From 88a4bddc89ba26827d66c95da3ea528c71daca0a Mon Sep 17 00:00:00 2001 From: uermel Date: Tue, 7 Jan 2025 14:24:49 -0800 Subject: [PATCH 01/10] grid01 migrated --- ingestion_tools/dataset_configs/10426.yaml | 52 +++++++++++++++++----- 1 file changed, 40 insertions(+), 12 deletions(-) diff --git a/ingestion_tools/dataset_configs/10426.yaml b/ingestion_tools/dataset_configs/10426.yaml index 308eec46a..8a4a4bdd5 100644 --- a/ingestion_tools/dataset_configs/10426.yaml +++ b/ingestion_tools/dataset_configs/10426.yaml @@ -1,15 +1,20 @@ -annotations: [] -collection_metadata: -- sources: +alignments: +- metadata: + format: IMOD + method_type: fiducial_based + sources: - source_multi_glob: list_globs: - - mdocs/{mdoc_name} -dataset_keyphotos: + - alignmentfiles/{run_name}_binalign8_fid.tlt + - alignmentfiles/{run_name}_binalign8_fid.xf + +annotations: [] + +collection_metadata: - sources: - - literal: - value: - snapshot: null - thumbnail: null + - source_glob: + list_glob: 'mdocs/{mdoc_name}' + datasets: - metadata: authors: &id001 @@ -68,6 +73,7 @@ datasets: - literal: value: - '10426' + depositions: - metadata: authors: *id001 @@ -84,20 +90,38 @@ depositions: - literal: value: - 10306 + +deposition_keyphotos: +- sources: + - literal: + value: + snapshot: null #"cryoetportal-rawdatasets-dev/deposition_key_photos/deposition_10306_snapshot.png" + thumbnail: null #"cryoetportal-rawdatasets-dev/deposition_key_photos/deposition_10306_thumbnail.png" + frames: - sources: - source_glob: - list_glob: frames/{frame_prefix}*.mrc + list_glob: 'frames/{frame_prefix}*.mrc' + +gains: [] + +rawtilts: + - sources: + - source_glob: + list_glob: 'rawtilts/{run_name}.rawtlt' + runs: - sources: - source_glob: list_glob: tomograms_bin8/* match_regex: \.rec$ name_regex: (.*)_binalign8.rec + standardization_config: deposition_id: 10306 run_data_map_file: run_to_data_map.tsv source_prefix: kem_sochacki_06_2024/grid01/ + tiltseries: - metadata: acceleration_voltage: 300000 @@ -124,7 +148,9 @@ tiltseries: total_flux: float {tilt_series_total_flux} sources: - source_glob: - list_glob: validation_placeholder/for_unavailable_ts.st + list_glob: 'tilt_series/{run_name}_binalign8.st' + match_regex: ^.*\.st$ + tomograms: - metadata: affine_transformation_matrix: @@ -160,9 +186,11 @@ tomograms: voxel_spacing: 8.66 sources: - source_glob: - list_glob: tomograms_bin8/{run_name}_binalign8.rec + list_glob: 'tomograms_bin8/{run_name}_binalign8.rec' match_regex: (.*)\.rec + version: 1.1.0 + voxel_spacings: - sources: - literal: From 3803726f670d762b5985293ab968d8234c0103cb Mon Sep 17 00:00:00 2001 From: uermel Date: Tue, 7 Jan 2025 15:08:31 -0800 Subject: [PATCH 02/10] all migrated. --- ingestion_tools/dataset_configs/10426.yaml | 2 +- ingestion_tools/dataset_configs/10427.yaml | 43 ++++++++++++++++------ ingestion_tools/dataset_configs/10428.yaml | 43 ++++++++++++++++------ ingestion_tools/dataset_configs/10429.yaml | 43 ++++++++++++++++------ ingestion_tools/dataset_configs/10430.yaml | 43 ++++++++++++++++------ ingestion_tools/dataset_configs/10431.yaml | 43 ++++++++++++++++------ ingestion_tools/dataset_configs/10432.yaml | 43 ++++++++++++++++------ ingestion_tools/dataset_configs/10433.yaml | 41 ++++++++++++++++----- ingestion_tools/dataset_configs/10434.yaml | 43 ++++++++++++++++------ ingestion_tools/dataset_configs/10435.yaml | 43 ++++++++++++++++------ 10 files changed, 287 insertions(+), 100 deletions(-) diff --git a/ingestion_tools/dataset_configs/10426.yaml b/ingestion_tools/dataset_configs/10426.yaml index 8a4a4bdd5..086f5dc20 100644 --- a/ingestion_tools/dataset_configs/10426.yaml +++ b/ingestion_tools/dataset_configs/10426.yaml @@ -83,7 +83,7 @@ depositions: and evaluation of the unroofing method for preparation of plasma membranes and associated proteins. deposition_identifier: 10306 - deposition_title: Unroofed eukaryotic cells. + deposition_title: Human plasma membranes isolated using the unroofing method. deposition_types: - dataset sources: diff --git a/ingestion_tools/dataset_configs/10427.yaml b/ingestion_tools/dataset_configs/10427.yaml index 3a1a1c648..1a846e1cb 100644 --- a/ingestion_tools/dataset_configs/10427.yaml +++ b/ingestion_tools/dataset_configs/10427.yaml @@ -1,15 +1,20 @@ -annotations: [] -collection_metadata: -- sources: +alignments: +- metadata: + format: IMOD + method_type: fiducial_based + sources: - source_multi_glob: list_globs: - - mdocs/{mdoc_name} -dataset_keyphotos: + - alignmentfiles/{run_name}_binalign8_fid.tlt + - alignmentfiles/{run_name}_binalign8_fid.xf + +annotations: [] + +collection_metadata: - sources: - - literal: - value: - snapshot: null - thumbnail: null + - source_glob: + list_glob: 'mdocs/{mdoc_name}' + datasets: - metadata: authors: &id001 @@ -68,11 +73,13 @@ datasets: - literal: value: - '10427' + depositions: - sources: - literal: value: - 10306 + frames: - sources: - parent_filters: @@ -229,16 +236,26 @@ frames: source_glob: list_glob: frames/*.tif match_regex: (tomo_unroof_control_c2d1_01692_\-50\.0\.tif|tomo_unroof_control_c2d1_01691_\-48\.0\.tif|tomo_unroof_control_c2d1_01690_\-46\.0\.tif|tomo_unroof_control_c2d1_01689_\-44\.0\.tif|tomo_unroof_control_c2d1_01688_\-42\.0\.tif|tomo_unroof_control_c2d1_01687_\-40\.0\.tif|tomo_unroof_control_c2d1_01686_\-38\.0\.tif|tomo_unroof_control_c2d1_01678_\-36\.0\.tif|tomo_unroof_control_c2d1_01677_\-34\.0\.tif|tomo_unroof_control_c2d1_01676_\-32\.0\.tif|tomo_unroof_control_c2d1_01672_\-30\.0\.tif|tomo_unroof_control_c2d1_01671_\-28\.0\.tif|tomo_unroof_control_c2d1_01670_\-26\.0\.tif|tomo_unroof_control_c2d1_01666_\-24\.0\.tif|tomo_unroof_control_c2d1_01665_\-22\.0\.tif|tomo_unroof_control_c2d1_01664_\-20\.0\.tif|tomo_unroof_control_c2d1_01660_\-18\.0\.tif|tomo_unroof_control_c2d1_01659_\-16\.0\.tif|tomo_unroof_control_c2d1_01658_\-14\.0\.tif|tomo_unroof_control_c2d1_01654_\-12\.0\.tif|tomo_unroof_control_c2d1_01653_\-10\.0\.tif|tomo_unroof_control_c2d1_01652_\-8\.0\.tif|tomo_unroof_control_c2d1_01648_\-6\.0\.tif|tomo_unroof_control_c2d1_01647_\-4\.0\.tif|tomo_unroof_control_c2d1_01646_\-2\.0\.tif|tomo_unroof_control_c2d1_01642_\-0\.0\.tif|tomo_unroof_control_c2d1_01643_2\.0\.tif|tomo_unroof_control_c2d1_01644_4\.0\.tif|tomo_unroof_control_c2d1_01645_6\.0\.tif|tomo_unroof_control_c2d1_01649_8\.0\.tif|tomo_unroof_control_c2d1_01650_10\.0\.tif|tomo_unroof_control_c2d1_01651_12\.0\.tif|tomo_unroof_control_c2d1_01655_14\.0\.tif|tomo_unroof_control_c2d1_01656_16\.0\.tif|tomo_unroof_control_c2d1_01657_18\.0\.tif|tomo_unroof_control_c2d1_01661_20\.0\.tif|tomo_unroof_control_c2d1_01662_22\.0\.tif|tomo_unroof_control_c2d1_01663_24\.0\.tif|tomo_unroof_control_c2d1_01667_26\.0\.tif|tomo_unroof_control_c2d1_01668_28\.0\.tif|tomo_unroof_control_c2d1_01669_30\.0\.tif|tomo_unroof_control_c2d1_01673_32\.0\.tif|tomo_unroof_control_c2d1_01674_34\.0\.tif|tomo_unroof_control_c2d1_01675_36\.0\.tif|tomo_unroof_control_c2d1_01679_38\.0\.tif|tomo_unroof_control_c2d1_01680_40\.0\.tif|tomo_unroof_control_c2d1_01681_42\.0\.tif|tomo_unroof_control_c2d1_01682_44\.0\.tif|tomo_unroof_control_c2d1_01683_46\.0\.tif|tomo_unroof_control_c2d1_01684_48\.0\.tif|tomo_unroof_control_c2d1_01685_50\.0\.tif) + +gains: [] + +rawtilts: + - sources: + - source_glob: + list_glob: 'rawtilts/{run_name}.rawtlt' + runs: - sources: - source_glob: list_glob: tomograms_bin8/* match_regex: \.rec$ name_regex: (.*)_binalign8.rec + standardization_config: deposition_id: 10306 run_data_map_file: run_to_data_map.tsv source_prefix: kem_sochacki_06_2024/grid02/ + tiltseries: - metadata: acceleration_voltage: 300000 @@ -265,7 +282,9 @@ tiltseries: total_flux: float {tilt_series_total_flux} sources: - source_glob: - list_glob: validation_placeholder/for_unavailable_ts.st + list_glob: 'tilt_series/{run_name}_binalign8.st' + match_regex: ^.*\.st$ + tomograms: - metadata: affine_transformation_matrix: @@ -304,9 +323,11 @@ tomograms: voxel_spacing: 8.627 sources: - source_glob: - list_glob: tomograms_bin8/{run_name}_binalign8.rec + list_glob: 'tomograms_bin8/{run_name}_binalign8.rec' match_regex: (.*)\.rec + version: 1.1.0 + voxel_spacings: - sources: - literal: diff --git a/ingestion_tools/dataset_configs/10428.yaml b/ingestion_tools/dataset_configs/10428.yaml index 166b6ed6e..c99299130 100644 --- a/ingestion_tools/dataset_configs/10428.yaml +++ b/ingestion_tools/dataset_configs/10428.yaml @@ -1,15 +1,20 @@ -annotations: [] -collection_metadata: -- sources: +alignments: +- metadata: + format: IMOD + method_type: fiducial_based + sources: - source_multi_glob: list_globs: - - mdocs/{mdoc_name} -dataset_keyphotos: + - alignmentfiles/{run_name}_bin8_align_fid.tlt + - alignmentfiles/{run_name}_bin8_align_fid.xf + +annotations: [] + +collection_metadata: - sources: - - literal: - value: - snapshot: null - thumbnail: null + - source_glob: + list_glob: 'mdocs/{mdoc_name}' + datasets: - metadata: authors: &id001 @@ -70,25 +75,37 @@ datasets: - literal: value: - '10428' + depositions: - sources: - literal: value: - 10306 + frames: - sources: - source_glob: list_glob: frames/{frame_prefix}*.tif + +gains: [] + +rawtilts: + - sources: + - source_glob: + list_glob: 'rawtilts/{run_name}.rawtlt' + runs: - sources: - source_glob: list_glob: tomograms_bin8/* match_regex: \.rec$ name_regex: (.