scitex 2.5.0__py3-none-any.whl → 2.7.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- scitex/__init__.py +19 -8
- scitex/__main__.py +2 -1
- scitex/__version__.py +1 -1
- scitex/_optional_deps.py +13 -20
- scitex/ai/__init__.py +5 -0
- scitex/ai/_gen_ai/_Anthropic.py +3 -1
- scitex/ai/_gen_ai/_BaseGenAI.py +3 -2
- scitex/ai/_gen_ai/_DeepSeek.py +1 -1
- scitex/ai/_gen_ai/_Google.py +3 -2
- scitex/ai/_gen_ai/_Llama.py +4 -2
- scitex/ai/_gen_ai/_OpenAI.py +3 -1
- scitex/ai/_gen_ai/_PARAMS.py +1 -0
- scitex/ai/_gen_ai/_Perplexity.py +3 -1
- scitex/ai/_gen_ai/__init__.py +1 -0
- scitex/ai/_gen_ai/_format_output_func.py +3 -1
- scitex/ai/classification/CrossValidationExperiment.py +8 -14
- scitex/ai/classification/examples/timeseries_cv_demo.py +128 -112
- scitex/ai/classification/reporters/_BaseClassificationReporter.py +2 -0
- scitex/ai/classification/reporters/_ClassificationReporter.py +30 -45
- scitex/ai/classification/reporters/_MultiClassificationReporter.py +8 -11
- scitex/ai/classification/reporters/_SingleClassificationReporter.py +126 -182
- scitex/ai/classification/reporters/__init__.py +1 -1
- scitex/ai/classification/reporters/reporter_utils/_Plotter.py +213 -119
- scitex/ai/classification/reporters/reporter_utils/__init__.py +28 -36
- scitex/ai/classification/reporters/reporter_utils/aggregation.py +125 -143
- scitex/ai/classification/reporters/reporter_utils/data_models.py +128 -120
- scitex/ai/classification/reporters/reporter_utils/reporting.py +507 -340
- scitex/ai/classification/reporters/reporter_utils/storage.py +4 -1
- scitex/ai/classification/reporters/reporter_utils/validation.py +141 -154
- scitex/ai/classification/timeseries/_TimeSeriesBlockingSplit.py +204 -129
- scitex/ai/classification/timeseries/_TimeSeriesCalendarSplit.py +215 -171
- scitex/ai/classification/timeseries/_TimeSeriesMetadata.py +17 -17
- scitex/ai/classification/timeseries/_TimeSeriesSlidingWindowSplit.py +67 -143
- scitex/ai/classification/timeseries/_TimeSeriesSlidingWindowSplit_v01-not-using-n_splits.py +67 -143
- scitex/ai/classification/timeseries/_TimeSeriesStrategy.py +12 -13
- scitex/ai/classification/timeseries/_TimeSeriesStratifiedSplit.py +231 -144
- scitex/ai/classification/timeseries/__init__.py +2 -4
- scitex/ai/classification/timeseries/_normalize_timestamp.py +3 -0
- scitex/ai/clustering/_pca.py +0 -1
- scitex/ai/clustering/_umap.py +1 -2
- scitex/ai/feature_extraction/__init__.py +10 -8
- scitex/ai/feature_extraction/vit.py +0 -1
- scitex/ai/feature_selection/feature_selection.py +3 -8
- scitex/ai/metrics/_calc_conf_mat.py +2 -0
- scitex/ai/metrics/_calc_feature_importance.py +3 -7
- scitex/ai/metrics/_calc_pre_rec_auc.py +5 -5
- scitex/ai/metrics/_calc_roc_auc.py +4 -2
- scitex/ai/metrics/_calc_seizure_prediction_metrics.py +35 -20
- scitex/ai/metrics/_calc_silhouette_score.py +1 -3
- scitex/ai/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger.py +0 -3
- scitex/ai/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger2020.py +0 -3
- scitex/ai/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger913A.py +0 -3
- scitex/ai/optim/_optimizers.py +1 -1
- scitex/ai/plt/__init__.py +6 -1
- scitex/ai/plt/_plot_feature_importance.py +1 -3
- scitex/ai/plt/_plot_learning_curve.py +9 -24
- scitex/ai/plt/_plot_optuna_study.py +4 -3
- scitex/ai/plt/_plot_pre_rec_curve.py +9 -15
- scitex/ai/plt/_plot_roc_curve.py +6 -8
- scitex/ai/plt/_stx_conf_mat.py +121 -122
- scitex/ai/sampling/undersample.py +3 -2
- scitex/ai/sklearn/__init__.py +2 -2
- scitex/ai/training/_LearningCurveLogger.py +23 -10
- scitex/ai/utils/_check_params.py +0 -1
- scitex/benchmark/__init__.py +15 -25
- scitex/benchmark/benchmark.py +124 -117
- scitex/benchmark/monitor.py +117 -107
- scitex/benchmark/profiler.py +61 -58
- scitex/bridge/__init__.py +110 -0
- scitex/bridge/_helpers.py +149 -0
- scitex/bridge/_plt_vis.py +529 -0
- scitex/bridge/_protocol.py +283 -0
- scitex/bridge/_stats_plt.py +261 -0
- scitex/bridge/_stats_vis.py +265 -0
- scitex/browser/__init__.py +0 -2
- scitex/browser/auth/__init__.py +0 -0
- scitex/browser/auth/google.py +16 -11
- scitex/browser/automation/CookieHandler.py +2 -3
- scitex/browser/collaboration/__init__.py +3 -0
- scitex/browser/collaboration/auth_helpers.py +3 -1
- scitex/browser/collaboration/collaborative_agent.py +2 -0
- scitex/browser/collaboration/interactive_panel.py +2 -2
- scitex/browser/collaboration/shared_session.py +20 -11
- scitex/browser/collaboration/standard_interactions.py +1 -0
- scitex/browser/core/BrowserMixin.py +12 -30
- scitex/browser/core/ChromeProfileManager.py +9 -24
- scitex/browser/debugging/_browser_logger.py +15 -25
- scitex/browser/debugging/_failure_capture.py +9 -2
- scitex/browser/debugging/_highlight_element.py +15 -6
- scitex/browser/debugging/_show_grid.py +5 -6
- scitex/browser/debugging/_sync_session.py +4 -3
- scitex/browser/debugging/_test_monitor.py +14 -5
- scitex/browser/debugging/_visual_cursor.py +46 -35
- scitex/browser/interaction/click_center.py +4 -3
- scitex/browser/interaction/click_with_fallbacks.py +7 -10
- scitex/browser/interaction/close_popups.py +79 -66
- scitex/browser/interaction/fill_with_fallbacks.py +8 -8
- scitex/browser/pdf/__init__.py +3 -1
- scitex/browser/pdf/click_download_for_chrome_pdf_viewer.py +11 -10
- scitex/browser/pdf/detect_chrome_pdf_viewer.py +3 -6
- scitex/browser/remote/CaptchaHandler.py +109 -96
- scitex/browser/remote/ZenRowsAPIClient.py +91 -97
- scitex/browser/remote/ZenRowsBrowserManager.py +138 -112
