIRE(client.Get("/statistics/data_collection", good)->status == 200);
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// Back from Inactive; the next start without tokens leaves the dataset open.
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REQUIRE(client.Post("/initialize")->status == 200);
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start(nlohmann::json::object());
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REQUIRE(client.Get("/statistics/data_collection")->status == 200);
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REQUIRE(client.Get("/statistics/data_collection", wrong)->status == 200);
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// And with new tokens, the old ones no longer open it.
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start({{"tokens", {"secret-3"}}});
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const httplib::Headers newer{{"Authorization", "Bearer secret-3"}};
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REQUIRE(client.Get("/statistics/data_collection", good)->status == 401);
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REQUIRE(client.Get("/statistics/data_collection", newer)->status == 200);
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}
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}
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