*)_bin8_align.rec + standardization_config: deposition_id: 10306 run_data_map_file: run_to_data_map.tsv source_prefix: kem_sochacki_06_2024/grid03/ + tiltseries: - metadata: acceleration_voltage: 300000 @@ -115,7 +132,9 @@ tiltseries: total_flux: float {tilt_series_total_flux} sources: - source_glob: - list_glob: validation_placeholder/for_unavailable_ts.st + list_glob: 'tilt_series/{run_name}_bin8_align.st' + match_regex: ^.*\.st$ + tomograms: - metadata: affine_transformation_matrix: @@ -154,9 +173,11 @@ tomograms: voxel_spacing: 8.627 sources: - source_glob: - list_glob: tomograms_bin8/{run_name}_bin8_align.rec + list_glob: 'tomograms_bin8/{run_name}_bin8_align.rec' match_regex: (.*)\.rec + version: 1.1.0 + voxel_spacings: - sources: - literal: diff --git a/ingestion_tools/dataset_configs/10429.yaml b/ingestion_tools/dataset_configs/10429.yaml index 45630ab47..149f06507 100644 --- a/ingestion_tools/dataset_configs/10429.yaml +++ b/ingestion_tools/dataset_configs/10429.yaml @@ -1,15 +1,20 @@ -annotations: [] -collection_metadata: -- sources: +alignments: +- metadata: + format: IMOD + method_type: fiducial_based + sources: - source_multi_glob: list_globs: - - mdocs/{mdoc_name} -dataset_keyphotos: + - alignmentfiles/{run_name}_bin8_align_fid.tlt + - alignmentfiles/{run_name}_bin8_align_fid.xf + +annotations: [] + +collection_metadata: - sources: - - literal: - value: - snapshot: null - thumbnail: null + - source_glob: + list_glob: 'mdocs/{mdoc_name}' + datasets: - metadata: authors: &id001 @@ -70,25 +75,37 @@ datasets: - literal: value: - '10429' + depositions: - sources: - literal: value: - 10306 + frames: - sources: - source_glob: list_glob: frames/{frame_prefix}*.mrc + +gains: [] + +rawtilts: + - sources: + - source_glob: + list_glob: 'rawtilts/{run_name}.rawtlt' + runs: - sources: - source_glob: list_glob: tomograms_bin8/* match_regex: \.rec$ name_regex: (.*)_bin8_align.rec + standardization_config: deposition_id: 10306 run_data_map_file: run_to_data_map.tsv source_prefix: kem_sochacki_06_2024/grid04/ + tiltseries: - metadata: acceleration_voltage: 300000 @@ -115,7 +132,9 @@ tiltseries: total_flux: float {tilt_series_total_flux} sources: - source_glob: - list_glob: validation_placeholder/for_unavailable_ts.st + list_glob: 'tilt_series/{run_name}_bin8_align.st' + match_regex: ^.*\.st$ + tomograms: - metadata: affine_transformation_matrix: @@ -154,9 +173,11 @@ tomograms: voxel_spacing: 8.464 sources: - source_glob: - list_glob: tomograms_bin8/{run_name}_bin8_align.rec + list_glob: 'tomograms_bin8/{run_name}_bin8_align.rec' match_regex: (.*)\.rec + version: 1.1.0 + voxel_spacings: - sources: - literal: diff --git a/ingestion_tools/dataset_configs/10430.yaml b/ingestion_tools/dataset_configs/10430.yaml index 54090a9a8..bad8fef42 100644 --- a/ingestion_tools/dataset_configs/10430.yaml +++ b/ingestion_tools/dataset_configs/10430.yaml @@ -1,15 +1,20 @@ -annotations: [] -collection_metadata: -- sources: +alignments: +- metadata: + format: IMOD + method_type: fiducial_based + sources: - source_multi_glob: list_globs: - - mdocs/{mdoc_name} -dataset_keyphotos: + - alignmentfiles/{run_name}_fid.tlt + - alignmentfiles/{run_name}_fid.xf + +annotations: [] + +collection_metadata: - sources: - - literal: - value: - snapshot: null - thumbnail: null + - source_glob: + list_glob: 'mdocs/{mdoc_name}' + datasets: - metadata: authors: &id001 @@ -78,17 +83,27 @@ depositions: frames: - sources: - source_glob: - list_glob: frames/{frame_prefix}*.mrc + list_glob: 'frames/{frame_prefix}*.mrc' + +gains: [] + +rawtilts: + - sources: + - source_glob: + list_glob: 'rawtilts/{run_name}.rawtlt' + runs: - sources: - source_glob: list_glob: tomograms_bin10/* match_regex: \.mrc$ name_regex: (.*)_b10_rec.mrc + standardization_config: deposition_id: 10306 run_data_map_file: run_to_data_map.tsv source_prefix: kem_sochacki_06_2024/grid05/ + tiltseries: - metadata: acceleration_voltage: 300000 @@ -115,7 +130,9 @@ tiltseries: total_flux: float {tilt_series_total_flux} sources: - source_glob: - list_glob: validation_placeholder/for_unavailable_ts.st + list_glob: 'tiltseries/{run_name}.mrc' + match_regex: ^.*\.mrc$ + tomograms: - metadata: affine_transformation_matrix: @@ -154,9 +171,11 @@ tomograms: voxel_spacing: 10.825 sources: - source_glob: - list_glob: tomograms_bin10/{run_name}_b10_rec.mrc + list_glob: 'tomograms_bin10/{run_name}_b10_rec.mrc' match_regex: (.*)\.mrc + version: 1.1.0 + voxel_spacings: - sources: - literal: diff --git a/ingestion_tools/dataset_configs/10431.yaml b/ingestion_tools/dataset_configs/10431.yaml index 5ed5a1f13..a1a254edc 100644 --- a/ingestion_tools/dataset_configs/10431.yaml +++ b/ingestion_tools/dataset_configs/10431.yaml @@ -1,15 +1,20 @@ -annotations: [] -collection_metadata: -- sources: +alignments: +- metadata: + format: IMOD + method_type: fiducial_based + sources: - source_multi_glob: list_globs: - - mdocs/{mdoc_name} -dataset_keyphotos: + - alignmentfiles/{run_name}_bin8_align_fid.tlt + - alignmentfiles/{run_name}_bin8_align_fid.xf + +annotations: [] + +collection_metadata: - sources: - - literal: - value: - snapshot: null - thumbnail: null + - source_glob: + list_glob: 'mdocs/{mdoc_name}' + datasets: - metadata: authors: &id001 @@ -72,25 +77,37 @@ datasets: - literal: value: - '10431' + depositions: - sources: - literal: value: - 10306 + frames: - sources: - source_glob: list_glob: frames/{frame_prefix}*.mrc + +gains: [] + +rawtilts: + - sources: + - source_glob: + list_glob: 'rawtilts/{run_name}.rawtlt' + runs: - sources: - source_glob: list_glob: tomograms_bin8/* match_regex: \.rec$ name_regex: (.*)_bin8_align.rec + standardization_config: deposition_id: 10306 run_data_map_file: run_to_data_map.tsv source_prefix: kem_sochacki_06_2024/grid06/ + tiltseries: - metadata: acceleration_voltage: 300000 @@ -117,7 +134,9 @@ tiltseries: total_flux: float {tilt_series_total_flux} sources: - source_glob: - list_glob: validation_placeholder/for_unavailable_ts.st + list_glob: 'tilt_series/{run_name}_bin8_align.st' + match_regex: ^.*\.st$ + tomograms: - metadata: affine_transformation_matrix: @@ -156,9 +175,11 @@ tomograms: voxel_spacing: 8.464 sources: - source_glob: - list_glob: tomograms_bin8/{run_name}_bin8_align.rec + list_glob: 'tomograms_bin8/{run_name}_bin8_align.rec' match_regex: (.*)\.rec + version: 1.1.0 + voxel_spacings: - sources: - literal: diff --git a/ingestion_tools/dataset_configs/10432.yaml b/ingestion_tools/dataset_configs/10432.yaml index fd3873214..f25de6103 100644 --- a/ingestion_tools/dataset_configs/10432.yaml +++ b/ingestion_tools/dataset_configs/10432.yaml @@ -1,15 +1,20 @@ -annotations: [] -collection_metadata: -- sources: +alignments: +- metadata: + format: IMOD + method_type: fiducial_based + sources: - source_multi_glob: list_globs: - - mdocs/{mdoc_name} -dataset_keyphotos: + - alignmentfiles/{run_name}_bin8_align_fid.tlt + - alignmentfiles/{run_name}_bin8_align_fid.xf + +annotations: [] + +collection_metadata: - sources: - - literal: - value: - snapshot: null - thumbnail: null + - source_glob: + list_glob: 'mdocs/{mdoc_name}' + datasets: - metadata: authors: &id001 @@ -72,25 +77,37 @@ datasets: - literal: value: - '10432' + depositions: - sources: - literal: value: - 10306 + frames: - sources: - source_glob: list_glob: frames/{frame_prefix}*.tif + +gains: [] + +rawtilts: + - sources: + - source_glob: + list_glob: 'rawtilts/{run_name}.rawtlt' + runs: - sources: - source_glob: list_glob: tomograms_bin8/* match_regex: \.rec$ name_regex: (.*)_bin8_align.rec + standardization_config: deposition_id: 10306 run_data_map_file: run_to_data_map.tsv source_prefix: kem_sochacki_06_2024/grid07/ + tiltseries: - metadata: acceleration_voltage: 300000 @@ -117,7 +134,9 @@ tiltseries: total_flux: float {tilt_series_total_flux} sources: - source_glob: - list_glob: validation_placeholder/for_unavailable_ts.st + list_glob: 'tilt_series/{run_name}_bin8_align.st' + match_regex: ^.*\.st$ + tomograms: - metadata: affine_transformation_matrix: @@ -156,9 +175,11 @@ tomograms: voxel_spacing: 8.627 sources: - source_glob: - list_glob: tomograms_bin8/{run_name}_bin8_align.rec + list_glob: 'tomograms_bin8/{run_name}_bin8_align.rec' match_regex: (.*)\.rec + version: 1.1.0 + voxel_spacings: - sources: - literal: diff --git a/ingestion_tools/dataset_configs/10433.yaml b/ingestion_tools/dataset_configs/10433.yaml index a1a220b7a..52c4010e7 100644 --- a/ingestion_tools/dataset_configs/10433.yaml +++ b/ingestion_tools/dataset_configs/10433.yaml @@ -1,15 +1,20 @@ -annotations: [] -collection_metadata: -- sources: +alignments: +- metadata: + format: IMOD + method_type: fiducial_based + sources: - source_multi_glob: list_globs: - - mdocs/{mdoc_name} -dataset_keyphotos: + - alignmentfiles/{run_name}_bin8_align_fid.tlt + - alignmentfiles/{run_name}_bin8_align_fid.xf + +annotations: [] + +collection_metadata: - sources: - - literal: - value: - snapshot: null - thumbnail: null + - source_glob: + list_glob: 'mdocs/{mdoc_name}' + datasets: - metadata: authors: &id001 @@ -72,25 +77,37 @@ datasets: - literal: value: - '10433' + depositions: - sources: - literal: value: - 10306 + frames: - sources: - source_glob: list_glob: frames/{frame_prefix}*.tif + +gains: [] + +rawtilts: + - sources: + - source_glob: + list_glob: 'rawtilts/{run_name}.rawtlt' + runs: - sources: - source_glob: list_glob: tomograms_bin8/* match_regex: \.rec$ name_regex: (.