- scitex/browser/stealth/HumanBehavior.py +4 -9
- scitex/browser/stealth/StealthManager.py +11 -26
- scitex/capture/__init__.py +17 -17
- scitex/capture/__main__.py +2 -3
- scitex/capture/capture.py +23 -51
- scitex/capture/cli.py +14 -39
- scitex/capture/gif.py +5 -9
- scitex/capture/mcp_server.py +7 -20
- scitex/capture/session.py +4 -3
- scitex/capture/utils.py +18 -53
- scitex/cli/__init__.py +1 -1
- scitex/cli/cloud.py +158 -116
- scitex/cli/config.py +224 -0
- scitex/cli/main.py +41 -40
- scitex/cli/scholar.py +60 -27
- scitex/cli/security.py +14 -20
- scitex/cli/web.py +87 -90
- scitex/cli/writer.py +51 -45
- scitex/cloud/__init__.py +14 -11
- scitex/cloud/_matplotlib_hook.py +6 -6
- scitex/config/README.md +313 -0
- scitex/config/{PriorityConfig.py → _PriorityConfig.py} +114 -17
- scitex/config/_ScitexConfig.py +319 -0
- scitex/config/__init__.py +41 -9
- scitex/config/_paths.py +325 -0
- scitex/config/default.yaml +81 -0
- scitex/context/_suppress_output.py +2 -3
- scitex/db/_BaseMixins/_BaseBackupMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseBatchMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseBlobMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseImportExportMixin.py +1 -3
- scitex/db/_BaseMixins/_BaseIndexMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseMaintenanceMixin.py +1 -3
- scitex/db/_BaseMixins/_BaseQueryMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseRowMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseTableMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseTransactionMixin.py +1 -3
- scitex/db/_BaseMixins/__init__.py +1 -1
- scitex/db/__init__.py +9 -1
- scitex/db/__main__.py +8 -21
- scitex/db/_check_health.py +15 -31
- scitex/db/_delete_duplicates.py +7 -4
- scitex/db/_inspect.py +22 -38
- scitex/db/_inspect_optimized.py +89 -85
- scitex/db/_postgresql/_PostgreSQL.py +0 -1
- scitex/db/_postgresql/_PostgreSQLMixins/_BlobMixin.py +3 -1
- scitex/db/_postgresql/_PostgreSQLMixins/_ConnectionMixin.py +1 -3
- scitex/db/_postgresql/_PostgreSQLMixins/_ImportExportMixin.py +1 -3
- scitex/db/_postgresql/_PostgreSQLMixins/_MaintenanceMixin.py +1 -4
- scitex/db/_postgresql/_PostgreSQLMixins/_QueryMixin.py +3 -3
- scitex/db/_postgresql/_PostgreSQLMixins/_RowMixin.py +3 -1
- scitex/db/_postgresql/_PostgreSQLMixins/_TransactionMixin.py +1 -3
- scitex/db/_postgresql/__init__.py +1 -1
- scitex/db/_sqlite3/_SQLite3.py +2 -4
- scitex/db/_sqlite3/_SQLite3Mixins/_ArrayMixin.py +11 -12
- scitex/db/_sqlite3/_SQLite3Mixins/_ArrayMixin_v01-need-_hash-col.py +19 -14
- scitex/db/_sqlite3/_SQLite3Mixins/_BatchMixin.py +3 -1
- scitex/db/_sqlite3/_SQLite3Mixins/_BlobMixin.py +7 -7
- scitex/db/_sqlite3/_SQLite3Mixins/_ColumnMixin.py +118 -111
- scitex/db/_sqlite3/_SQLite3Mixins/_ConnectionMixin.py +8 -10
- scitex/db/_sqlite3/_SQLite3Mixins/_GitMixin.py +17 -45
- scitex/db/_sqlite3/_SQLite3Mixins/_ImportExportMixin.py +1 -3
- scitex/db/_sqlite3/_SQLite3Mixins/_IndexMixin.py +3 -1
- scitex/db/_sqlite3/_SQLite3Mixins/_QueryMixin.py +3 -4
- scitex/db/_sqlite3/_SQLite3Mixins/_RowMixin.py +9 -9
- scitex/db/_sqlite3/_SQLite3Mixins/_TableMixin.py +18 -11
- scitex/db/_sqlite3/_SQLite3Mixins/__init__.py +1 -0
- scitex/db/_sqlite3/__init__.py +1 -1
- scitex/db/_sqlite3/_delete_duplicates.py +13 -11
- scitex/decorators/__init__.py +29 -4
- scitex/decorators/_auto_order.py +43 -43
- scitex/decorators/_batch_fn.py +12 -6
- scitex/decorators/_cache_disk.py +8 -9
- scitex/decorators/_cache_disk_async.py +8 -7
- scitex/decorators/_combined.py +19 -13
- scitex/decorators/_converters.py +16 -3
- scitex/decorators/_deprecated.py +32 -22
- scitex/decorators/_numpy_fn.py +18 -4
- scitex/decorators/_pandas_fn.py +17 -5
- scitex/decorators/_signal_fn.py +17 -3
- scitex/decorators/_torch_fn.py +32 -15
- scitex/decorators/_xarray_fn.py +23 -9
- scitex/dev/_analyze_code_flow.py +0 -2
- scitex/dict/_DotDict.py +15 -19
- scitex/dict/_flatten.py +1 -0
- scitex/dict/_listed_dict.py +1 -0
- scitex/dict/_pop_keys.py +1 -0
- scitex/dict/_replace.py +1 -0
- scitex/dict/_safe_merge.py +1 -0
- scitex/dict/_to_str.py +2 -3
- scitex/dsp/__init__.py +13 -4
- scitex/dsp/_crop.py +3 -1
- scitex/dsp/_detect_ripples.py +3 -1
- scitex/dsp/_modulation_index.py +3 -1
- scitex/dsp/_time.py +3 -1
- scitex/dsp/_wavelet.py +0 -1
- scitex/dsp/example.py +0 -5
- scitex/dsp/filt.py +4 -0
- scitex/dsp/utils/__init__.py +4 -1
- scitex/dsp/utils/pac.py +3 -3
- scitex/dt/_normalize_timestamp.py +4 -1
- scitex/errors.py +3 -6
- scitex/etc/__init__.py +1 -1
- scitex/gen/_DimHandler.py +6 -6
- scitex/gen/__init__.py +5 -1
- scitex/gen/_deprecated_close.py +1 -0
- scitex/gen/_deprecated_start.py +5 -3
- scitex/gen/_detect_environment.py +44 -41
- scitex/gen/_detect_notebook_path.py +51 -47
- scitex/gen/_embed.py +1 -1
- scitex/gen/_get_notebook_path.py +81 -62
- scitex/gen/_inspect_module.py +0 -1
- scitex/gen/_norm.py +16 -7
- scitex/gen/_norm_cache.py +78 -65
- scitex/gen/_print_config.py +0 -3
- scitex/gen/_src.py +2 -3
- scitex/gen/_title_case.py +3 -2
- scitex/gen/_to_even.py +8 -8
- scitex/gen/_transpose.py +3 -3
- scitex/gen/misc.py +0 -3
- scitex/gists/_SigMacro_processFigure_S.py +2 -2
- scitex/gists/_SigMacro_toBlue.py +2 -2
- scitex/gists/__init__.py +4 -1
- scitex/git/_branch.py +19 -11
- scitex/git/_clone.py +23 -15
- scitex/git/_commit.py +10 -12
- scitex/git/_init.py +15 -38
- scitex/git/_remote.py +9 -3
- scitex/git/_result.py +3 -0
- scitex/git/_retry.py +2 -5
- scitex/git/_types.py +4 -0
- scitex/git/_validation.py +8 -8
