scitex 2.5.0__py3-none-any.whl → 2.7.3__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 +25 -10
- 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/audio/README.md +52 -0
- scitex/audio/__init__.py +384 -0
- scitex/audio/__main__.py +129 -0
- scitex/audio/_tts.py +334 -0
- scitex/audio/engines/__init__.py +44 -0
- scitex/audio/engines/base.py +275 -0
- scitex/audio/engines/elevenlabs_engine.py +143 -0
- scitex/audio/engines/gtts_engine.py +162 -0
- scitex/audio/engines/pyttsx3_engine.py +131 -0
- scitex/audio/mcp_server.py +757 -0
- 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/dev/plt/__init__.py +272 -0
- scitex/dev/plt/plot_mpl_axhline.py +28 -0
- scitex/dev/plt/plot_mpl_axhspan.py +28 -0
- scitex/dev/plt/plot_mpl_axvline.py +28 -0
- scitex/dev/plt/plot_mpl_axvspan.py +28 -0
- scitex/dev/plt/plot_mpl_bar.py +29 -0
- scitex/dev/plt/plot_mpl_barh.py +29 -0
- scitex/dev/plt/plot_mpl_boxplot.py +28 -0
- scitex/dev/plt/plot_mpl_contour.py +31 -0
- scitex/dev/plt/plot_mpl_contourf.py +31 -0
- scitex/dev/plt/plot_mpl_errorbar.py +30 -0
- scitex/dev/plt/plot_mpl_eventplot.py +28 -0
- scitex/dev/plt/plot_mpl_fill.py +30 -0
- scitex/dev/plt/plot_mpl_fill_between.py +31 -0
- scitex/dev/plt/plot_mpl_hexbin.py +28 -0
- scitex/dev/plt/plot_mpl_hist.py +28 -0
- scitex/dev/plt/plot_mpl_hist2d.py +28 -0
- scitex/dev/plt/plot_mpl_imshow.py +29 -0
- scitex/dev/plt/plot_mpl_pcolormesh.py +31 -0
- scitex/dev/plt/plot_mpl_pie.py +29 -0
- scitex/dev/plt/plot_mpl_plot.py +29 -0
- scitex/dev/plt/plot_mpl_quiver.py +31 -0
- scitex/dev/plt/plot_mpl_scatter.py +28 -0
- scitex/dev/plt/plot_mpl_stackplot.py +31 -0
- scitex/dev/plt/plot_mpl_stem.py +29 -0
- scitex/dev/plt/plot_mpl_step.py +29 -0
- scitex/dev/plt/plot_mpl_violinplot.py +28 -0
- scitex/dev/plt/plot_sns_barplot.py +29 -0
- scitex/dev/plt/plot_sns_boxplot.py +29 -0
- scitex/dev/plt/plot_sns_heatmap.py +28 -0
- scitex/dev/plt/plot_sns_histplot.py +29 -0
- scitex/dev/plt/plot_sns_kdeplot.py +29 -0
- scitex/dev/plt/plot_sns_lineplot.py +31 -0
- scitex/dev/plt/plot_sns_scatterplot.py +29 -0
- scitex/dev/plt/plot_sns_stripplot.py +29 -0
- scitex/dev/plt/plot_sns_swarmplot.py +29 -0
- scitex/dev/plt/plot_sns_violinplot.py +29 -0
- scitex/dev/plt/plot_stx_bar.py +29 -0
- scitex/dev/plt/plot_stx_barh.py +29 -0
- scitex/dev/plt/plot_stx_box.py +28 -0
- scitex/dev/plt/plot_stx_boxplot.py +28 -0
- scitex/dev/plt/plot_stx_conf_mat.py +28 -0
- scitex/dev/plt/plot_stx_contour.py +31 -0
- scitex/dev/plt/plot_stx_ecdf.py +28 -0
- scitex/dev/plt/plot_stx_errorbar.py +30 -0
- scitex/dev/plt/plot_stx_fill_between.py +31 -0
- scitex/dev/plt/plot_stx_fillv.py +28 -0
- scitex/dev/plt/plot_stx_heatmap.py +28 -0
- scitex/dev/plt/plot_stx_image.py +28 -0
- scitex/dev/plt/plot_stx_imshow.py +28 -0
- scitex/dev/plt/plot_stx_joyplot.py +28 -0
- scitex/dev/plt/plot_stx_kde.py +28 -0
- scitex/dev/plt/plot_stx_line.py +28 -0
- scitex/dev/plt/plot_stx_mean_ci.py +28 -0
- scitex/dev/plt/plot_stx_mean_std.py +28 -0
- scitex/dev/plt/plot_stx_median_iqr.py +28 -0
- scitex/dev/plt/plot_stx_raster.py +28 -0
- scitex/dev/plt/plot_stx_rectangle.py +28 -0
- scitex/dev/plt/plot_stx_scatter.py +29 -0
- scitex/dev/plt/plot_stx_shaded_line.py +29 -0
- scitex/dev/plt/plot_stx_violin.py +28 -0
- scitex/dev/plt/plot_stx_violinplot.py +28 -0
- 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/fig/__init__.py +352 -0
- scitex/{vis → fig}/backend/__init__.py +3 -3
- scitex/{vis/backend/export.py → fig/backend/_export.py} +1 -1
- scitex/{vis/backend/parser.py → fig/backend/_parser.py} +2 -4
- scitex/{vis/backend/render.py → fig/backend/_render.py} +1 -1
- scitex/{vis → fig}/canvas.py +16 -4
- scitex/{vis → fig}/editor/__init__.py +0 -0
- scitex/{vis → fig}/editor/_dearpygui_editor.py +450 -304
- scitex/fig/editor/_defaults.py +300 -0
- scitex/fig/editor/_edit.py +751 -0
- scitex/{vis → fig}/editor/_flask_editor.py +8 -8
- scitex/{vis → fig}/editor/_mpl_editor.py +63 -48
- scitex/{vis → fig}/editor/_qt_editor.py +391 -160
- scitex/{vis → fig}/editor/_tkinter_editor.py +146 -89
- scitex/fig/editor/flask_editor/__init__.py +21 -0
- scitex/fig/editor/flask_editor/_bbox.py +1276 -0
- scitex/fig/editor/flask_editor/_core.py +624 -0
- scitex/fig/editor/flask_editor/_plotter.py +601 -0
- scitex/fig/editor/flask_editor/_renderer.py +739 -0
- scitex/{vis/editor/flask_editor/utils.py → fig/editor/flask_editor/_utils.py} +13 -14
- scitex/{vis → fig}/editor/flask_editor/templates/__init__.py +6 -6
- scitex/fig/editor/flask_editor/templates/_html.py +834 -0
- scitex/fig/editor/flask_editor/templates/_scripts.py +3136 -0
- scitex/fig/editor/flask_editor/templates/_styles.py +1346 -0
- scitex/{vis → fig}/io/__init__.py +18 -6
- scitex/fig/io/_bundle.py +973 -0
- scitex/{vis/io/canvas.py → fig/io/_canvas.py} +9 -5
- scitex/{vis/io/data.py → fig/io/_data.py} +14 -10
- scitex/{vis/io/directory.py → fig/io/_directory.py} +7 -4
- scitex/{vis/io/export.py → fig/io/_export.py} +16 -13
- scitex/{vis/io/load.py → fig/io/_load.py} +2 -2
- scitex/{vis/io/panel.py → fig/io/_panel.py} +22 -14
- scitex/{vis/io/save.py → fig/io/_save.py} +1 -1
- scitex/{vis → fig}/model/__init__.py +8 -8
- scitex/{vis/model/annotations.py → fig/model/_annotations.py} +3 -5