*)_bin8_align.rec + standardization_config: deposition_id: 10306 run_data_map_file: run_to_data_map.tsv source_prefix: kem_sochacki_06_2024/grid08/ + tiltseries: - metadata: acceleration_voltage: 300000 @@ -117,7 +134,9 @@ tiltseries: total_flux: float {tilt_series_total_flux} sources: - source_glob: - list_glob: validation_placeholder/for_unavailable_ts.st + list_glob: 'raw_tilt_series/{run_name}_bin8_align.st' + match_regex: ^.*\.st$ + tomograms: - metadata: affine_transformation_matrix: @@ -158,7 +177,9 @@ tomograms: - source_glob: list_glob: tomograms_bin8/{run_name}_bin8_align.rec match_regex: (.*)\.rec + version: 1.1.0 + voxel_spacings: - sources: - literal: diff --git a/ingestion_tools/dataset_configs/10434.yaml b/ingestion_tools/dataset_configs/10434.yaml index 82470ce5d..0766aedcc 100644 --- a/ingestion_tools/dataset_configs/10434.yaml +++ b/ingestion_tools/dataset_configs/10434.yaml @@ -1,15 +1,20 @@ -annotations: [] -collection_metadata: -- sources: +alignments: +- metadata: + format: IMOD + method_type: fiducial_based + sources: - source_multi_glob: list_globs: - - mdocs/{mdoc_name} -dataset_keyphotos: + - alignmentfiles/{run_name}_bin8_align_fid.tlt + - alignmentfiles/{run_name}_bin8_align_fid.xf + +annotations: [] + +collection_metadata: - sources: - - literal: - value: - snapshot: null - thumbnail: null + - source_glob: + list_glob: 'mdocs/{mdoc_name}' + datasets: - metadata: authors: &id001 @@ -72,25 +77,37 @@ datasets: - literal: value: - '10434' + depositions: - sources: - literal: value: - 10306 + frames: - sources: - source_glob: list_glob: frames/{frame_prefix}*.tif + +gains: [] + +rawtilts: + - sources: + - source_glob: + list_glob: 'rawtilts/{run_name}.rawtlt' + runs: - sources: - source_glob: list_glob: tomograms_bin8/* match_regex: \.rec$ name_regex: (.*)_bin8_align.rec + standardization_config: deposition_id: 10306 run_data_map_file: run_to_data_map.tsv source_prefix: kem_sochacki_06_2024/grid09/ + tiltseries: - metadata: acceleration_voltage: 300000 @@ -117,7 +134,9 @@ tiltseries: total_flux: float {tilt_series_total_flux} sources: - source_glob: - list_glob: validation_placeholder/for_unavailable_ts.st + list_glob: 'raw_tilt_series/{run_name}_bin8_align.st' + match_regex: ^.*\.st$ + tomograms: - metadata: affine_transformation_matrix: @@ -156,9 +175,11 @@ tomograms: voxel_spacing: 8.627 sources: - source_glob: - list_glob: tomograms_bin8/{run_name}_bin8_align.rec + list_glob: 'tomograms_bin8/{run_name}_bin8_align.rec' match_regex: (.*)\.rec + version: 1.1.0 + voxel_spacings: - sources: - literal: diff --git a/ingestion_tools/dataset_configs/10435.yaml b/ingestion_tools/dataset_configs/10435.yaml index 14fc66137..3badfa162 100644 --- a/ingestion_tools/dataset_configs/10435.yaml +++ b/ingestion_tools/dataset_configs/10435.yaml @@ -1,15 +1,20 @@ -annotations: [] -collection_metadata: -- sources: +alignments: +- metadata: + format: IMOD + method_type: fiducial_based + sources: - source_multi_glob: list_globs: - - mdocs/{mdoc_name} -dataset_keyphotos: + - alignmentfiles/{run_name}_bin8_align_fid.tlt + - alignmentfiles/{run_name}_bin8_align_fid.xf + +annotations: [] + +collection_metadata: - sources: - - literal: - value: - snapshot: null - thumbnail: null + - source_glob: + list_glob: 'mdocs/{mdoc_name}' + datasets: - metadata: authors: &id001 @@ -72,25 +77,37 @@ datasets: - literal: value: - '10435' + depositions: - sources: - literal: value: - 10306 + frames: - sources: - source_glob: list_glob: frames/{frame_prefix}*.tif + +gains: [] + +rawtilts: + - sources: + - source_glob: + list_glob: 'rawtilts/{run_name}.rawtlt' + runs: - sources: - source_glob: list_glob: tomograms_bin8/* match_regex: \.rec$ name_regex: (.*)_bin8_align.rec + standardization_config: deposition_id: 10306 run_data_map_file: run_to_data_map.tsv source_prefix: kem_sochacki_06_2024/grid10/ + tiltseries: - metadata: acceleration_voltage: 300000 @@ -117,7 +134,9 @@ tiltseries: total_flux: float {tilt_series_total_flux} sources: - source_glob: - list_glob: validation_placeholder/for_unavailable_ts.st + list_glob: 'raw_tilt_series/{run_name}_bin8_align.st' + match_regex: ^.*\.st + tomograms: - metadata: affine_transformation_matrix: @@ -156,9 +175,11 @@ tomograms: voxel_spacing: 8.627 sources: - source_glob: - list_glob: tomograms_bin8/{run_name}_bin8_align.rec + list_glob: 'tomograms_bin8/{run_name}_bin8_align.rec' match_regex: (.*)\.rec + version: 1.1.0 + voxel_spacings: - sources: - literal: From 3e29f65647de03cab883cd1ddacd3a57b9fff585 Mon Sep 17 00:00:00 2001 From: uermel Date: Tue, 7 Jan 2025 15:43:13 -0800 Subject: [PATCH 03/10] prep for new annotations --- ingestion_tools/dataset_configs/10431.yaml | 38 ++++++++++++++++++++-- 1 file changed, 35 insertions(+), 3 deletions(-) diff --git a/ingestion_tools/dataset_configs/10431.yaml b/ingestion_tools/dataset_configs/10431.yaml index a1a254edc..ccc925905 100644 --- a/ingestion_tools/dataset_configs/10431.yaml +++ b/ingestion_tools/dataset_configs/10431.yaml @@ -8,8 +8,6 @@ alignments: - alignmentfiles/{run_name}_bin8_align_fid.tlt - alignmentfiles/{run_name}_bin8_align_fid.xf -annotations: [] - collection_metadata: - sources: - source_glob: @@ -52,7 +50,7 @@ datasets: with 0.7 bar of paraformaldehyde prior to vitrification. dataset_identifier: 10431 dataset_title: Unroofing Grid06 - dates: + dates: &dataset_dates deposition_date: '2024-07-01' last_modified_date: '2024-07-01' release_date: '2024-07-05' @@ -78,6 +76,40 @@ datasets: value: - '10431' +annotations: [] +#TODO: Uncomment when RELION 5 support is added +# - metadata: +# annotation_method: Segmentation using EMAN2, refinement using Dynamo and RELION +# annotation_object: +# id: GO:0030118 +# name: clathrin coat +# annotation_publications: 10.1101/2024.06.27.600657 +# annotation_software: EMAN2, Dynamo, RELION 4, RELION 5 +# method_links: +# - custom_name: EMAN2 website +# link: https://blake.bcm.edu/emanwiki/EMAN2 +# link_type: website +# - custom_name: Dynamo website +# link: https://www.dynamo-em.org//w/index.php?title=Main_Page +# link_type: source_code +# - custom_name: RELION on GitHub +# link: https://github.com/3dem/relion +# link_type: source_code +# authors: *id001 +# dates: *dataset_dates +# ground_truth_status: false +# is_curator_recommended: true +# method_type: hybrid +# version: 1.0 +# sources: +# - OrientedPoint: +# binning: 10 +# file_format: relion5_star +# glob_strings: +# - 'clathrin_aqb1_refined_particles.star' +# is_visualization_default: true +# order: xyz + depositions: - sources: - literal: From f792022b0ad042b581dee357da69a39598169221 Mon Sep 17 00:00:00 2001 From: Manasa Venkatakrishnan Date: Tue, 7 Jan 2025 15:59:07 -0800 Subject: [PATCH 04/10] Updating schema build --- schema/poetry.lock | 95 ++++++++++++++++++++++++++++++++++++++++++- schema/pyproject.toml | 15 ++++++- 2 files changed, 107 insertions(+), 3 deletions(-) diff --git a/schema/poetry.lock b/schema/poetry.lock index d8415e55b..5efd44eed 100644 --- a/schema/poetry.lock +++ b/schema/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.0.0 and should not be changed by hand. [[package]] name = "aiohappyeyeballs" @@ -6,6 +6,7 @@ version = "2.4.4" description = "Happy Eyeballs for asyncio" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "aiohappyeyeballs-2.4.4-py3-none-any.whl", hash = "sha256:a980909d50efcd44795c4afeca523296716d50cd756ddca6af8c65b996e27de8"}, {file = "aiohappyeyeballs-2.4.4.tar.gz", hash = "sha256:5fdd7d87889c63183afc18ce9271f9b0a7d32c2303e394468dd45d514a757745"}, @@ -17,6 +18,7 @@ version = "3.10.11" description = "Async http client/server framework (asyncio)" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "aiohttp-3.10.11-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:5077b1a5f40ffa3ba1f40d537d3bec4383988ee51fbba6b74aa8fb1bc466599e"}, {file = "aiohttp-3.10.11-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:8d6a14a4d93b5b3c2891fca94fa9d41b2322a68194422bef0dd5ec1e57d7d298"}, @@ -128,6 +130,7 @@ version = "1.3.1" description = "aiosignal: a list of registered asynchronous callbacks" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "aiosignal-1.3.1-py3-none-any.whl", hash = "sha256:f8376fb07dd1e86a584e4fcdec80b36b7f81aac666ebc724e2c090300dd83b17"}, {file = "aiosignal-1.3.1.tar.gz", hash = "sha256:54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc"}, @@ -142,6 +145,7 @@ version = "0.7.0" description = "Reusable constraint types to use with typing.Annotated" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"}, {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, @@ -153,6 +157,7 @@ version = "4.9.3" description = "ANTLR 4.9.3 runtime for Python 3.7" optional = false python-versions = "*" +groups = ["main"] files = [ {file = "antlr4-python3-runtime-4.9.3.tar.gz", hash = "sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b"}, ] @@ -163,6 +168,7 @@ version = "1.3.0" description = "Better dates & times for Python" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "arrow-1.3.0-py3-none-any.whl", hash = "sha256:c728b120ebc00eb84e01882a6f5e7927a53960aa990ce7dd2b10f39005a67f80"}, {file = "arrow-1.3.0.tar.gz", hash = "sha256:d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85"}, @@ -182,6 +188,7 @@ version = "2.0.4" description = "Simple LRU cache for asyncio" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "async-lru-2.0.4.tar.gz", hash = "sha256:b8a59a5df60805ff63220b2a0c5b5393da5521b113cd5465a44eb037d81a5627"}, {file = "async_lru-2.0.4-py3-none-any.whl", hash = "sha256:ff02944ce3c288c5be660c42dbcca0742b32c3b279d6dceda655190240b99224"}, @@ -193,6 +200,7 @@ version = "23.2.0" description = "Classes Without Boilerplate" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"}, {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"}, @@ -212,6 +220,7 @@ version = "24.4.2" description = "The uncompromising code formatter." optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "black-24.4.