- scitex/git/_workflow.py +4 -4
- scitex/io/__init__.py +2 -1
- scitex/io/_glob.py +2 -2
- scitex/io/_json2md.py +3 -3
- scitex/io/_load.py +6 -8
- scitex/io/_load_cache.py +71 -71
- scitex/io/_load_configs.py +2 -3
- scitex/io/_load_modules/_H5Explorer.py +6 -12
- scitex/io/_load_modules/_ZarrExplorer.py +3 -3
- scitex/io/_load_modules/_bibtex.py +62 -63
- scitex/io/_load_modules/_canvas.py +4 -9
- scitex/io/_load_modules/_catboost.py +7 -2
- scitex/io/_load_modules/_hdf5.py +2 -0
- scitex/io/_load_modules/_image.py +5 -1
- scitex/io/_load_modules/_matlab.py +3 -1
- scitex/io/_load_modules/_optuna.py +0 -1
- scitex/io/_load_modules/_pdf.py +38 -29
- scitex/io/_load_modules/_sqlite3.py +1 -0
- scitex/io/_load_modules/_txt.py +2 -0
- scitex/io/_load_modules/_xml.py +9 -9
- scitex/io/_load_modules/_zarr.py +12 -10
- scitex/io/_metadata.py +76 -37
- scitex/io/_qr_utils.py +18 -13
- scitex/io/_save.py +220 -63
- scitex/io/_save_modules/__init__.py +7 -2
- scitex/io/_save_modules/_bibtex.py +66 -61
- scitex/io/_save_modules/_canvas.py +5 -6
- scitex/io/_save_modules/_catboost.py +2 -2
- scitex/io/_save_modules/_csv.py +4 -4
- scitex/io/_save_modules/_excel.py +5 -9
- scitex/io/_save_modules/_hdf5.py +9 -21
- scitex/io/_save_modules/_html.py +5 -5
- scitex/io/_save_modules/_image.py +105 -8
- scitex/io/_save_modules/_joblib.py +2 -2
- scitex/io/_save_modules/_json.py +51 -6
- scitex/io/_save_modules/_listed_dfs_as_csv.py +2 -1
- scitex/io/_save_modules/_listed_scalars_as_csv.py +2 -1
- scitex/io/_save_modules/_matlab.py +2 -2
- scitex/io/_save_modules/_numpy.py +6 -8
- scitex/io/_save_modules/_pickle.py +4 -4
- scitex/io/_save_modules/_plotly.py +3 -3
- scitex/io/_save_modules/_tex.py +23 -25
- scitex/io/_save_modules/_text.py +2 -2
- scitex/io/_save_modules/_yaml.py +9 -9
- scitex/io/_save_modules/_zarr.py +15 -15
- scitex/io/utils/__init__.py +2 -1
- scitex/io/utils/h5_to_zarr.py +173 -155
- scitex/linalg/__init__.py +1 -1
- scitex/linalg/_geometric_median.py +4 -3
- scitex/logging/_Tee.py +5 -7
- scitex/logging/__init__.py +18 -19
- scitex/logging/_config.py +4 -1
- scitex/logging/_context.py +6 -5
- scitex/logging/_formatters.py +2 -3
- scitex/logging/_handlers.py +19 -20
- scitex/logging/_levels.py +9 -17
- scitex/logging/_logger.py +74 -15
- scitex/logging/_print_capture.py +17 -17
- scitex/nn/_BNet.py +1 -3
- scitex/nn/_Filters.py +6 -2
- scitex/nn/_ModulationIndex.py +3 -1
- scitex/nn/_PAC.py +3 -2
- scitex/nn/_PSD.py +0 -1
- scitex/nn/__init__.py +16 -3
- scitex/path/_clean.py +10 -8
- scitex/path/_find.py +1 -1
- scitex/path/_get_spath.py +1 -2
- scitex/path/_mk_spath.py +1 -1
- scitex/path/_symlink.py +5 -10
- scitex/pd/__init__.py +4 -1
- scitex/pd/_force_df.py +24 -24
- scitex/pd/_get_unique.py +1 -0
- scitex/pd/_merge_columns.py +1 -1
- scitex/pd/_round.py +11 -7
- scitex/pd/_to_xy.py +0 -1
- scitex/plt/REQUESTS.md +191 -0
- scitex/plt/__init__.py +185 -87
- scitex/plt/_subplots/_AxesWrapper.py +22 -6
- scitex/plt/_subplots/_AxisWrapper.py +100 -39
- scitex/plt/_subplots/_AxisWrapperMixins/_AdjustmentMixin.py +74 -52
- scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin.py +183 -73
- scitex/plt/_subplots/_AxisWrapperMixins/_SeabornMixin.py +61 -45
- scitex/plt/_subplots/_AxisWrapperMixins/_TrackingMixin.py +26 -14
- scitex/plt/_subplots/_AxisWrapperMixins/_UnitAwareMixin.py +80 -73
- scitex/plt/_subplots/_FigWrapper.py +93 -60
- scitex/plt/_subplots/_SubplotsWrapper.py +135 -68
- scitex/plt/_subplots/__init__.py +10 -0
- scitex/plt/_subplots/_export_as_csv.py +89 -47
- scitex/plt/_subplots/_export_as_csv_formatters/__init__.py +1 -0
- scitex/plt/_subplots/_export_as_csv_formatters/_format_annotate.py +6 -4
- scitex/plt/_subplots/_export_as_csv_formatters/_format_bar.py +88 -38
- scitex/plt/_subplots/_export_as_csv_formatters/_format_barh.py +25 -31
- scitex/plt/_subplots/_export_as_csv_formatters/_format_boxplot.py +53 -23
- scitex/plt/_subplots/_export_as_csv_formatters/_format_contour.py +38 -25
- scitex/plt/_subplots/_export_as_csv_formatters/_format_contourf.py +17 -9
- scitex/plt/_subplots/_export_as_csv_formatters/_format_errorbar.py +70 -124
- scitex/plt/_subplots/_export_as_csv_formatters/_format_eventplot.py +12 -10
- scitex/plt/_subplots/_export_as_csv_formatters/_format_fill.py +31 -17
- scitex/plt/_subplots/_export_as_csv_formatters/_format_fill_between.py +33 -21
- scitex/plt/_subplots/_export_as_csv_formatters/_format_hexbin.py +14 -4
- scitex/plt/_subplots/_export_as_csv_formatters/_format_hist.py +43 -29
- scitex/plt/_subplots/_export_as_csv_formatters/_format_hist2d.py +14 -4
- scitex/plt/_subplots/_export_as_csv_formatters/_format_imshow.py +27 -11
- scitex/plt/_subplots/_export_as_csv_formatters/_format_imshow2d.py +7 -5
- scitex/plt/_subplots/_export_as_csv_formatters/_format_matshow.py +9 -7
- scitex/plt/_subplots/_export_as_csv_formatters/_format_pie.py +15 -6
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot.py +85 -46
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_box.py +52 -27
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_imshow.py +1 -0
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_kde.py +16 -17
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_scatter.py +7 -5
- scitex/plt/_subplots/_export_as_csv_formatters/_format_quiver.py +10 -8
- scitex/plt/_subplots/_export_as_csv_formatters/_format_scatter.py +17 -6
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_barplot.py +43 -26
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_boxplot.py +68 -47