- scitex/{vis/model/axes.py → fig/model/_axes.py} +2 -2
- scitex/{vis/model/figure.py → fig/model/_figure.py} +1 -1
- scitex/{vis/model/guides.py → fig/model/_guides.py} +2 -2
- scitex/{vis/model/plot.py → fig/model/_plot.py} +3 -5
- scitex/{vis/model/plot_types.py → fig/model/_plot_types.py} +0 -0
- scitex/{vis/model/styles.py → fig/model/_styles.py} +1 -1
- scitex/{vis → fig}/utils/__init__.py +3 -3
- scitex/{vis/utils/defaults.py → fig/utils/_defaults.py} +1 -2
- scitex/{vis/utils/validate.py → fig/utils/_validate.py} +3 -9
- 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 +12 -27
- scitex/io/_bundle.py +434 -0
- scitex/io/_flush.py +5 -2
- scitex/io/_glob.py +2 -2
- scitex/io/_json2md.py +3 -3
- scitex/io/_load.py +104 -8
- scitex/io/_load_cache.py +71 -71
- scitex/io/_load_configs.py +2 -3
- scitex/io/_load_modules/_H5Explorer.py +11 -14
- scitex/io/_load_modules/_ZarrExplorer.py +3 -3
- scitex/io/_load_modules/_bibtex.py +62 -63
- scitex/io/_load_modules/_canvas.py +6 -11
- scitex/io/_load_modules/_catboost.py +7 -2
- scitex/io/_load_modules/_hdf5.py +2 -0
- scitex/io/_load_modules/_image.py +7 -4
- scitex/io/_load_modules/_matlab.py +3 -1
- scitex/io/_load_modules/_optuna.py +0 -1
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- scitex/scholar/url_finder/translators/individual/oxford.py +25 -19
- scitex/scholar/url_finder/translators/individual/oxford_dictionaries_premium.py +3 -1
- scitex/scholar/url_finder/translators/individual/ozon_ru.py +3 -1
- scitex/scholar/url_finder/translators/individual/plos.py +9 -12
- scitex/scholar/url_finder/translators/individual/polygon.py +3 -1
- scitex/scholar/url_finder/translators/individual/primo.py +3 -1
- scitex/scholar/url_finder/translators/individual/project_muse.py +3 -1
- scitex/scholar/url_finder/translators/individual/pubfactory_journals.py +3 -1
- scitex/scholar/url_finder/translators/individual/pubmed.py +71 -65
- scitex/scholar/url_finder/translators/individual/pubmed_central.py +8 -6
- scitex/scholar/url_finder/translators/individual/rechtspraak_nl.py +3 -1
- scitex/scholar/url_finder/translators/individual/sage_journals.py +25 -17
- scitex/scholar/url_finder/translators/individual/sciencedirect.py +36 -17
- scitex/scholar/url_finder/translators/individual/semantics_visual_library.py +3 -1
- scitex/scholar/url_finder/translators/individual/silverchair.py +70 -52
- scitex/scholar/url_finder/translators/individual/sora.py +3 -1
- scitex/scholar/url_finder/translators/individual/springer.py +15 -11
- scitex/scholar/url_finder/translators/individual/ssrn.py +3 -3
- scitex/scholar/url_finder/translators/individual/stanford_encyclopedia_of_philosophy.py +3 -1
- scitex/scholar/url_finder/translators/individual/superlib.py +3 -1
- scitex/scholar/url_finder/translators/individual/treesearch.py +3 -1
- scitex/scholar/url_finder/translators/individual/university_of_chicago_press_books.py +3 -1
- scitex/scholar/url_finder/translators/individual/vlex.py +3 -1
- scitex/scholar/url_finder/translators/individual/web_of_science.py +3 -1
- scitex/scholar/url_finder/translators/individual/web_of_science_nextgen.py +3 -1
- scitex/scholar/url_finder/translators/individual/wiley.py +31 -25
- scitex/scholar/url_finder/translators/individual/wilson_center_digital_archive.py +3 -1
- scitex/scholar/utils/bibtex/_parse_bibtex.py +3 -3
- scitex/scholar/utils/cleanup/_cleanup_scholar_processes.py +5 -9
- scitex/scholar/utils/text/_TextNormalizer.py +249 -176
- scitex/scholar/utils/validation/DOIValidator.py +31 -28
- scitex/scholar/utils/validation/__init__.py +0 -0
- scitex/scholar/utils/validation/validate_library_dois.py +61 -57
- scitex/scholar/zotero/__init__.py +1 -1
- scitex/security/cli.py +7 -20
- scitex/security/github.py +45 -32
- scitex/session/__init__.py +8 -9
- scitex/session/_decorator.py +49 -42
- scitex/session/_lifecycle.py +39 -39
- scitex/session/_manager.py +24 -20
- scitex/sh/__init__.py +4 -3
- scitex/sh/_execute.py +10 -7
- scitex/sh/_security.py +3 -3
- scitex/sh/_types.py +2 -3
- scitex/stats/__init__.py +174 -6
- scitex/stats/_schema.py +42 -569
- scitex/stats/auto/__init__.py +188 -0
- scitex/stats/auto/_context.py +331 -0
- scitex/stats/auto/_formatting.py +679 -0
- scitex/stats/auto/_rules.py +901 -0
- scitex/stats/auto/_selector.py +554 -0
- scitex/stats/auto/_styles.py +721 -0
- scitex/stats/correct/__init__.py +4 -4
- scitex/stats/correct/_correct_bonferroni.py +43 -34
- scitex/stats/correct/_correct_fdr.py +14 -40
- scitex/stats/correct/_correct_fdr_.py +39 -46
- scitex/stats/correct/_correct_holm.py +14 -32
- scitex/stats/correct/_correct_sidak.py +36 -21
- scitex/stats/descriptive/_circular.py +20 -21
- scitex/stats/descriptive/_describe.py +19 -5
- scitex/stats/descriptive/_nan.py +5 -7
- scitex/stats/descriptive/_real.py +4 -3
- scitex/stats/effect_sizes/__init__.py +10 -11
- scitex/stats/effect_sizes/_cliffs_delta.py +35 -32
- scitex/stats/effect_sizes/_cohens_d.py +30 -31
- scitex/stats/effect_sizes/_epsilon_squared.py +19 -22
- scitex/stats/effect_sizes/_eta_squared.py +23 -27
- scitex/stats/effect_sizes/_prob_superiority.py +18 -21
- scitex/stats/io/__init__.py +29 -0
- scitex/stats/io/_bundle.py +156 -0
- scitex/stats/posthoc/__init__.py +3 -3
- scitex/stats/posthoc/_dunnett.py +75 -55