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:dd1b5a14e417189db4c7b64a6540f31730713d173f0b63e55fabd52d61d8fdce"}, {file = "black-24.4.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:8e537d281831ad0e71007dcdcbe50a71470b978c453fa41ce77186bbe0ed6021"}, @@ -256,6 +265,7 @@ version = "2024.7.4" description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.6" +groups = ["main"] files = [ {file = "certifi-2024.7.4-py3-none-any.whl", hash = "sha256:c198e21b1289c2ab85ee4e67bb4b4ef3ead0892059901a8d5b622f24a1101e90"}, {file = "certifi-2024.7.4.tar.gz", hash = "sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b"}, @@ -267,6 +277,7 @@ version = "0.2.1" description = "rdflib collections flattening graph" optional = false python-versions = "*" +groups = ["main"] files = [ {file = "CFGraph-0.2.1.tar.gz", hash = "sha256:b57fe7044a10b8ff65aa3a8a8ddc7d4cd77bf511b42e57289cd52cbc29f8fe74"}, ] @@ -280,6 +291,7 @@ version = "5.2.0" description = "Universal encoding detector for Python 3" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "chardet-5.2.0-py3-none-any.whl", hash = "sha256:e1cf59446890a00105fe7b7912492ea04b6e6f06d4b742b2c788469e34c82970"}, {file = "chardet-5.2.0.tar.gz", hash = "sha256:1b3b6ff479a8c414bc3fa2c0852995695c4a026dcd6d0633b2dd092ca39c1cf7"}, @@ -291,6 +303,7 @@ version = "3.3.2" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." optional = false python-versions = ">=3.7.0" +groups = ["main"] files = [ {file = "charset-normalizer-3.3.2.tar.gz", hash = "sha256:f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5"}, {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:25baf083bf6f6b341f4121c2f3c548875ee6f5339300e08be3f2b2ba1721cdd3"}, @@ -390,6 +403,7 @@ version = "8.1.7" description = "Composable command line interface toolkit" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"}, {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"}, @@ -404,6 +418,8 @@ version = "0.4.6" description = "Cross-platform colored terminal text." optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" +groups = ["main"] +markers = "platform_system == \"Windows\" or sys_platform == \"win32\"" files = [ {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"}, {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"}, @@ -415,6 +431,7 @@ version = "0.7.10" description = "Idiomatic conversion between URIs and compact URIs (CURIEs)." optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "curies-0.7.10-py3-none-any.whl", hash = "sha256:ad80f420dd76b6f3e921a245370ff6ab7473c48c29c17254970c03cd2e58af5f"}, {file = "curies-0.7.10.tar.gz", hash = "sha256:98a7ceb94710fab3a02727a7f85ba0719dd22be5fc8b5f2ad1d7d4cfc47d64ce"}, @@ -439,6 +456,7 @@ version = "1.2.14" description = "Python @deprecated decorator to deprecate old python classes, functions or methods." optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +groups = ["main"] files = [ {file = "Deprecated-1.2.14-py2.py3-none-any.whl", hash = "sha256:6fac8b097794a90302bdbb17b9b815e732d3c4720583ff1b198499d78470466c"}, {file = "Deprecated-1.2.14.tar.gz", hash = "sha256:e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3"}, @@ -456,6 +474,7 @@ version = "1.1.0" description = "An implementation of lxml.xmlfile for the standard library" optional = false python-versions = ">=3.6" +groups = ["main"] files = [ {file = "et_xmlfile-1.1.0-py3-none-any.whl", hash = "sha256:a2ba85d1d6a74ef63837eed693bcb89c3f752169b0e3e7ae5b16ca5e1b3deada"}, {file = "et_xmlfile-1.1.0.tar.gz", hash = "sha256:8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c"}, @@ -467,6 +486,7 @@ version = "1.5.1" description = "Validates fully-qualified domain names against RFC 1123, so that they are acceptable to modern bowsers" optional = false python-versions = ">=2.7, !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, <4" +groups = ["main"] files = [ {file = "fqdn-1.5.1-py3-none-any.whl", hash = "sha256:3a179af3761e4df6eb2e026ff9e1a3033d3587bf980a0b1b2e1e5d08d7358014"}, {file = "fqdn-1.5.1.tar.gz", hash = "sha256:105ed3677e767fb5ca086a0c1f4bb66ebc3c100be518f0e0d755d9eae164d89f"}, @@ -478,6 +498,7 @@ version = "1.4.1" description = "A list-like structure which implements collections.abc.MutableSequence" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "frozenlist-1.4.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:f9aa1878d1083b276b0196f2dfbe00c9b7e752475ed3b682025ff20c1c1f51ac"}, {file = "frozenlist-1.4.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:29acab3f66f0f24674b7dc4736477bcd4bc3ad4b896f5f45379a67bce8b96868"}, @@ -564,6 +585,7 @@ version = "0.20.3" description = "Simple Python interface for Graphviz" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "graphviz-0.20.3-py3-none-any.whl", hash = "sha256:81f848f2904515d8cd359cc611faba817598d2feaac4027b266aa3eda7b3dde5"}, {file = "graphviz-0.20.3.zip", hash = "sha256:09d6bc81e6a9fa392e7ba52135a9d49f1ed62526f96499325930e87ca1b5925d"}, @@ -580,6 +602,8 @@ version = "3.0.3" description = "Lightweight in-process concurrent programming" optional = false python-versions = ">=3.7" +groups = ["main"] +markers = "python_version < \"3.13\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")" files = [ {file = "greenlet-3.0.3-cp310-cp310-macosx_11_0_universal2.whl", hash = "sha256:9da2bd29ed9e4f15955dd1595ad7bc9320308a3b766ef7f837e23ad4b4aac31a"}, {file = "greenlet-3.0.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:d353cadd6083fdb056bb46ed07e4340b0869c305c8ca54ef9da3421acbdf6881"}, @@ -651,6 +675,7 @@ version = "0.9.1" description = "Honey Badger reader - a generic file/url/string open and read tool" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "hbreader-0.9.1-py3-none-any.whl", hash = "sha256:9a6e76c9d1afc1b977374a5dc430a1ebb0ea0488205546d4678d6e31cc5f6801"}, {file = "hbreader-0.9.1.tar.gz", hash = "sha256:d2c132f8ba6276d794c66224c3297cec25c8079d0a4cf019c061611e0a3b94fa"}, @@ -662,6 +687,7 @@ version = "3.7" description = "Internationalized Domain Names in Applications (IDNA)" optional = false python-versions = ">=3.5" +groups = ["main"] files = [ {file = "idna-3.7-py3-none-any.whl", hash = "sha256:82fee1fc78add43492d3a1898bfa6d8a904cc97d8427f683ed8e798d07761aa0"}, {file = "idna-3.7.tar.gz", hash = "sha256:028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc"}, @@ -673,6 +699,7 @@ version = "2.0.0" description = "brain-dead simple config-ini parsing" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"}, {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"}, @@ -684,6 +711,7 @@ version = "0.6.1" description = "An ISO 8601 date/time/duration parser and formatter" optional = false python-versions = "*" +groups = ["main"] files = [ {file = "isodate-0.6.1-py2.py3-none-any.whl", hash = "sha256:0751eece944162659049d35f4f549ed815792b38793f07cf73381c1c87cbed96"}, {file = "isodate-0.6.1.tar.gz", hash = "sha256:48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9"}, @@ -698,6 +726,7 @@ version = "20.11.0" description = "Operations with ISO 8601 durations" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "isoduration-20.11.0-py3-none-any.whl", hash = "sha256:b2904c2a4228c3d44f409c8ae8e2370eb21a26f7ac2ec5446df141dde3452042"}, {file = "isoduration-20.11.0.tar.gz", hash = "sha256:ac2f9015137935279eac671f94f89eb00584f940f5dc49462a0c4ee692ba1bd9"}, @@ -712,6 +741,7 @@ version = "3.1.4" description = "A very fast and expressive template engine." optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "jinja2-3.1.4-py3-none-any.whl", hash = "sha256:bc5dd2abb727a5319567b7a813e6a2e7318c39f4f487cfe6c89c6f9c7d25197d"}, {file = "jinja2-3.1.4.tar.gz", hash = "sha256:4a3aee7acbbe7303aede8e9648d13b8bf88a429282aa6122a993f0ac800cb369"}, @@ -729,6 +759,7 @@ version = "0.1.9" description = "Python library for denormalizing nested dicts or json objects to tables and back" optional = false python-versions = ">=3.7.0" +groups = ["main"] files = [ {file = "json_flattener-0.1.9-py3-none-any.whl", hash = "sha256:6b027746f08bf37a75270f30c6690c7149d5f704d8af1740c346a3a1236bc941"}, {file = "json_flattener-0.1.9.tar.gz", hash = "sha256:84cf8523045ffb124301a602602201665fcb003a171ece87e6f46ed02f7f0c15"}, @@ -744,6 +775,7 @@ version = "1.3.1" description = 