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_heatmap.py +52 -64
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_histplot.py +55 -50
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_jointplot.py +9 -11
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_kdeplot.py +63 -29
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_lineplot.py +4 -4
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_pairplot.py +6 -4
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_scatterplot.py +44 -40
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_stripplot.py +46 -39
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_swarmplot.py +46 -39
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_violinplot.py +75 -94
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stem.py +12 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_step.py +12 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_streamplot.py +10 -8
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_conf_mat.py +17 -15
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_ecdf.py +10 -9
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- scitex/template/clone_singularity.py +6 -7
- scitex/template/clone_writer_directory.py +6 -7
- scitex/tex/_preview.py +26 -11
- scitex/tex/_to_vec.py +10 -7
- scitex/torch/__init__.py +11 -1
- scitex/types/_ArrayLike.py +2 -0
- scitex/types/_is_listed_X.py +3 -3
- scitex/units.py +110 -77
- scitex/utils/_compress_hdf5.py +3 -3
- scitex/utils/_email.py +8 -4
- scitex/utils/_notify.py +14 -8
- scitex/utils/_search.py +6 -6
- scitex/utils/_verify_scitex_format.py +17 -42
- scitex/utils/_verify_scitex_format_v01.py +12 -34
- scitex/utils/template.py +4 -3
- scitex/vis/__init__.py +0 -0
- scitex/vis/backend/__init__.py +3 -3
- scitex/vis/backend/{export.py → _export.py} +1 -1
- scitex/vis/backend/{parser.py → _parser.py} +1 -3
- scitex/vis/backend/{render.py → _render.py} +1 -1
- scitex/vis/canvas.py +15 -3
- scitex/vis/editor/__init__.py +0 -0
- scitex/vis/editor/_dearpygui_editor.py +450 -304
- scitex/vis/editor/_defaults.py +114 -123
- scitex/vis/editor/_edit.py +38 -26
- scitex/vis/editor/_flask_editor.py +8 -8
- scitex/vis/editor/_mpl_editor.py +63 -48
- scitex/vis/editor/_qt_editor.py +210 -159
- scitex/vis/editor/_tkinter_editor.py +146 -89
- scitex/vis/editor/flask_editor/__init__.py +10 -10
- scitex/vis/editor/flask_editor/_bbox.py +529 -0
- scitex/vis/editor/flask_editor/{core.py → _core.py} +45 -29
- scitex/vis/editor/flask_editor/_plotter.py +567 -0
- scitex/vis/editor/flask_editor/_renderer.py +393 -0
- scitex/vis/editor/flask_editor/{utils.py → _utils.py} +13 -14
- scitex/vis/editor/flask_editor/templates/__init__.py +5 -5
- scitex/vis/editor/flask_editor/templates/{html.py → _html.py} +234 -16
- scitex/vis/editor/flask_editor/templates/_scripts.py +1261 -0
- scitex/vis/editor/flask_editor/templates/{styles.py → _styles.py} +192 -2
- scitex/vis/io/__init__.py +5 -5
- scitex/vis/io/{canvas.py → _canvas.py} +8 -4
- scitex/vis/io/{data.py → _data.py} +13 -9
- scitex/vis/io/{directory.py → _directory.py} +7 -4
- scitex/vis/io/{export.py → _export.py} +15 -12
- scitex/vis/io/{load.py → _load.py} +1 -1
- scitex/vis/io/{panel.py → _panel.py} +21 -13
- scitex/vis/io/{save.py → _save.py} +0 -0
- scitex/vis/model/__init__.py +7 -7
- scitex/vis/model/{annotations.py → _annotations.py} +2 -4
- scitex/vis/model/{axes.py → _axes.py} +1 -1
- scitex/vis/model/{figure.py → _figure.py} +0 -0
- scitex/vis/model/{guides.py → _guides.py} +1 -1
- scitex/vis/model/{plot.py → _plot.py} +2 -4
- scitex/vis/model/{plot_types.py → _plot_types.py} +0 -0
- scitex/vis/model/{styles.py → _styles.py} +0 -0
- scitex/vis/utils/__init__.py +2 -2
- scitex/vis/utils/{defaults.py → _defaults.py} +1 -2
- scitex/vis/utils/{validate.py → _validate.py} +3 -9
- scitex/web/__init__.py +7 -1
- scitex/web/_scraping.py +54 -38
- scitex/web/_search_pubmed.py +30 -14
- scitex/writer/.legacy/Writer_v01-refactored.py +4 -4
- scitex/writer/.legacy/_compile.py +18 -28
- scitex/writer/Writer.py +8 -21
- scitex/writer/__init__.py +11 -11
- scitex/writer/_clone_writer_project.py +2 -6
- scitex/writer/_compile/__init__.py +1 -0
- scitex/writer/_compile/_parser.py +1 -0
- scitex/writer/_compile/_runner.py +35 -38
- scitex/writer/_compile/_validator.py +1 -0
- scitex/writer/_compile/manuscript.py +1 -0
- scitex/writer/_compile/revision.py +1 -0
- scitex/writer/_compile/supplementary.py +1 -0
- scitex/writer/_compile_async.py +5 -12
- scitex/writer/_project/__init__.py +1 -0
- scitex/writer/_project/_create.py +10 -25
- scitex/writer/_project/_trees.py +4 -9
- scitex/writer/_project/_validate.py +2 -3
- scitex/writer/_validate_tree_structures.py +7 -18
- scitex/writer/dataclasses/__init__.py +8 -10
- scitex/writer/dataclasses/config/_CONSTANTS.py +2 -3
- scitex/writer/dataclasses/config/_WriterConfig.py +4 -9
- scitex/writer/dataclasses/contents/_ManuscriptContents.py +14 -25
- scitex/writer/dataclasses/contents/_RevisionContents.py +21 -16
- scitex/writer/dataclasses/contents/_SupplementaryContents.py +21 -24
- scitex/writer/dataclasses/core/_Document.py +2 -3
- scitex/writer/dataclasses/core/_DocumentSection.py +8 -23
- scitex/writer/dataclasses/results/_CompilationResult.py +2 -3
- scitex/writer/dataclasses/results/_LaTeXIssue.py +3 -6
- scitex/writer/dataclasses/results/_SaveSectionsResponse.py +20 -9
- scitex/writer/dataclasses/results/_SectionReadResponse.py +24 -10
- scitex/writer/dataclasses/tree/_ConfigTree.py +7 -4