- scitex/stats/posthoc/_games_howell.py +61 -43
- scitex/stats/posthoc/_tukey_hsd.py +42 -34
- scitex/stats/power/__init__.py +2 -2
- scitex/stats/power/_power.py +56 -56
- scitex/stats/tests/__init__.py +1 -1
- scitex/stats/tests/correlation/__init__.py +1 -1
- scitex/stats/tests/correlation/_test_pearson.py +28 -38
- scitex/stats/utils/__init__.py +14 -17
- scitex/stats/utils/_effect_size.py +85 -78
- scitex/stats/utils/_formatters.py +49 -43
- scitex/stats/utils/_normalizers.py +7 -14
- scitex/stats/utils/_power.py +56 -56
- scitex/str/__init__.py +1 -0
- scitex/str/_clean_path.py +3 -3
- scitex/str/_factor_out_digits.py +86 -58
- scitex/str/_format_plot_text.py +180 -111
- scitex/str/_latex.py +19 -19
- scitex/str/_latex_fallback.py +9 -10
- scitex/str/_parse.py +3 -6
- scitex/str/_print_debug.py +13 -13
- scitex/str/_printc.py +2 -0
- scitex/str/_search.py +3 -3
- scitex/template/.legacy/_clone_project.py +9 -13
- scitex/template/__init__.py +10 -2
- scitex/template/_clone_project.py +7 -2
- scitex/template/_copy.py +1 -0
- scitex/template/_customize.py +3 -6
- scitex/template/_git_strategy.py +2 -3
- scitex/template/_rename.py +1 -0
- scitex/template/clone_pip_project.py +6 -7
- scitex/template/clone_research.py +7 -10
- scitex/template/clone_singularity.py +6 -7
- scitex/template/clone_writer_directory.py +6 -7
- scitex/tex/__init__.py +4 -0
- scitex/tex/_export.py +890 -0
- 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/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-2.7.3.dist-info}/METADATA +14 -10
- {scitex-2.5.0.dist-info → scitex-2.7.3.dist-info}/RECORD +1149 -985
- scitex/db/_sqlite3/_SQLite3Mixins/_ColumnMixin_v01-indentation-issues.py +0 -583
- scitex/io/memo.md +0 -2827
- scitex/plt/_subplots/TODO.md +0 -53
- scitex/plt/_subplots/_AxisWrapperMixins/_AdjustmentMixin.py +0 -537
- scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin.py +0 -1499
- scitex/plt/_subplots/_AxisWrapperMixins/_SeabornMixin.py +0 -431
- scitex/plt/_subplots/_export_as_csv_formatters.py +0 -112
- scitex/vis/__init__.py +0 -177
- scitex/vis/editor/_defaults.py +0 -244
- scitex/vis/editor/_edit.py +0 -378
- scitex/vis/editor/flask_editor/__init__.py +0 -21
- scitex/vis/editor/flask_editor/bbox.py +0 -216
- scitex/vis/editor/flask_editor/core.py +0 -152
- scitex/vis/editor/flask_editor/plotter.py +0 -130
- scitex/vis/editor/flask_editor/renderer.py +0 -184
- scitex/vis/editor/flask_editor/templates/html.py +0 -295
- scitex/vis/editor/flask_editor/templates/scripts.py +0 -614
- scitex/vis/editor/flask_editor/templates/styles.py +0 -549
- /scitex/{vis → fig}/README.md +0 -0
- /scitex/{vis → fig}/docs/CANVAS_ARCHITECTURE.md +0 -0
- {scitex-2.5.0.dist-info → scitex-2.7.3.dist-info}/WHEEL +0 -0
- {scitex-2.5.0.dist-info → scitex-2.7.3.dist-info}/entry_points.txt +0 -0
- {scitex-2.5.0.dist-info → scitex-2.7.3.dist-info}/licenses/LICENSE +0 -0
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@@ -40,7 +40,7 @@ class ORCIDTranslator:
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# XML namespaces used in ORCID API responses
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NAMESPACES = {
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"work": "http://www.orcid.org/ns/work",
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"activities": "http://www.orcid.org/ns/activities"
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"activities": "http://www.orcid.org/ns/activities",
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@classmethod
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return None
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# Remove URL prefix if present and clean extra UI text
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orcid = orcid_text.replace(
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orcid = orcid_text.replace("https://orcid.org/", "").strip()
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# Extract just the ORCID ID pattern (0000-0000-0000-0000)
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put_codes = {}
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# Find all work groups
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for group in root.findall(
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for group in root.findall(".//activities:group", cls.NAMESPACES):
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"""
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url = f"{cls.API_BASE}/{orcid}/work/{put_code}"
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headers = {
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"Accept": "application/vnd.citationstyles.csl+json"
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}
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headers = {"Accept": "application/vnd.citationstyles.csl+json"}
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metadata = await ORCIDTranslator.fetch_work_metadata(
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metadata = await ORCIDTranslator.fetch_work_metadata(
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orcid, first_code
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)
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if
