bartels-rausch
2ec52b7ee7
beamtime/nappFileList.m - Fix h5 LensMode: translate numeric codes to descriptive text (e.g. 1 -> T_HiPPHAXPES) to match what .ibw files already store, applied across all three h5read fallback branches, not just the oldest-format one beamtime/nappGenerateSpectra.m - Bug fixes beamtime/nappPlot.m - Bug fixes import/importData.m (new) - Ground script for one beamtime: import (nappFileList, nappGenerateSpectra), sample/spot and photon-energy assignment per row range, campaign metadata (CustomProperties) and column descriptions/units set inline, tidy-up, and export to .csv/.mat/.h5 (via nappExportH5). Leaves FileList in the workspace for PublishReport.m and callOpenbisSync.m to run against afterward. import/nappExportH5.m (new) - Export FileList + campaign metadata + raw source files to a self-contained HDF5 archive - Low-level HDF5 API (H5F/H5G/H5D/H5A/H5T/H5S/H5P) to fix H5FD_truncate/"too many open files" errors from the top-level h5create/h5write functions each reopening the file internally - Explicit rowIndex attribute per row group, since HDF5 group listing order isn't guaranteed to match table row order openBIS/ (new) - nappSyncToOpenbis.py, callOpenbisSync.m, testpybis.m, README.md - openBIS sync pipeline: create-or-update per row matched by $name, correct lowercase property codes, timestamp formatting, parent linking, raw file upload, plot/photo/video thumbnail embedding, config/engine split for maintainability -- see README.md for full details
46 lines
2.2 KiB
Matlab
46 lines
2.2 KiB
Matlab
%% 1. Point at the venv (always needed fresh after restart)
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pyenv('Version', '/Users/bartels-rausch/matlab-pybis-venv/bin/python3')
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%% 2. Import (first time this session -- guaranteed to read from disk)
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py.sys.path().append('/Users/bartels-rausch');
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py.importlib.import_module('nappSyncToOpenbis');
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%% 3. Your connection details
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openbisUrl = "https://openbis-psi.labnotebook.ch";
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spaceCode = "5505_BEAMTIMES";
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collectionId = [];
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objectType = "LAC_EXPERIMENTAL_STEP_BEAMTIME";
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parentIdentifier = "/5505_BEAMTIMES/ENTRY783";
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verifyCertificates = false;
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username = "bartels-rausch_admin";
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password = input('openBIS password: ', 's');
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clc
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%% 4. Rebuild the test data (also fresh, in case anything upstream changed)
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testRows = FileList(11:12,:);
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metaCols = {'name','folder','creationDate','lastModifiedDatenum','sample', ...
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'sampleTemp_dC','cellPressure_mbar','iceTemp_dC','comment','regionName', ...
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'scientaLensMode','scientaAcquisitionMode','scientaDwellTime_ms', ...
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'scientaPassEnergy_eV','scientaSequenceIterations','scientaRegionIterations', ...
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'scientaEkinStep_eV','xRayEkin_eV','xRayEkinRange_eV','scientaEkinRange_eV', ...
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'smplX_mm','smplY_mm','smplZ_mm'};
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metaCols = intersect(metaCols, testRows.Properties.VariableNames, 'stable');
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testTable = testRows(:, metaCols);
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testTable.resultImages = repmat({{}}, height(testTable), 1);
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rowsJsonTest = jsonencode(table2struct(testTable));
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campaignProps = struct( ...
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'campaignLocation', FileList.Properties.CustomProperties.campaignLocation, ...
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'team', FileList.Properties.CustomProperties.team, ...
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'projectName', FileList.Properties.CustomProperties.projectName);
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campaignPropsJson = jsonencode(campaignProps);
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%% 5. The actual test
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resultJson = py.nappSyncToOpenbis.sync_rows(rowsJsonTest, openbisUrl, spaceCode, ...
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pyargs('collection', collectionId, 'object_type', objectType, ...
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'username', username, 'password', password, ...
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'campaign_props_json', campaignPropsJson, 'upload_files', false, ...
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'parent_identifier', parentIdentifier, ...
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'verify_certificates', verifyCertificates));
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results = struct2table(jsondecode(char(resultJson)));
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disp(results.message{1}) |