- scitex/writer/dataclasses/tree/_ManuscriptTree.py +10 -13
- scitex/writer/dataclasses/tree/_RevisionTree.py +16 -17
- scitex/writer/dataclasses/tree/_ScriptsTree.py +10 -5
- scitex/writer/dataclasses/tree/_SharedTree.py +10 -13
- scitex/writer/dataclasses/tree/_SupplementaryTree.py +15 -14
- scitex/writer/utils/.legacy_git_retry.py +3 -8
- scitex/writer/utils/_parse_latex_logs.py +2 -3
- scitex/writer/utils/_parse_script_args.py +20 -23
- scitex/writer/utils/_watch.py +5 -5
- {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/METADATA +4 -10
- {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/RECORD +1071 -975
- scitex/db/_sqlite3/_SQLite3Mixins/_ColumnMixin_v01-indentation-issues.py +0 -583
- scitex/plt/_subplots/_export_as_csv_formatters.py +0 -112
- scitex/vis/editor/flask_editor/bbox.py +0 -216
- scitex/vis/editor/flask_editor/plotter.py +0 -130
- scitex/vis/editor/flask_editor/renderer.py +0 -184
- scitex/vis/editor/flask_editor/templates/scripts.py +0 -614
- {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/WHEEL +0 -0
- {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/entry_points.txt +0 -0
- {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/licenses/LICENSE +0 -0
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@@ -31,39 +31,39 @@ class DataciteJSONTranslator:
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"priority": 100,
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# Type mappings from DataCite/CSL to Zotero
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"article": "preprint",
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"book": "book",
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"chapter": "bookSection",
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"article-journal": "journalArticle",
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"article-magazine": "magazineArticle",
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"article-newspaper": "newspaperArticle",
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"thesis": "thesis",
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"entry-encyclopedia": "encyclopediaArticle",
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"entry-dictionary": "dictionaryEntry",
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"paper-conference": "conferencePaper",
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"personal_communication": "letter",
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"manuscript": "manuscript",
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"interview": "interview",
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"motion_picture": "film",
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"graphic": "artwork",
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"report": "report",
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"legal_case": "case",
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"patent": "patent",
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"legislation": "statute",
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contrib_type = contributor.get("contributorType", "").lower()
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if contrib_type == "editor":
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role = "editor"
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elif contrib_type == "producer":
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role = "producer"
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if contributor.get("familyName") and contributor.get("givenName"):
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item["creators"].append(
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{
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"lastName": contributor["familyName"],
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"firstName": contributor["givenName"],
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"creatorType": role,
|
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}
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)
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elif contributor.get("nameType") == "Personal":
|
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name = contributor.get("name", "")
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item["creators"].append(
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{
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"lastName": names[-1],
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"firstName": " ".join(names[:-1]),
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"creatorType": role,
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}
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)
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item[
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'fieldMode': True
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})
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item["creators"].append(
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{"lastName": name, "creatorType": role, "fieldMode": True}
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)
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else:
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item[
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item["creators"].append(
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{
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"lastName": contributor.get("name", ""),