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if
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authors = metadata[
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if "author" in metadata:
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authors = metadata["author"]
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'a[href*="/pdf/"]',
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".download-pdf a",
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"href", timeout=1000
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base_url = await page.evaluate(
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base_url = await page.evaluate(
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base_url = re.sub(r
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elif not pdf_link.startswith("http"):
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base_url = await page.evaluate("window.location.href")
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base_url = re.sub(r"/[^/]*$", "", base_url)
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pdf_urls.append(pdf_link)
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'a[href*="lookinside"]',
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".book-preview a",
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preview_link = await page.locator(selector).first.get_attribute(
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preview_link = await page.locator(selector).first.get_attribute(
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"href", timeout=1000
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)
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if preview_link and ".pdf" in preview_link.lower():
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base_url = await page.evaluate("window.location.origin")
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preview_link = f"{base_url}{preview_link}"
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elif not preview_link.startswith(
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base_url = await page.evaluate(
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base_url = re.sub(r
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elif not preview_link.startswith("http"):
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base_url = await page.evaluate("window.location.href")
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base_url = re.sub(r"/[^/]*$", "", base_url)
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preview_link = f"{base_url}/{preview_link}"
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@@ -127,13 +131,15 @@ class OxfordTranslator(BaseTranslator):
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# Method 3: Extract ISBN and attempt to construct PDF URL
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# (Usually doesn't work for OUP, but worth trying)
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try:
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isbn_text = await page.locator('p:has-text("ISBN:")').first.inner_text(
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isbn_text = await page.locator('p:has-text("ISBN:")').first.inner_text(
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timeout=2000
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)
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isbn_match = re.search(r"ISBN:\s*(\d{10,13})", isbn_text)
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if isbn_match:
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isbn = isbn_match.group(1)
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# Some academic publishers provide PDFs via ISBN
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# This is speculative and may not work
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base_url = await page.evaluate(
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+
base_url = await page.evaluate("window.location.origin")
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potential_pdf = f"{base_url}/academic/pdf/{isbn}.pdf"
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# We don't add this speculatively without verification
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except Exception:
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@@ -12,7 +12,9 @@ class OxfordDictionariesPremiumTranslator(BaseTranslator):
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"""Oxford Dictionaries Premium."""
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LABEL = "Oxford Dictionaries Premium"
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-
URL_TARGET_PATTERN =
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+
URL_TARGET_PATTERN = (
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+
r"^https?://premium\.oxforddictionaries\.com/(translate|definition)/"
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+
)
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@classmethod
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def matches_url(cls, url: str) -> bool:
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@@ -12,7 +12,9 @@ class OzonRuTranslator(BaseTranslator):
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"""OZON.ru."""