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"creatorType": role,
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"fieldMode": True,
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}
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)
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# Extract publisher
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publisher = data.get(
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publisher = data.get("publisher")
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item[
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item["publisher"] = publisher.get("name", "")
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else:
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item[
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item["publisher"] = publisher
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# Extract DOI
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item[
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if data.get("doi"):
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item["DOI"] = data["doi"]
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# Extract URL
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item[
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if data.get("url"):
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item["url"] = data["url"]
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# Extract dates
|
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for date_info in data.get(
|
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date_type = date_info.get(
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date_value = date_info.get(
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for date_info in data.get("dates", []):
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date_type = date_info.get("dateType", "").lower()
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date_value = date_info.get("date", "")
|
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|
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if date_type ==
|
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item[
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+
if date_type == "issued" and date_value:
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+
item["date"] = date_value[:10] if len(date_value) >= 10 else date_value
|
|
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256
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# Extract publication year
|
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if data.get(
|
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|
-
if not item.get(
|
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item[
|
|
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|
+
if data.get("publicationYear"):
|
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if not item.get("date"):
|
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item["date"] = str(data["publicationYear"])
|
|
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|
|
247
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|
# Extract descriptions (abstract)
|
|
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|
-
for desc in data.get(
|
|
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|
-
if desc.get(
|
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item[
|
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+
for desc in data.get("descriptions", []):
|
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if desc.get("descriptionType", "").lower() == "abstract":
|
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item["abstractNote"] = desc.get("description", "")
|
|
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266
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break
|
|
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267
|
|
|
253
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|
# Extract subjects as tags
|
|
254
|
-
for subject in data.get(
|
|
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|
-
subject_text = subject.get(
|
|
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|
+
for subject in data.get("subjects", []):
|
|
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|
+
subject_text = subject.get("subject", "").strip()
|
|
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271
|
if subject_text:
|
|
257
|
-
item[
|
|
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|
+
item["tags"].append({"tag": subject_text})
|
|
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273
|
|
|
259
274
|
# Extract language
|
|
260
|
-
if data.get(
|
|
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|
-
item[
|
|
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|
+
if data.get("language"):
|
|
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|
+
item["language"] = data["language"]
|
|
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277
|
|
|
263
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|
return item
|
|
@@ -35,35 +35,37 @@ class DataverseTranslator:
|
|
|
35
35
|
"inRepository": True,
|
|
36
36
|
"translatorType": 4,
|
|
37
37
|
"browserSupport": "gcsibv",
|
|
38
|
-
"lastUpdated": "2023-05-01 12:09:04"
|
|
38
|
+
"lastUpdated": "2023-05-01 12:09:04",
|
|
39
39
|
}
|
|
40
40
|
|
|
41
41
|
def detect_web(self, doc: BeautifulSoup, url: str) -> str:
|
|
42
42
|
"""Detect if page is Dataverse dataset or search."""