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LABEL = "OZON.ru"
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-
URL_TARGET_PATTERN =
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+
URL_TARGET_PATTERN = (
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+
r"^https?://www\.ozon\.ru/(context/detail/id/|\?context=search)"
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+
)
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@classmethod
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def matches_url(cls, url: str) -> bool:
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@@ -60,7 +60,7 @@ class PLoSTranslator(BaseTranslator):
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try:
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pdf_url = await page.locator(
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'meta[name="citation_pdf_url"]'
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-
).first.get_attribute(
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+
).first.get_attribute("content", timeout=3000)
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if pdf_url:
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pdf_urls.append(pdf_url)
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return pdf_urls
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@@ -72,11 +72,11 @@ class PLoSTranslator(BaseTranslator):
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try:
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pdf_link = await page.locator(
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'a[href*="/article/file"][href*="type=printable"]'
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-
).first.get_attribute(
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+
).first.get_attribute("href", timeout=2000)
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if pdf_link:
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# Make absolute URL if needed
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-
if pdf_link.startswith(
|
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-
base_url = await page.evaluate(
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+
if pdf_link.startswith("/"):
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+
base_url = await page.evaluate("window.location.origin")
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pdf_link = f"{base_url}{pdf_link}"
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pdf_urls.append(pdf_link)
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return pdf_urls
|
|
@@ -86,18 +86,15 @@ class PLoSTranslator(BaseTranslator):
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86
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# Method 3: Construct PDF URL from DOI if present
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# Pattern: https://journals.plos.org/journal/article/file?id=DOI&type=printable
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try:
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-
doi = await page.locator(
|
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90
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-
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91
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-
)
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|
-
current_url = await page.evaluate(
|
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89
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+
doi = await page.locator('meta[name="citation_doi"]').first.get_attribute(
|
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90
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+
"content", timeout=2000
|
|
91
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+
)
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+
current_url = await page.evaluate("window.location.href")
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|
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|
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94
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|
if doi:
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|
# Extract journal name from URL
|
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|
# Pattern: journals.plos.org/{journal}/article?id=...
|
|
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|
-
journal_match = re.search(
|
|
98
|
-
r'journals\.plos\.org/([^/]+)/',
|
|
99
|
-
current_url
|
|
100
|
-
)
|
|
97
|
+
journal_match = re.search(r"journals\.plos\.org/([^/]+)/", current_url)
|
|
101
98
|
if journal_match:
|
|
102
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|
journal = journal_match.group(1)
|
|
103
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|
pdf_url = f"https://journals.plos.org/{journal}/article/file?id={doi}&type=printable"
|
|
@@ -12,7 +12,9 @@ class PolygonTranslator(BaseTranslator):
|
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|
12
12
|
"""Polygon."""
|
|
13
13
|
|
|
14
14
|
LABEL = "Polygon"
|
|
15
|
-
URL_TARGET_PATTERN =
|
|
15
|
+
URL_TARGET_PATTERN = (
|
|
16
|
+
r"^https?://(www\.)?(polygon|heroesneverdie|riftherald|theflyingcourier)\.com"
|
|
17
|
+
)
|
|
16
18
|
|
|
17
19
|
@classmethod
|
|
18
20
|
def matches_url(cls, url: str) -> bool:
|
|
@@ -12,7 +12,9 @@ class PrimoTranslator(BaseTranslator):
|
|
|
12
12
|
"""Primo."""
|
|
13
13
|
|
|
14
14
|
LABEL = "Primo"
|
|
15
|
-
URL_TARGET_PATTERN =
|
|
15
|
+
URL_TARGET_PATTERN = (
|
|
16
|
+
r"/primo_library/|/nebis/|^https?://www\.recherche-portal\.ch/zbz/"
|
|
17
|
+
)
|
|
16
18
|
|
|
17
19
|
@classmethod
|
|
18
20
|
def matches_url(cls, url: str) -> bool:
|
|
@@ -12,7 +12,9 @@ class ProjectMUSETranslator(BaseTranslator):
|
|
|
12
12
|
"""Project MUSE."""
|
|
13
13
|
|
|
14
14
|
LABEL = "Project MUSE"
|
|
15
|
-
URL_TARGET_PATTERN =
|
|
15
|
+
URL_TARGET_PATTERN = (
|
|
16
|
+
r"^https?://[^/]*muse\.jhu\.edu/(book/|pub/|article/|issue/|search\?)"
|
|
17
|
+
)
|
|
16
18
|
|
|
17
19
|
@classmethod
|
|
18
20
|
def matches_url(cls, url: str) -> bool:
|
|
@@ -12,7 +12,9 @@ class PubFactoryJournalsTranslator(BaseTranslator):
|
|
|
12
12
|
"""PubFactory Journals."""