|
|
43
|
-
if not doc.select_one(
|
|
44
|
-
return
|
|
43
|
+
if not doc.select_one("#dataverseHeader"):
|
|
44
|
+
return ""
|
|
45
45
|
|
|
46
|
-
if
|
|
47
|
-
return
|
|
46
|
+
if "/dataset.xhtml" in url:
|
|
47
|
+
return "dataset"
|
|
48
48
|
elif self.get_search_results(doc, check_only=True):
|
|
49
|
-
return
|
|
49
|
+
return "multiple"
|
|
50
50
|
|
|
51
|
-
return
|
|
51
|
+
return ""
|
|
52
52
|
|
|
53
|
-
def get_search_results(
|
|
53
|
+
def get_search_results(
|
|
54
|
+
self, doc: BeautifulSoup, check_only: bool = False
|
|
55
|
+
) -> Optional[Dict[str, str]]:
|
|
54
56
|
"""Extract search results."""
|
|
55
57
|
items = {}
|
|
56
58
|
rows = doc.select('.datasetResult a[href*="/dataset.xhtml"]')
|
|
57
59
|
|
|
58
60
|
for row in rows:
|
|
59
|
-
href = row.get(
|
|
61
|
+
href = row.get("href")
|
|
60
62
|
title = row.get_text(strip=True)
|
|
61
63
|
|
|
62
64
|
if not href or not title:
|
|
63
65
|
continue
|
|
64
66
|
|
|
65
67
|
if check_only:
|
|
66
|
-
return {
|
|
68
|
+
return {"found": "true"}
|
|
67
69
|
|
|
68
70
|
items[href] = title
|
|
69
71
|
|
|
@@ -73,7 +75,7 @@ class DataverseTranslator:
|
|
|
73
75
|
"""Main extraction method."""
|
|
74
76
|
page_type = self.detect_web(doc, url)
|
|
75
77
|
|
|
76
|
-
if page_type ==
|
|
78
|
+
if page_type == "multiple":
|
|
77
79
|
return self.get_search_results(doc, check_only=False)
|
|
78
80
|
else:
|
|
79
81
|
return self.scrape(doc, url)
|
|
@@ -81,11 +83,11 @@ class DataverseTranslator:
|
|
|
81
83
|
def scrape(self, doc: BeautifulSoup, url: str) -> Dict[str, Any]:
|
|
82
84
|
"""Scrape dataset metadata."""
|
|
83
85
|
item = {
|
|
84
|
-
|
|
85
|
-
|
|
86
|
-
|
|
87
|
-
|
|
88
|
-
|
|
86
|
+
"itemType": "dataset",
|
|
87
|
+
"url": url,
|
|
88
|
+
"creators": [],
|
|
89
|
+
"tags": [],
|
|
90
|
+
"attachments": [],
|
|
89
91
|
}
|
|
90
92
|
|
|
91
93
|
# Parse JSON-LD schema
|
|
@@ -95,92 +97,94 @@ class DataverseTranslator:
|
|
|
95
97
|
schema = json.loads(ld_json_tag.string)
|
|
96
98
|
|
|
97
99
|
# Extract license
|
|
98
|
-
license_info = schema.get(
|
|
100
|
+
license_info = schema.get("license")
|
|
99
101
|
if isinstance(license_info, dict):
|
|
100
|
-
license_info = license_info.get(
|
|
102
|
+
license_info = license_info.get("text", "")
|
|
101
103
|
if license_info:
|
|
102
104
|
# Clean HTML tags from license text
|
|
103
|
-
item[
|
|
105
|
+
item["rights"] = re.sub(r"<[^>]+>", "", str(license_info)).strip()
|
|
104
106
|
|
|
105
107
|
# Extract abstract
|
|
106
|
-
if schema.get(
|
|
107
|
-
item[
|
|
108
|
+
if schema.get("description"):
|
|
109
|
+
item["abstractNote"] = schema["description"]
|
|
108
110
|
|
|
109
111
|
# Extract version
|
|
110
|
-
version = schema.get(
|
|
112
|
+
version = schema.get("version")
|
|
111
113
|
if version and version > 1:
|
|
112
|
-
item[
|
|
114
|
+
item["versionNumber"] = str(version)
|
|
113
115
|
|
|
114
116
|
except (json.JSONDecodeError, KeyError):
|
|
115
117
|
pass
|
|
116
118
|
|
|
117
119
|
# Extract library catalog (repository name)
|
|
118
|
-
breadcrumb = doc.select_one(
|
|
120
|
+
breadcrumb = doc.select_one("#breadcrumbLnk0")
|
|
119
121
|
if breadcrumb:
|
|
120
|
-
item[
|
|
122
|
+
item["libraryCatalog"] = breadcrumb.get_text(strip=True)
|
|
121
123
|
|
|
122
124
|
# Extract title from meta tags
|
|
123
|
-
title_tag = doc.find(
|
|
124
|
-
if title_tag and title_tag.get(
|
|
125
|
-
title = title_tag[
|
|
125
|
+