|
|
13
13
|
|
|
14
14
|
LABEL = "PubFactory Journals"
|
|
15
|
-
URL_TARGET_PATTERN =
|
|
15
|
+
URL_TARGET_PATTERN = (
|
|
16
|
+
r"^https://([^/]+/view/journals/.+\.xml|[^.]*journals\.[^/]+/search)\b"
|
|
17
|
+
)
|
|
16
18
|
|
|
17
19
|
@classmethod
|
|
18
20
|
def matches_url(cls, url: str) -> bool:
|
|
@@ -56,37 +56,37 @@ class PubMedTranslator(BaseTranslator):
|
|
|
56
56
|
"""
|
|
57
57
|
try:
|
|
58
58
|
content = await page.content()
|
|
59
|
-
soup = BeautifulSoup(content,
|
|
59
|
+
soup = BeautifulSoup(content, "html.parser")
|
|
60
60
|
|
|
61
61
|
# Strategy 1: meta tags
|
|
62
|
-
for meta_name in [
|
|
63
|
-
meta = soup.find(
|
|
64
|
-
if meta and meta.get(
|
|
65
|
-
pmid = meta[
|
|
62
|
+
for meta_name in ["ncbi_uidlist", "ncbi_article_id", "uid"]:
|
|
63
|
+
meta = soup.find("meta", attrs={"name": meta_name})
|
|
64
|
+
if meta and meta.get("content"):
|
|
65
|
+
pmid = meta["content"].strip()
|
|
66
66
|
if pmid.isdigit():
|
|
67
67
|
return pmid
|
|
68
68
|
|
|
69
69
|
# Strategy 2: input element
|
|
70
|
-
input_elem = soup.find(
|
|
71
|
-
if input_elem and input_elem.get(
|
|
72
|
-
pmid = input_elem[
|
|
70
|
+
input_elem = soup.find("input", attrs={"id": "absid"})
|
|
71
|
+
if input_elem and input_elem.get("value"):
|
|
72
|
+
pmid = input_elem["value"].strip()
|
|
73
73
|
if pmid.isdigit():
|
|
74
74
|
return pmid
|
|
75
75
|
|
|
76
76
|
# Strategy 3: link href patterns
|
|
77
|
-
for rel in [
|
|
78
|
-
link = soup.find(
|
|
79
|
-
if link and link.get(
|
|
80
|
-
match = re.search(r
|
|
77
|
+
for rel in ["canonical", "handheld"]:
|
|
78
|
+
link = soup.find("link", attrs={"rel": rel})
|
|
79
|
+
if link and link.get("href"):
|
|
80
|
+
match = re.search(r"/(\d+)(?:/|$)", link["href"])
|
|
81
81
|
if match:
|
|
82
82
|
return match.group(1)
|
|
83
83
|
|
|
84
84
|
# Strategy 4: bookshelf PubMed record links
|
|
85
|
-
maincontent = soup.find(id=
|
|
85
|
+
maincontent = soup.find(id="maincontent")
|
|
86
86
|
if maincontent:
|
|
87
|
-
pubmed_link = maincontent.find(
|
|
88
|
-
|
|
89
|
-
|
|
87
|
+
pubmed_link = maincontent.find(
|
|
88
|
+
"a", attrs={"title": re.compile(r"PubMed record")}
|
|
89
|
+
)
|
|
90
90
|
if pubmed_link:
|
|
91
91
|
pmid = pubmed_link.get_text(strip=True)
|
|
92
92
|
if pmid.isdigit():
|
|
@@ -94,11 +94,11 @@ class PubMedTranslator(BaseTranslator):
|
|
|
94
94
|
|
|
95
95
|
# Strategy 5: URL extraction
|
|
96
96
|
url = page.url
|
|
97
|
-
match = re.search(r
|
|
97
|
+
match = re.search(r"/pubmed/(\d+)", url)
|
|
98
98
|
if match:
|
|
99
99
|
return match.group(1)
|
|
100
100
|
|
|
101
|
-
match = re.search(r
|
|
101
|
+
match = re.search(r"pubmed\.ncbi\.nlm\.nih\.gov/(\d+)", url)
|
|
102
102
|
if match:
|
|
103
103
|
return match.group(1)
|
|
104
104
|
|
|
@@ -119,11 +119,11 @@ class PubMedTranslator(BaseTranslator):
|
|
|
119
119
|
"""
|
|
120
120
|
try:
|
|
121
121
|
params = {
|
|
122
|
-
|
|
123
|
-
|
|
124
|
-
|
|
125
|
-
|
|
126
|
-
|
|
122
|
+
"db": "PubMed",
|
|
123
|
+
"tool": "ZoteroTranslatorsPython",
|
|
124
|
+
"retmode": "xml",
|
|
125
|
+
"rettype": "citation",
|
|
126
|
+
"id": pmid,
|
|
127
127
|
}
|
|
128
128
|
|
|
129
129
|
async with httpx.AsyncClient(timeout=30.0) as client:
|
|
@@ -132,13 +132,16 @@ class PubMedTranslator(BaseTranslator):
|
|
|
132
132
|
xml_text = response.text
|
|
133
133
|
|
|
134
134
|
# Check if valid PubMed data was returned (case-insensitive)
|
|
135
|
-
if
|
|
135
|
+
if (
|
|
136
|
+
"pubmedarticle" not in xml_text.lower()
|
|
137
|
+
and "pubmedbookarticle" not in xml_text.lower()
|
|
138
|
+
):
|
|
136
139
|
logger.warning(f"No PubMed data found for PMID {pmid}")
|
|
137
140
|
return None
|
|
138
141
|
|
|
139
142
|
# Parse XML to extract metadata
|
|
140
143
|
metadata = cls._parse_pubmed_xml(xml_text)
|
|
141
|
-
metadata[
|
|
144
|
+
metadata["pmid"] = pmid
|
|
142
145
|
return metadata
|
|
143
146
|
|
|
144
147
|
except Exception as e:
|
|
@@ -155,54 +158,56 @@ class PubMedTranslator(BaseTranslator):
|
|
|
155
158
|
Returns:
|
|
156
159
|
Dictionary containing parsed metadata
|
|
157
160
|
"""
|
|
158
|
-
soup = BeautifulSoup(xml_text,
|
|
161
|
+
soup = BeautifulSoup(xml_text, "xml")
|
|
159
162
|
metadata = {}
|
|
160
163
|
|
|
161
164
|
try:
|
|
162
165
|
# Extract article title
|
|
163
|
-
article_title = soup.find(
|
|
166
|
+
article_title = soup.find("ArticleTitle")
|
|
164
167
|
if article_title:
|
|
165
|
-
metadata[
|
|
168
|
+
metadata["title"] = article_title.get_text(strip=True)