title_tag = doc.find("meta", {"property": "og:title"})
|
|
126
|
+
if title_tag and title_tag.get("content"):
|
|
127
|
+
title = title_tag["content"]
|
|
126
128
|
# Handle "Replication Data for:" pattern
|
|
127
|
-
if re.match(r
|
|
128
|
-
match = re.match(r
|
|
129
|
+
if re.match(r"^(Replication )?[Dd]ata for:", title):
|
|
130
|
+
match = re.match(r"(^(Replication )?[Dd]ata for:.*?)(:|$)", title)
|
|
129
131
|
if match:
|
|
130
|
-
item[
|
|
131
|
-
item[
|
|
132
|
+
item["shortTitle"] = match.group(1)
|
|
133
|
+
item["title"] = title
|
|
132
134
|
|
|
133
135
|
# Extract DOI
|
|
134
|
-
doi_tag = doc.find(
|
|
135
|
-
if doi_tag and doi_tag.get(
|
|
136
|
-
item[
|
|
136
|
+
doi_tag = doc.find("meta", {"property": "citation_doi"})
|
|
137
|
+
if doi_tag and doi_tag.get("content"):
|
|
138
|
+
item["DOI"] = doi_tag["content"]
|
|
137
139
|
|
|
138
140
|
# Extract repository
|
|
139
|
-
repo_tag = doc.find(
|
|
140
|
-
if repo_tag and repo_tag.get(
|
|
141
|
-
item[
|
|
141
|
+
repo_tag = doc.find("meta", {"property": "citation_publisher"})
|
|
142
|
+
if repo_tag and repo_tag.get("content"):
|
|
143
|
+
item["repository"] = repo_tag["content"]
|
|
142
144
|
|
|
143
145
|
# Extract creators
|
|
144
|
-
author_tags = doc.find_all(
|
|
146
|
+
author_tags = doc.find_all("meta", {"property": "citation_author"})
|
|
145
147
|
for author_tag in author_tags:
|
|
146
|
-
author_name = author_tag.get(
|
|
148
|
+
author_name = author_tag.get("content", "")
|
|
147
149
|
if author_name:
|
|
148
150
|
names = author_name.split()
|
|
149
151
|
if len(names) >= 2:
|
|
150
|
-
item[
|
|
151
|
-
|
|
152
|
-
|
|
153
|
-
|
|
154
|
-
|
|
152
|
+
item["creators"].append(
|
|
153
|
+
{
|
|
154
|
+
"firstName": " ".join(names[:-1]),
|
|
155
|
+
"lastName": names[-1],
|
|
156
|
+
"creatorType": "author",
|
|
157
|
+
}
|
|
158
|
+
)
|
|
155
159
|
else:
|
|
156
|
-
item[
|
|
157
|
-
|
|
158
|
-
|
|
159
|
-
|
|
160
|
-
|
|
160
|
+
item["creators"].append(
|
|
161
|
+
{
|
|
162
|
+
"lastName": author_name,
|
|
163
|
+
"creatorType": "author",
|
|
164
|
+
"fieldMode": True,
|
|
165
|
+
}
|
|
166
|
+
)
|
|
161
167
|
|
|
162
168
|
# Extract date
|
|
163
|
-
date_tag = doc.find(
|
|
164
|
-
if date_tag and date_tag.get(
|
|
165
|
-
item[
|
|
169
|
+
date_tag = doc.find("meta", {"property": "citation_publication_date"})
|
|
170
|
+
if date_tag and date_tag.get("content"):
|
|
171
|
+
item["date"] = date_tag["content"]
|
|
166
172
|
|
|
167
173
|
# Extract language
|
|
168
|
-
lang_tag = doc.find(
|
|
169
|
-
if lang_tag and lang_tag.get(
|
|
170
|
-
item[
|
|
174
|
+
lang_tag = doc.find("meta", {"property": "og:locale"})
|
|
175
|
+
if lang_tag and lang_tag.get("content"):
|
|
176
|
+
item["language"] = lang_tag["content"]
|
|
171
177
|
|
|
172
178
|
# Extract keywords as tags
|
|
173
|
-
keywords_tags = doc.find_all(
|
|
179
|
+
keywords_tags = doc.find_all("meta", {"property": "citation_keywords"})
|
|
174
180
|
for kw_tag in keywords_tags:
|
|
175
|
-
keyword = kw_tag.get(
|
|
181
|
+
keyword = kw_tag.get("content", "").strip()
|
|
176
182
|
if keyword:
|
|
177
|
-
item[
|
|
183
|
+
item["tags"].append({"tag": keyword})
|
|
178
184
|
|
|
179
185
|
# Add snapshot attachment
|
|
180
|
-
item[
|
|
181
|
-
|
|
182
|
-
|
|
183
|
-
'url': url
|
|
184
|
-
})
|
|
186
|
+
item["attachments"].append(
|
|
187
|
+
{"title": "Snapshot", "mimeType": "text/html", "url": url}
|
|
188
|
+
)
|
|
185
189
|
|
|
186
190
|
return item
|