|
|
166
169
|
|
|
167
170
|
# Extract authors
|
|
168
171
|
authors = []
|
|
169
|
-
for author in soup.find_all(
|
|
170
|
-
last_name = author.find(
|
|
171
|
-
fore_name = author.find(
|
|
172
|
+
for author in soup.find_all("Author"):
|
|
173
|
+
last_name = author.find("LastName")
|
|
174
|
+
fore_name = author.find("ForeName")
|
|
172
175
|
if last_name:
|
|
173
176
|
author_name = last_name.get_text(strip=True)
|
|
174
177
|
if fore_name:
|
|
175
178
|
author_name = f"{fore_name.get_text(strip=True)} {author_name}"
|
|
176
179
|
authors.append(author_name)
|
|
177
|
-
metadata[
|
|
180
|
+
metadata["authors"] = authors
|
|
178
181
|
|
|
179
182
|
# Extract DOI
|
|
180
|
-
article_ids = soup.find_all(
|
|
183
|
+
article_ids = soup.find_all("ArticleId", attrs={"IdType": "doi"})
|
|
181
184
|
if article_ids:
|
|
182
|
-
metadata[
|
|
185
|
+
metadata["doi"] = article_ids[0].get_text(strip=True)
|
|
183
186
|
|
|
184
187
|
# Extract abstract
|
|
185
|
-
abstract = soup.find(
|
|
188
|
+
abstract = soup.find("AbstractText")
|
|
186
189
|
if abstract:
|
|
187
|
-
metadata[
|
|
190
|
+
metadata["abstract"] = abstract.get_text(strip=True)
|
|
188
191
|
|
|
189
192
|
# Extract journal information
|
|
190
|
-
journal = soup.find(
|
|
193
|
+
journal = soup.find("Journal")
|
|
191
194
|
if journal:
|
|
192
|
-
journal_title = journal.find(
|
|
195
|
+
journal_title = journal.find("Title")
|
|
193
196
|
if journal_title:
|
|
194
|
-
metadata[
|
|
197
|
+
metadata["journal"] = journal_title.get_text(strip=True)
|
|
195
198
|
|
|
196
|
-
journal_abbrev = journal.find(
|
|
199
|
+
journal_abbrev = journal.find("ISOAbbreviation")
|
|
197
200
|
if journal_abbrev:
|
|
198
|
-
metadata[
|
|
201
|
+
metadata["journal_abbreviation"] = journal_abbrev.get_text(
|
|
202
|
+
strip=True
|
|
203
|
+
)
|
|
199
204
|
|
|
200
205
|
# Extract publication date
|
|
201
|
-
pub_date = soup.find(
|
|
206
|
+
pub_date = soup.find("PubDate")
|
|
202
207
|
if pub_date:
|
|
203
|
-
year = pub_date.find(
|
|
204
|
-
month = pub_date.find(
|
|
205
|
-
day = pub_date.find(
|
|
208
|
+
year = pub_date.find("Year")
|
|
209
|
+
month = pub_date.find("Month")
|
|
210
|
+
day = pub_date.find("Day")
|
|
206
211
|
date_parts = []
|
|
207
212
|
if year:
|
|
208
213
|
date_parts.append(year.get_text(strip=True))
|
|
@@ -210,21 +215,21 @@ class PubMedTranslator(BaseTranslator):
|
|
|
210
215
|
date_parts.append(month.get_text(strip=True))
|
|
211
216
|
if day:
|
|
212
217
|
date_parts.append(day.get_text(strip=True))
|
|
213
|
-
metadata[
|
|
218
|
+
metadata["date"] = "-".join(date_parts)
|
|
214
219
|
|
|
215
220
|
# Extract volume and issue
|
|
216
|
-
volume = soup.find(
|
|
221
|
+
volume = soup.find("Volume")
|
|
217
222
|
if volume:
|
|
218
|
-
metadata[
|
|
223
|
+
metadata["volume"] = volume.get_text(strip=True)
|
|
219
224
|
|
|
220
|
-
issue = soup.find(
|
|
225
|
+
issue = soup.find("Issue")
|
|
221
226
|
if issue:
|
|
222
|
-
metadata[
|
|
227
|
+
metadata["issue"] = issue.get_text(strip=True)
|
|
223
228
|
|
|
224
229
|
# Extract pages
|
|
225
|
-
medline_pgn = soup.find(
|
|
230
|
+
medline_pgn = soup.find("MedlinePgn")
|
|
226
231
|
if medline_pgn:
|
|
227
|
-
metadata[
|
|
232
|
+
metadata["pages"] = medline_pgn.get_text(strip=True)
|
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except Exception as e:
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logger.error(f"Error parsing PubMed XML: {e}")
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@@ -242,31 +247,31 @@ class PubMedTranslator(BaseTranslator):
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try:
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content = await page.content()
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-
soup = BeautifulSoup(content,
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+
soup = BeautifulSoup(content, "html.parser")
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# Look for "Full Text Links" section
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-
full_text_section = soup.find(
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+
full_text_section = soup.find("div", class_=re.compile(r"full-text-links"))
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if full_text_section:
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-
links = full_text_section.find_all(
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+
links = full_text_section.find_all("a", href=True)
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for link in links:
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-
href = link[
|
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+
href = link["href"]
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# Filter for likely PDF links
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254
|
-
if any(x in href.lower() for x in [
|
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+
if any(x in href.lower() for x in [".pdf", "download", "pdf"]):
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pdf_urls.append(href)
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|
# Look for LinkOut resources
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-
linkout_section = soup.find(
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+
linkout_section = soup.find("div", attrs={"id": "link-out"})
|
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259
264
|
if linkout_section:
|
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-
links = linkout_section.find_all(
|
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+
links = linkout_section.find_all("a", href=True)
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266
|
for link in links:
|
|
262
|
-
href = link[
|
|
263
|
-
if
|
|
267
|
+
href = link["href"]
|
|
268
|
+
if "pdf" in href.lower():
|
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264
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|
pdf_urls.append(href)
|
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265
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|
|
|
266
271
|
# PMC (PubMed Central) link - free full text
|
|
267
|
-
pmc_link = soup.find(
|
|
268
|
-
if pmc_link and pmc_link.get(
|
|
269
|
-
pdf_urls.append(pmc_link[
|
|
272
|
+
pmc_link = soup.find("a", attrs={"data-ga-action": "PMC article"})
|
|
273
|
+
if pmc_link and pmc_link.get("href"):
|
|
274
|
+
pdf_urls.append(pmc_link["href"])
|
|
270
275
|
|
|
271
276
|
except Exception as e:
|
|
272
277
|
logger.error(f"Error extracting PDF URLs: {e}")
|
|
@@ -292,7 +297,7 @@ async def main():
|
|
|
292
297
|
page = await browser.new_page()
|
|
293
298
|
|
|
294
299
|
try:
|
|
295
|
-
await page.goto(test_url, wait_until=
|
|
300
|
+
await page.goto(test_url, wait_until="domcontentloaded", timeout=30000)
|
|
296
301
|
|
|
297
302
|
# Extract PMID
|
|
298
303
|
pmid = await PubMedTranslator.extract_pmid_from_page(page)
|
|
@@ -321,4 +326,5 @@ async def main():
|
|
|
321
326
|
|
|
322
327
|
if __name__ == "__main__":
|
|
323
328
|
import asyncio
|
|
329
|
+
|
|
324
330
|
asyncio.run(main())
|
|
@@ -12,7 +12,9 @@ class PubMedCentralTranslator(BaseTranslator):
|
|
|
12
12
|
"""PubMed Central."""
|
|
13
13
|
|
|
14
14
|
LABEL = "PubMed Central"
|
|
15
|
-
URL_TARGET_PATTERN =
|
|
15
|
+
URL_TARGET_PATTERN = (
|
|
16
|
+
r"^https://(www\.)?(pmc\.ncbi\.nlm\.nih\.gov/|ncbi\.nlm\.nih\.gov/pmc)"
|
|
17
|
+
)
|
|
16
18
|
|
|
17
19
|
@classmethod
|
|
18
20
|
def matches_url(cls, url: str) -> bool:
|
|
@@ -37,7 +39,7 @@ class PubMedCentralTranslator(BaseTranslator):
|
|
|
37
39
|
current_url = page.url
|
|
38
40
|
|
|
39
41
|
# Check if already viewing a PDF
|
|
40
|
-
if re.search(r
|
|
42
|
+
if re.search(r"/pdf/.+\.pdf", current_url):
|
|
41
43
|
return [current_url]
|
|
42
44
|
|
|
43
45
|
# Try multiple selectors (from JavaScript translator lines 70-74)
|
|
@@ -53,12 +55,12 @@ class PubMedCentralTranslator(BaseTranslator):
|
|
|
53
55
|
try:
|
|
54
56
|
elements = await page.query_selector_all(selector)
|
|
55
57
|
for element in elements:
|
|
56
|
-
href = await element.get_attribute(
|
|
57
|
-
if href and
|
|
58
|
+
href = await element.get_attribute("href")
|
|
59
|
+
if href and ".pdf" in href.lower():
|
|
58
60
|
# Make absolute URL if relative
|
|
59
|
-
if href.startswith(
|
|
61
|
+
if href.startswith("/"):
|
|
60
62
|
href = f"https://www.ncbi.nlm.nih.gov{href}"
|
|
61
|
-
elif not href.startswith(
|
|
63
|
+
elif not href.startswith("http"):
|
|
62
64
|
href = f"https://www.ncbi.nlm.nih.gov/pmc/{href}"
|
|
63
65
|
|
|
64
66
|
if href not in pdf_urls:
|
|
@@ -12,7 +12,9 @@ class RechtspraakNlTranslator(BaseTranslator):
|
|
|
12
12
|
"""Rechtspraak.nl."""
|
|
13
13
|
|
|
14
14
|
LABEL = "Rechtspraak.nl"
|
|
15
|
-
URL_TARGET_PATTERN =
|
|
15
|
+
URL_TARGET_PATTERN = (
|
|
16
|
+
r"^https?://(uitspraken\.rechtspraak|linkeddata\.overheid)\.nl/"
|
|
17
|
+
)
|
|
16
18
|
|
|
17
19
|
@classmethod
|
|
18
20
|
def matches_url(cls, url: str) -> bool:
|