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hash = "sha256:2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1"}, @@ -1239,6 +1290,7 @@ version = "3.11" description = "Python Lex & Yacc" optional = false python-versions = "*" +groups = ["main"] files = [ {file = "ply-3.11-py2.py3-none-any.whl", hash = "sha256:096f9b8350b65ebd2fd1346b12452efe5b9607f7482813ffca50c22722a807ce"}, {file = "ply-3.11.tar.gz", hash = "sha256:00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3"}, @@ -1250,6 +1302,7 @@ version = "0.1.12" description = "A python API for working with ID prefixes" optional = false python-versions = ">=3.7,<4.0" +groups = ["main"] files = [ {file = "prefixcommons-0.1.12-py3-none-any.whl", hash = "sha256:16dbc0a1f775e003c724f19a694fcfa3174608f5c8b0e893d494cf8098ac7f8b"}, {file = "prefixcommons-0.1.12.tar.gz", hash = "sha256:22c4e2d37b63487b3ab48f0495b70f14564cb346a15220f23919eb0c1851f69f"}, @@ -1267,6 +1320,7 @@ version = "0.2.4" description = "A python library for retrieving semantic prefix maps" optional = false python-versions = "<4.0,>=3.8" +groups = ["main"] files = [ {file = "prefixmaps-0.2.4-py3-none-any.whl", hash = "sha256:89bf0e6fb08c276f754f9624c42adf2e87c64ee92a3dde1f7eff01f22d85b512"}, {file = "prefixmaps-0.2.4.tar.gz", hash = "sha256:ae86a1b31189d0516d199756d5808f75f44b39e86546c356cc78c0fe8d2078af"}, @@ -1282,6 +1336,7 @@ version = "0.2.1" description = "Accelerated property cache" optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = "propcache-0.2.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:6b3f39a85d671436ee3d12c017f8fdea38509e4f25b28eb25877293c98c243f6"}, {file = "propcache-0.2.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:39d51fbe4285d5db5d92a929e3e21536ea3dd43732c5b177c7ef03f918dff9f2"}, @@ -1373,6 +1428,7 @@ version = "2.8.2" description = "Data validation using Python type hints" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "pydantic-2.8.2-py3-none-any.whl", hash = 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description = "PyShExC - Python ShEx compiler" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "PyShExC-0.9.1-py2.py3-none-any.whl", hash = "sha256:efc55ed5cb2453e9df569b03e282505e96bb06597934288f3b23dd980ef10028"}, {file = "PyShExC-0.9.1.tar.gz", hash = "sha256:35a9975d4b9afeb20ef710fb6680871756381d0c39fbb5470b3b506581a304d3"}, @@ -1566,6 +1627,7 @@ version = "8.2.2" description = "pytest: simple powerful testing with Python" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "pytest-8.2.2-py3-none-any.whl", hash = "sha256:c434598117762e2bd304e526244f67bf66bbd7b5d6cf22138be51ff661980343"}, {file = "pytest-8.2.2.tar.gz", hash = "sha256:de4bb8104e201939ccdc688b27a89a7be2079b22e2bd2b07f806b6ba71117977"}, @@ -1586,6 +1648,7 @@ version = "2015.11.4" description = "Configures logging and allows tweaking the log level with a py.test flag" optional = false python-versions = "*" +groups = ["main"] files = [ {file = "pytest-logging-2015.11.4.tar.gz", hash = "sha256:cec5c85ecf18aab7b2ead5498a31b9f758680ef5a902b9054ab3f2bdbb77c896"}, ] @@ -1599,6 +1662,7 @@ version = "2.9.0.post0" description = "Extensions to the standard Python datetime module" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" +groups = ["main"] files = [ {file = "python-dateutil-2.9.0.post0.tar.gz", hash = "sha256:37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3"}, {file = "python_dateutil-2.9.0.post0-py2.py3-none-any.whl", hash = "sha256:a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427"}, @@ -1613,6 +1677,7 @@ version = "0.4.0" description = "A pure Python implementation of the trie data structure." optional = false python-versions = "*" +groups = ["main"] files = [ {file = "PyTrie-0.4.0-py3-none-any.whl", hash = "sha256:f687c224ee8c66cda8e8628a903011b692635ffbb08d4b39c5f92b18eb78c950"}, {file = "PyTrie-0.4.0.tar.gz", hash = "sha256:8f4488f402d3465993fb6b6efa09866849ed8cda7903b50647b7d0342b805379"}, @@ -1627,6 +1692,7 @@ version = "6.0.1" description = "YAML parser and emitter for Python" optional = false python-versions = ">=3.6" +groups = ["main"] files = [ {file = "PyYAML-6.0.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:d858aa552c999bc8a8d57426ed01e40bef403cd8ccdd0fc5f6f04a00414cac2a"}, {file = "PyYAML-6.0.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:fd66fc5d0da6d9815ba2cebeb4205f95818ff4b79c3ebe268e75d961704af52f"}, @@ -1687,6 +1753,7 @@ version = "7.0.0" description = "RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information." optional = false python-versions = ">=3.8.1,<4.0.0" +groups = ["main"] files = [ {file = "rdflib-7.0.0-py3-none-any.whl", hash = "sha256:0438920912a642c866a513de6fe8a0001bd86ef975057d6962c79ce4771687cd"}, {file = "rdflib-7.0.0.tar.gz", hash = "sha256:9995eb8569428059b8c1affd26b25eac510d64f5043d9ce8c84e0d0036e995ae"}, @@ -1708,6 +1775,7 @@ version = "0.6.1" description = "rdflib extension adding JSON-LD parser and serializer" optional = false python-versions = "*" +groups = ["main"] files = [ {file = "rdflib-jsonld-0.6.1.tar.gz", hash = "sha256:eda5a42a2e09f80d4da78e32b5c684bccdf275368f1541e6b7bcddfb1382a0e0"}, {file = "rdflib_jsonld-0.6.1-py2.py3-none-any.whl", hash = "sha256:bcf84317e947a661bae0a3f2aee1eced697075fc4ac4db6065a3340ea0f10fc2"}, @@ -1722,6 +1790,7 @@ version = "1.0.3" description = "Shim for rdflib 5 and 6 incompatibilities" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "rdflib_shim-1.0.3-py3-none-any.whl", hash = "sha256:7a853e7750ef1e9bf4e35dea27d54e02d4ed087de5a9e0c329c4a6d82d647081"}, {file = "rdflib_shim-1.0.3.tar.gz", hash = "sha256:d955d11e2986aab42b6830ca56ac6bc9c893abd1d049a161c6de2f1b99d4fc0d"}, @@ -1737,6 +1806,7 @@ version = "0.35.1" description = "JSON Referencing + Python" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "referencing-0.35.1-py3-none-any.whl", hash = "sha256:eda6d3234d62814d1c64e305c1331c9a3a6132da475ab6382eaa997b21ee75de"}, {file = "referencing-0.35.1.tar.gz", hash = "sha256:25b42124a6c8b632a425174f24087783efb348a6f1e0008e63cd4466fedf703c"}, @@ -1752,6 +1822,7 @@ version = "2.32.3" description = "Python HTTP for Humans." optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "requests-2.32.3-py3-none-any.whl", hash = "sha256:70761cfe03c773ceb22aa2f671b4757976145175cdfca038c02654d061d6dcc6"}, {file = "requests-2.32.3.tar.gz", hash = "sha256:55365417734eb18255590a9ff9eb97e9e1da868d4ccd6402399eaf68af20a760"}, @@ -1773,6 +1844,7 @@ version = "0.1.4" description = "A pure python RFC3339 validator" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +groups = ["main"] files = [ {file = "rfc3339_validator-0.1.4-py2.py3-none-any.whl", hash = "sha256:24f6ec1eda14ef823da9e36ec7113124b39c04d50a4d3d3a3c2859577e7791fa"}, {file = "rfc3339_validator-0.1.4.tar.gz", hash = "sha256:138a2abdf93304ad60530167e51d2dfb9549521a836871b88d7f4695d0022f6b"}, @@ -1787,6 +1859,7 @@ version = "1.3.8" description = "Parsing and validation of URIs (RFC 3986) and IRIs (RFC 3987)" optional = false python-versions = "*" +groups = ["main"] files = [ {file = "rfc3987-1.3.8-py2.py3-none-any.whl", hash = "sha256:10702b1e51e5658843460b189b185c0366d2cf4cff716f13111b0ea9fd2dce53"}, {file = "rfc3987-1.3.8.tar.gz", hash = "sha256:d3c4d257a560d544e9826b38bc81db676890c79ab9d7ac92b39c7a253d5ca733"}, @@ -1798,6 +1871,7 @@ version = "0.19.0" description = "Python bindings to Rust's persistent data structures (rpds)" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "rpds_py-0.19.0-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:fb37bd599f031f1a6fb9e58ec62864ccf3ad549cf14bac527dbfa97123edcca4"}, {file = "rpds_py-0.19.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:3384d278df99ec2c6acf701d067147320b864ef6727405d6470838476e44d9e8"}, @@ -1906,6 +1980,7 @@ version = "0.18.6" description = "ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "ruamel.yaml-0.18.6-py3-none-any.whl", hash = "sha256:57b53ba33def16c4f3d807c0ccbc00f8a6081827e81ba2491691b76882d0c636"}, {file = "ruamel.yaml-0.18.6.tar.gz", hash = "sha256:8b27e6a217e786c6fbe5634d8f3f11bc63e0f80f6a5890f28863d9c45aac311b"}, @@ -1924,6 +1999,8 @@ version = "0.2.8" description = "C version of reader, parser and emitter for ruamel.yaml derived from libyaml" optional = false python-versions = ">=3.6" +groups = ["main"] +markers = "platform_python_implementation == \"CPython\" and python_version < \"3.13\"" files = [ {file = "ruamel.yaml.clib-0.2.8-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:b42169467c42b692c19cf539c38d4602069d8c1505e97b86387fcf7afb766e1d"}, {file = "ruamel.yaml.clib-0.2.8-cp310-cp310-macosx_13_0_arm64.whl", hash = "sha256:07238db9cbdf8fc1e9de2489a4f68474e70dffcb32232db7c08fa61ca0c7c462"}, @@ -1983,6 +2060,7 @@ version = "0.8.2" description = "ShExJSG - Astract Syntax Tree for the ShEx 2.0 language" optional = false python-versions = "*" +groups = ["main"] files = [ {file = "ShExJSG-0.8.2-py2.py3-none-any.whl", hash = "sha256:3b0d8432dd313bee9e1343382c5e02e9908dd941a7dd7342bf8c0200fe523766"}, {file = "ShExJSG-0.8.2.tar.gz", hash = "sha256:f17a629fc577fa344382bdee143cd9ff86588537f9f811f66cea6f63cdbcd0b6"}, @@ -1997,6 +2075,7 @@ version = "1.16.0" description = "Python 2 and 3 compatibility utilities" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" +groups = ["main"] files = [ {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"}, {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"}, @@ -2008,6 +2087,7 @@ version = "2.4.0" description = "Sorted Containers -- Sorted List, Sorted Dict, Sorted Set" optional = false python-versions = "*" +groups = ["main"] files = [ {file = "sortedcontainers-2.4.0-py2.py3-none-any.whl", hash = "sha256:a163dcaede0f1c021485e957a39245190e74249897e2ae4b2aa38595db237ee0"}, {file = "sortedcontainers-2.4.0.tar.gz", hash = "sha256:25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88"}, @@ -2019,6 +2099,7 @@ version = "0.5.1" description = "SPARQL Slurper for rdflib" optional = false python-versions = ">=3.7.4" +groups = ["main"] files = [ {file = "sparqlslurper-0.5.1-py3-none-any.whl", hash = "sha256:ae49b2d8ce3dd38df7a40465b228ad5d33fb7e11b3f248d195f9cadfc9cfff87"}, {file = "sparqlslurper-0.5.1.tar.gz", hash = "sha256:9282ebb064fc6152a58269d194cb1e7b275b0f095425a578d75b96dcc851f546"}, @@ -2035,6 +2116,7 @@ version = "2.0.0" description = "SPARQL Endpoint interface to Python" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "SPARQLWrapper-2.0.0-py3-none-any.whl", hash = "sha256:c99a7204fff676ee28e6acef327dc1ff8451c6f7217dcd8d49e8872f324a8a20"}, {file = "SPARQLWrapper-2.0.0.tar.gz", hash = "sha256:3fed3ebcc77617a4a74d2644b86fd88e0f32e7f7003ac7b2b334c026201731f1"}, @@ -2055,6 +2137,7 @@ version = "2.0.31" description = "Database Abstraction Library" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "SQLAlchemy-2.0.31-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:f2a213c1b699d3f5768a7272de720387ae0122f1becf0901ed6eaa1abd1baf6c"}, {file = "SQLAlchemy-2.0.31-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:9fea3d0884e82d1e33226935dac990b967bef21315cbcc894605db3441347443"}, @@ -2142,6 +2225,7 @@ version = "2.9.0.20240316" description = "Typing stubs for python-dateutil" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "types-python-dateutil-2.9.0.20240316.tar.gz", hash = "sha256:5d2f2e240b86905e40944dd787db6da9263f0deabef1076ddaed797351ec0202"}, {file = "types_python_dateutil-2.9.0.20240316-py3-none-any.whl", hash = "sha256:6b8cb66d960771ce5ff974e9dd45e38facb81718cc1e208b10b1baccbfdbee3b"}, @@ -2153,6 +2237,7 @@ version = "4.12.2" description = "Backported and Experimental Type Hints for Python 3.8+" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"}, {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"}, @@ -2164,6 +2249,7 @@ version = "1.3.0" description = "RFC 6570 URI Template Processor" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "uri-template-1.3.0.tar.gz", hash = "sha256:0e00f8eb65e18c7de20d595a14336e9f337ead580c70934141624b6d1ffdacc7"}, {file = "uri_template-1.3.0-py3-none-any.whl", hash = "sha256:a44a133ea12d44a0c0f06d7d42a52d71282e77e2f937d8abd5655b8d56fc1363"}, @@ -2178,6 +2264,7 @@ version = "2.2.2" description = "HTTP library with thread-safe connection pooling, file post, and more." optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "urllib3-2.2.2-py3-none-any.whl", hash = "sha256:a448b2f64d686155468037e1ace9f2d2199776e17f0a46610480d311f73e3472"}, {file = "urllib3-2.2.2.tar.gz", hash = "sha256:dd505485549a7a552833da5e6063639d0d177c04f23bc3864e41e5dc5f612168"}, @@ -2195,6 +2282,7 @@ version = "4.0.1" description = "Filesystem events monitoring" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "watchdog-4.0.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:da2dfdaa8006eb6a71051795856bedd97e5b03e57da96f98e375682c48850645"}, {file = "watchdog-4.0.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:e93f451f2dfa433d97765ca2634628b789b49ba8b504fdde5837cdcf25fdb53b"}, @@ -2239,6 +2327,7 @@ version = "24.6.0" description = "A library for working with the color formats defined by HTML and CSS." optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "webcolors-24.6.0-py3-none-any.whl", hash = "sha256:8cf5bc7e28defd1d48b9e83d5fc30741328305a8195c29a8e668fa45586568a1"}, {file = "webcolors-24.6.0.tar.gz", hash = "sha256:1d160d1de46b3e81e58d0a280d0c78b467dc80f47294b91b1ad8029d2cedb55b"}, @@ -2254,6 +2343,7 @@ version = "1.16.0" description = "Module for decorators, wrappers and monkey patching." optional = false python-versions = ">=3.6" +groups = ["main"] files = [ {file = "wrapt-1.16.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:ffa565331890b90056c01db69c0fe634a776f8019c143a5ae265f9c6bc4bd6d4"}, {file = "wrapt-1.16.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:e4fdb9275308292e880dcbeb12546df7f3e0f96c6b41197e0cf37d2826359020"}, @@ -2333,6 +2423,7 @@ version = "1.18.3" description = "Yet another URL library" optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = "yarl-1.18.3-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:7df647e8edd71f000a5208fe6ff8c382a1de8edfbccdbbfe649d263de07d8c34"}, {file = "yarl-1.18.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:c69697d3adff5aa4f874b19c0e4ed65180ceed6318ec856ebc423aa5850d84f7"}, @@ -2424,6 +2515,6 @@ multidict = ">=4.0" propcache = ">=0.2.0" [metadata] -lock-version = "2.0" +lock-version = "2.1" python-versions = "^3.11" content-hash = "397a7d253118dbd69f6e82c0bb6d84496c74483c3ec67e92a12e5f6c7efed0bd" diff --git a/schema/pyproject.toml b/schema/pyproject.toml index 541277ee8..bcf1b4fcf 100644 --- a/schema/pyproject.toml +++ b/schema/pyproject.toml @@ -1,3 +1,12 @@ +[project] +name = "schema_manager" +version = "1.0" +description = "Tools for managing schema of the CryoET Data Portal" +authors = [ + {name="CZI Imaging Team", email="cryoetdataportal@chanzuckerberg.com"}, +] +license = { text = "MIT" } + [tool.poetry] name = "schema_manager" version = "1.0" @@ -5,7 +14,7 @@ description = "Tools for managing schema of the CryoET Data Portal" authors = [ "CZI Imaging Team " ] -license = "MIT" +package-mode = false [tool.poetry.dependencies] python = "^3.11" @@ -60,3 +69,7 @@ show_error_codes = true ignore_missing_imports = true warn_unreachable = true strict = true + +[build-system] +requires = ["poetry-core==2.0.0"] +build-backend = "poetry.core.masonry.api" From e4746097d8d1fa89e078012541451547a8065e77 Mon Sep 17 00:00:00 2001 From: uermel Date: Wed, 8 Jan 2025 09:52:35 -0800 Subject: [PATCH 05/10] update dates, titles and sample type --- ingestion_tools/dataset_configs/10426.yaml | 19 +++++++++++-------- ingestion_tools/dataset_configs/10427.yaml | 18 +++++++++--------- ingestion_tools/dataset_configs/10428.yaml | 18 +++++++++--------- ingestion_tools/dataset_configs/10429.yaml | 18 +++++++++--------- ingestion_tools/dataset_configs/10430.yaml | 18 +++++++++--------- ingestion_tools/dataset_configs/10431.yaml | 18 +++++++++--------- ingestion_tools/dataset_configs/10432.yaml | 18 +++++++++--------- ingestion_tools/dataset_configs/10433.yaml | 18 +++++++++--------- ingestion_tools/dataset_configs/10434.yaml | 18 +++++++++--------- ingestion_tools/dataset_configs/10435.yaml | 18 +++++++++--------- 10 files changed, 92 insertions(+), 89 deletions(-) diff --git a/ingestion_tools/dataset_configs/10426.yaml b/ingestion_tools/dataset_configs/10426.yaml index 086f5dc20..4b0245601 100644 --- a/ingestion_tools/dataset_configs/10426.yaml +++ b/ingestion_tools/dataset_configs/10426.yaml @@ -49,11 +49,11 @@ datasets: 300 R2/2, 2 nm carbon grids prior to removing the apical membrane and cytoplasm with 0.7 bar of paraformaldehyde prior to vitrification. dataset_identifier: 10426 - dataset_title: Unroofing Grid01 - dates: &id003 + dataset_title: Plasma membranes isolated by unroofing - Grid 01 + dates: &dates deposition_date: '2024-07-01' - last_modified_date: '2024-07-01' - release_date: '2024-07-05' + last_modified_date: '2025-01-08' + release_date: '2025-01-08' funding: - funding_agency_name: Chan Zuckerberg Initiative grant_id: 2021-234544 @@ -68,7 +68,10 @@ datasets: taxonomy_id: 9606 sample_preparation: serum starved and grown on Quantifoil Au 300 R2/2, 2 nm carbon grids - sample_type: cell + sample_type: organelle + cell_component: + name: plasma membrane + id: GO:0005886 sources: - literal: value: @@ -78,12 +81,12 @@ depositions: - metadata: authors: *id001 cross_references: *id002 - dates: *id003 + dates: *dates deposition_description: Cryo-electron tomography datasets used in the development and evaluation of the unroofing method for preparation of plasma membranes and associated proteins. deposition_identifier: 10306 - deposition_title: Human plasma membranes isolated using the unroofing method. + deposition_title: Human plasma membranes isolated using the unroofing method deposition_types: - dataset sources: @@ -172,7 +175,7 @@ tomograms: - 1 authors: *id001 ctf_corrected: false - dates: *id003 + dates: *dates fiducial_alignment_status: FIDUCIAL is_visualization_default: true offset: diff --git a/ingestion_tools/dataset_configs/10427.yaml b/ingestion_tools/dataset_configs/10427.yaml index 1a846e1cb..80742784b 100644 --- a/ingestion_tools/dataset_configs/10427.yaml +++ b/ingestion_tools/dataset_configs/10427.yaml @@ -49,11 +49,11 @@ datasets: 300 R2/2, 2 nm carbon grids prior to removing the apical membrane and cytoplasm with 0.7 bar of paraformaldehyde prior to vitrification. dataset_identifier: 10427 - dataset_title: Unroofing Grid02 - dates: + dataset_title: Plasma membranes isolated by unroofing - Grid 02 + dates: &dates deposition_date: '2024-07-01' - last_modified_date: '2024-07-01' - release_date: '2024-07-05' + last_modified_date: '2025-01-08' + release_date: '2025-01-08' funding: - funding_agency_name: Chan Zuckerberg Initiative grant_id: 2021-234544 @@ -68,7 +68,10 @@ datasets: taxonomy_id: 9606 sample_preparation: serum starved and grown on Quantifoil Au 300 R2/2, 2 nm carbon grids - sample_type: cell + sample_type: organelle + cell_component: + name: plasma membrane + id: GO:0005886 sources: - literal: value: @@ -306,10 +309,7 @@ tomograms: - 1 authors: *id001 ctf_corrected: false - dates: - deposition_date: '2024-07-01' - last_modified_date: '2024-07-01' - release_date: '2024-07-05' + dates: *dates fiducial_alignment_status: FIDUCIAL is_visualization_default: true offset: diff --git a/ingestion_tools/dataset_configs/10428.yaml b/ingestion_tools/dataset_configs/10428.yaml index c99299130..4aa2bce0b 100644 --- a/ingestion_tools/dataset_configs/10428.yaml +++ b/ingestion_tools/dataset_configs/10428.yaml @@ -50,11 +50,11 @@ datasets: to removing the basal membrane and cytoplasm with 0.7 bar of paraformaldehyde prior to vitrification. dataset_identifier: 10428 - dataset_title: Unroofing Grid03 - dates: + dataset_title: Plasma membranes isolated by unroofing - Grid 03 + dates: &dates deposition_date: '2024-07-01' - last_modified_date: '2024-07-01' - release_date: '2024-07-05' + last_modified_date: '2025-01-08' + release_date: '2025-01-08' funding: - funding_agency_name: Chan Zuckerberg Initiative grant_id: 2021-234544 @@ -70,7 +70,10 @@ datasets: sample_preparation: Grown on coverslips coated with fibronectin + adhered to Quantifoil Au 300 R1.2/1.3 grids coated with poly-lysine + remove the basal membrane and cytoplasm with 0.7 bar of paraformaldehyde + vitrification. - sample_type: cell + sample_type: organelle + cell_component: + name: plasma membrane + id: GO:0005886 sources: - literal: value: @@ -156,10 +159,7 @@ tomograms: - 1 authors: *id001 ctf_corrected: false - dates: - deposition_date: '2024-07-01' - last_modified_date: '2024-07-01' - release_date: '2024-07-05' + dates: *dates fiducial_alignment_status: FIDUCIAL is_visualization_default: true offset: diff --git a/ingestion_tools/dataset_configs/10429.yaml b/ingestion_tools/dataset_configs/10429.yaml index 149f06507..5cf3613a6 100644 --- a/ingestion_tools/dataset_configs/10429.yaml +++ b/ingestion_tools/dataset_configs/10429.yaml @@ -50,11 +50,11 @@ datasets: to removing the basal membrane and cytoplasm with 0.7 bar of paraformaldehyde prior to vitrification. dataset_identifier: 10429 - dataset_title: Unroofing Grid04 - dates: + dataset_title: Plasma membranes isolated by unroofing - Grid 04 + dates: &dates deposition_date: '2024-07-01' - last_modified_date: '2024-07-01' - release_date: '2024-07-05' + last_modified_date: '2025-01-08' + release_date: '2025-01-08' funding: - funding_agency_name: Chan Zuckerberg Initiative grant_id: 2021-234544 @@ -70,7 +70,10 @@ datasets: sample_preparation: Grown on coverslips coated with fibronectin + adhered to Quantifoil Au 300 R1.2/1.3 grids coated with poly-lysine + remove the basal membrane and cytoplasm with 0.7 bar of paraformaldehyde + vitrification. - sample_type: cell + sample_type: organelle + cell_component: + name: plasma membrane + id: GO:0005886 sources: - literal: value: @@ -156,10 +159,7 @@ tomograms: - 1 authors: *id001 ctf_corrected: false - dates: - deposition_date: '2024-07-01' - last_modified_date: '2024-07-01' - release_date: '2024-07-05' + dates: *dates fiducial_alignment_status: FIDUCIAL is_visualization_default: true offset: diff --git a/ingestion_tools/dataset_configs/10430.yaml b/ingestion_tools/dataset_configs/10430.yaml index bad8fef42..82b6b9217 100644 --- a/ingestion_tools/dataset_configs/10430.yaml +++ b/ingestion_tools/dataset_configs/10430.yaml @@ -50,11 +50,11 @@ datasets: induced with doxycycline overnight then adhered to Quantifoil Cu 200 R2/2 grids coated with poly-lysine prior to removing the basal membrane and cytoplasm. dataset_identifier: 10430 - dataset_title: Unroofing Grid05 - dates: + dataset_title: Plasma membranes isolated by unroofing - Grid 05 + dates: &dates deposition_date: '2024-07-01' - last_modified_date: '2024-07-01' - release_date: '2024-07-05' + last_modified_date: '2025-01-08' + release_date: '2025-01-08' funding: - funding_agency_name: Chan Zuckerberg Initiative grant_id: 2021-234544 @@ -70,7 +70,10 @@ datasets: sample_preparation: Grown on coverslips coated with fibronectin + induced with tetracycline overnight + adhered to Quantifoil Cu 200 R2/2 grids coated with poly-lysine + remove the basal membrane and cytoplasm + paraformaldehyde + vitrification. - sample_type: cell + sample_type: organelle + cell_component: + name: plasma membrane + id: GO:0005886 sources: - literal: value: @@ -154,10 +157,7 @@ tomograms: - 1 authors: *id001 ctf_corrected: false - dates: - deposition_date: '2024-07-01' - last_modified_date: '2024-07-01' - release_date: '2024-07-05' + dates: *dates fiducial_alignment_status: FIDUCIAL is_visualization_default: true offset: diff --git a/ingestion_tools/dataset_configs/10431.yaml b/ingestion_tools/dataset_configs/10431.yaml index ccc925905..51fb3706a 100644 --- a/ingestion_tools/dataset_configs/10431.yaml +++ b/ingestion_tools/dataset_configs/10431.yaml @@ -49,11 +49,11 @@ datasets: grids coated with poly-lysine prior to removing the basal membrane and cytoplasm with 0.7 bar of paraformaldehyde prior to vitrification. dataset_identifier: 10431 - dataset_title: Unroofing Grid06 - dates: &dataset_dates + dataset_title: Plasma membranes isolated by unroofing - Grid 06 + dates: &dates deposition_date: '2024-07-01' - last_modified_date: '2024-07-01' - release_date: '2024-07-05' + last_modified_date: '2025-01-08' + release_date: '2025-01-08' funding: - funding_agency_name: Chan Zuckerberg Initiative grant_id: 2021-234544 @@ -70,7 +70,10 @@ datasets: tetracycline overnight + adhered to Quantifoil Au 300 R1.2/1.3 grids coated with poly-lysine + remove the basal membrane and cytoplasm + paraformaldehyde + vitrification. - sample_type: cell + sample_type: organelle + cell_component: + name: plasma membrane + id: GO:0005886 sources: - literal: value: @@ -190,10 +193,7 @@ tomograms: - 1 authors: *id001 ctf_corrected: false - dates: - deposition_date: '2024-07-01' - last_modified_date: '2024-07-01' - release_date: '2024-07-05' + dates: *dates fiducial_alignment_status: FIDUCIAL is_visualization_default: true offset: diff --git a/ingestion_tools/dataset_configs/10432.yaml b/ingestion_tools/dataset_configs/10432.yaml index f25de6103..c77bebf5e 100644 --- a/ingestion_tools/dataset_configs/10432.yaml +++ b/ingestion_tools/dataset_configs/10432.yaml @@ -51,11 +51,11 @@ datasets: coated with poly-lysine prior to removing the basal membrane and cytoplasm with 0.7 bar of paraformaldehyde. Unroofing occurred immediately prior to vitrification. dataset_identifier: 10432 - dataset_title: Unroofing Grid07 - dates: + dataset_title: Plasma membranes isolated by unroofing - Grid 07 + dates: &dates deposition_date: '2024-07-01' - last_modified_date: '2024-07-01' - release_date: '2024-07-05' + last_modified_date: '2025-01-08' + release_date: '2025-01-08' funding: - funding_agency_name: Chan Zuckerberg Initiative grant_id: 2021-234544 @@ -72,7 +72,10 @@ datasets: chain) + Grown on coverslips coated with fibronectin + adhered to Quantifoil Au 300 R1.2/1.3 grids coated with poly-lysine + remove the basal membrane and cytoplasm + 0.7 bar paraformaldehyde + vitrification. - sample_type: cell + sample_type: organelle + cell_component: + name: plasma membrane + id: GO:0005886 sources: - literal: value: @@ -158,10 +161,7 @@ tomograms: - 1 authors: *id001 ctf_corrected: false - dates: - deposition_date: '2024-07-01' - last_modified_date: '2024-07-01' - release_date: '2024-07-05' + dates: *dates fiducial_alignment_status: FIDUCIAL is_visualization_default: true offset: diff --git a/ingestion_tools/dataset_configs/10433.yaml b/ingestion_tools/dataset_configs/10433.yaml index 52c4010e7..a8520ac38 100644 --- a/ingestion_tools/dataset_configs/10433.yaml +++ b/ingestion_tools/dataset_configs/10433.yaml @@ -51,11 +51,11 @@ datasets: coated with poly-lysine prior to removing the basal membrane and cytoplasm with 0.7 bar of paraformaldehyde. Unroofing occurred immediately prior to vitrification. dataset_identifier: 10433 - dataset_title: Unroofing Grid08 - dates: + dataset_title: Plasma membranes isolated by unroofing - Grid 08 + dates: &dates deposition_date: '2024-07-01' - last_modified_date: '2024-07-01' - release_date: '2024-07-05' + last_modified_date: '2025-01-08' + release_date: '2025-01-08' funding: - funding_agency_name: Chan Zuckerberg Initiative grant_id: 2021-234544 @@ -72,7 +72,10 @@ datasets: chain) + Grown on coverslips coated with fibronectin + adhered to Quantifoil Au 300 R1.2/1.3 grids coated with poly-lysine + remove the basal membrane and cytoplasm + 0.7 bar paraformaldehyde + vitrification. - sample_type: cell + sample_type: organelle + cell_component: + name: plasma membrane + id: GO:0005886 sources: - literal: value: @@ -158,10 +161,7 @@ tomograms: - 1 authors: *id001 ctf_corrected: false - dates: - deposition_date: '2024-07-01' - last_modified_date: '2024-07-01' - release_date: '2024-07-05' + dates: *dates fiducial_alignment_status: FIDUCIAL is_visualization_default: true offset: diff --git a/ingestion_tools/dataset_configs/10434.yaml b/ingestion_tools/dataset_configs/10434.yaml index 0766aedcc..0507f9b25 100644 --- a/ingestion_tools/dataset_configs/10434.yaml +++ b/ingestion_tools/dataset_configs/10434.yaml @@ -51,11 +51,11 @@ datasets: to removing the basal membrane and cytoplasm with 0.7 bar of paraformaldehyde. Unroofing occurred immediately prior to vitrification. dataset_identifier: 10434 - dataset_title: Unroofing Grid09 - dates: + dataset_title: Plasma membranes isolated by unroofing - Grid 09 + dates: &dates deposition_date: '2024-07-01' - last_modified_date: '2024-07-01' - release_date: '2024-07-05' + last_modified_date: '2025-01-08' + release_date: '2025-01-08' funding: - funding_agency_name: Chan Zuckerberg Initiative grant_id: 2021-234544 @@ -72,7 +72,10 @@ datasets: coated with fibronectin + adhered to Quantifoil Au 300 R1.2/1.3 grids coated with poly-lysine + remove the basal membrane and cytoplasm + 0.7 bar paraformaldehyde + vitrification. - sample_type: cell + sample_type: organelle + cell_component: + name: plasma membrane + id: GO:0005886 sources: - literal: value: @@ -158,10 +161,7 @@ tomograms: - 1 authors: *id001 ctf_corrected: false - dates: - deposition_date: '2024-07-01' - last_modified_date: '2024-07-01' - release_date: '2024-07-05' + dates: *dates fiducial_alignment_status: FIDUCIAL is_visualization_default: true offset: diff --git a/ingestion_tools/dataset_configs/10435.yaml b/ingestion_tools/dataset_configs/10435.yaml index 3badfa162..a12bf230b 100644 --- a/ingestion_tools/dataset_configs/10435.yaml +++ b/ingestion_tools/dataset_configs/10435.yaml @@ -51,11 +51,11 @@ datasets: to removing the basal membrane and cytoplasm with 0.7 bar of paraformaldehyde. Unroofing occurred immediately prior to vitrification. dataset_identifier: 10435 - dataset_title: Unroofing Grid10 - dates: + dataset_title: Plasma membranes isolated by unroofing - Grid 10 + dates: &dates deposition_date: '2024-07-01' - last_modified_date: '2024-07-01' - release_date: '2024-07-05' + last_modified_date: '2025-01-08' + release_date: '2025-01-08' funding: - funding_agency_name: Chan Zuckerberg Initiative grant_id: 2021-234544 @@ -72,7 +72,10 @@ datasets: coated with fibronectin + adhered to Quantifoil Au 300 R1.2/1.3 grids coated with poly-lysine + remove the basal membrane and cytoplasm + 0.7 bar paraformaldehyde + vitrification. - sample_type: cell + sample_type: organelle + cell_component: + name: plasma membrane + id: GO:0005886 sources: - literal: value: @@ -158,10 +161,7 @@ tomograms: - 1 authors: *id001 ctf_corrected: false - dates: - deposition_date: '2024-07-01' - last_modified_date: '2024-07-01' - release_date: '2024-07-05' + dates: *dates fiducial_alignment_status: FIDUCIAL is_visualization_default: true offset: From bd51743f1631e91b3c166959121d3112c41951d5 Mon Sep 17 00:00:00 2001 From: uermel Date: Mon, 13 Jan 2025 10:13:22 -0800 Subject: [PATCH 06/10] update 3 dataset keyphotos. --- ingestion_tools/dataset_configs/10427.yaml | 7 +++++++ ingestion_tools/dataset_configs/10429.yaml | 7 +++++++ ingestion_tools/dataset_configs/10432.yaml | 7 +++++++ 3 files changed, 21 insertions(+) diff --git a/ingestion_tools/dataset_configs/10427.yaml b/ingestion_tools/dataset_configs/10427.yaml index 80742784b..870bb3a9b 100644 --- a/ingestion_tools/dataset_configs/10427.yaml +++ b/ingestion_tools/dataset_configs/10427.yaml @@ -77,6 +77,13 @@ datasets: value: - '10427' +dataset_keyphotos: +- sources: + - literal: + value: + snapshot: cryoetportal-rawdatasets-dev/kem_sochacki_06_2024/grid02/dataset_keyphotos/key-photo-snapshot.png + thumbnail: cryoetportal-rawdatasets-dev/kem_sochacki_06_2024/grid02/dataset_keyphotos/key-photo-thumbnail.png + depositions: - sources: - literal: diff --git a/ingestion_tools/dataset_configs/10429.yaml b/ingestion_tools/dataset_configs/10429.yaml index 5cf3613a6..524a9498e 100644 --- a/ingestion_tools/dataset_configs/10429.yaml +++ b/ingestion_tools/dataset_configs/10429.yaml @@ -79,6 +79,13 @@ datasets: value: - '10429' +dataset_keyphotos: +- sources: + - literal: + value: + snapshot: cryoetportal-rawdatasets-dev/kem_sochacki_06_2024/grid04/dataset_keyphotos/key-photo-snapshot.png + thumbnail: cryoetportal-rawdatasets-dev/kem_sochacki_06_2024/grid04/dataset_keyphotos/key-photo-thumbnail.png + depositions: - sources: - literal: diff --git a/ingestion_tools/dataset_configs/10432.yaml b/ingestion_tools/dataset_configs/10432.yaml index c77bebf5e..41e290a13 100644 --- a/ingestion_tools/dataset_configs/10432.yaml +++ b/ingestion_tools/dataset_configs/10432.yaml @@ -81,6 +81,13 @@ datasets: value: - '10432' +dataset_keyphotos: +- sources: + - literal: + value: + snapshot: cryoetportal-rawdatasets-dev/kem_sochacki_06_2024/grid07/dataset_keyphotos/key-photo-snapshot.png + thumbnail: cryoetportal-rawdatasets-dev/kem_sochacki_06_2024/grid07/dataset_keyphotos/key-photo-thumbnail.png + depositions: - sources: - literal: From fe939c217fd4445a273fb6198cc66356385c6684 Mon Sep 17 00:00:00 2001 From: uermel Date: Mon, 13 Jan 2025 10:29:28 -0800 Subject: [PATCH 07/10] update with final publication. --- ingestion_tools/dataset_configs/10426.yaml | 3 ++- ingestion_tools/dataset_configs/10427.yaml | 3 ++- ingestion_tools/dataset_configs/10428.yaml | 3 ++- ingestion_tools/dataset_configs/10429.yaml | 3 ++- ingestion_tools/dataset_configs/10430.yaml | 4 ++-- ingestion_tools/dataset_configs/10431.yaml | 4 ++-- ingestion_tools/dataset_configs/10432.yaml | 4 ++-- ingestion_tools/dataset_configs/10433.yaml | 4 ++-- ingestion_tools/dataset_configs/10434.yaml | 4 ++-- ingestion_tools/dataset_configs/10435.yaml | 4 ++-- 10 files changed, 20 insertions(+), 16 deletions(-) diff --git a/ingestion_tools/dataset_configs/10426.yaml b/ingestion_tools/dataset_configs/10426.yaml index 4b0245601..556bfd52b 100644 --- a/ingestion_tools/dataset_configs/10426.yaml +++ b/ingestion_tools/dataset_configs/10426.yaml @@ -41,7 +41,8 @@ datasets: id: CL:0000010 name: cultured cell cross_references: &id002 - publications: 10.1101/2024.06.27.600657 + publications: 10.1038/s41467-025-56045-z, 10.1101/2024.06.27.600657 + related_database_entries: EMD-44921, EMD-44909, EMD-44922, EMD-46973 dataset_description: Michalak, Sun, Sochacki et al. 2024 unroofing manuscript contains 10 grids. This is grid 1 of 10 and contains basal membranes of HSC3 cells. The cell line expresses EGFR-GFP as described in Panilla-Macua et al. diff --git a/ingestion_tools/dataset_configs/10427.yaml b/ingestion_tools/dataset_configs/10427.yaml index 870bb3a9b..1d7423523 100644 --- a/ingestion_tools/dataset_configs/10427.yaml +++ b/ingestion_tools/dataset_configs/10427.yaml @@ -41,7 +41,8 @@ datasets: id: CL:0000010 name: cultured cell cross_references: - publications: 10.1101/2024.06.27.600657 + publications: 10.1038/s41467-025-56045-z, 10.1101/2024.06.27.600657 + related_database_entries: EMD-44921, EMD-44909, EMD-44922, EMD-46973 dataset_description: Michalak, Sun, Sochacki et al. 2024 unroofing manuscript contains 10 grids. This is grid 2 of 10 and contains basal membranes of HSC3 cells. The cell line expresses EGFR-GFP as described in Panilla-Macua et al. diff --git a/ingestion_tools/dataset_configs/10428.yaml b/ingestion_tools/dataset_configs/10428.yaml index 4aa2bce0b..c89365cff 100644 --- a/ingestion_tools/dataset_configs/10428.yaml +++ b/ingestion_tools/dataset_configs/10428.yaml @@ -41,7 +41,8 @@ datasets: id: CL:0000010 name: cultured cell cross_references: - publications: 10.1101/2024.06.27.600657 + publications: 10.1038/s41467-025-56045-z, 10.1101/2024.06.27.600657 + related_database_entries: EMD-44921, EMD-44909, EMD-44922, EMD-46973 dataset_description: Michalak, Sun, Sochacki et al. 2024 unroofing manuscript contains 10 grids. This is grid 3 of 10 and contains apical membranes of HSC3 cells. The cell line expresses EGFR-GFP as described in Panilla-Macua et al. diff --git a/ingestion_tools/dataset_configs/10429.yaml b/ingestion_tools/dataset_configs/10429.yaml index 524a9498e..30a422c09 100644 --- a/ingestion_tools/dataset_configs/10429.yaml +++ b/ingestion_tools/dataset_configs/10429.yaml @@ -41,7 +41,8 @@ datasets: id: CL:0000010 name: cultured cell cross_references: - publications: 10.1101/2024.06.27.600657 + publications: 10.1038/s41467-025-56045-z, 10.1101/2024.06.27.600657 + related_database_entries: EMD-44921, EMD-44909, EMD-44922, EMD-46973 dataset_description: Michalak, Sun, Sochacki et al. 2024 unroofing manuscript contains 10 grids. This is grid 4 of 10 and contains apical membranes of HSC3 cells. The cell line expresses EGFR-GFP as described in Panilla-Macua et al. diff --git a/ingestion_tools/dataset_configs/10430.yaml b/ingestion_tools/dataset_configs/10430.yaml index 82b6b9217..a65a2d882 100644 --- a/ingestion_tools/dataset_configs/10430.yaml +++ b/ingestion_tools/dataset_configs/10430.yaml @@ -41,8 +41,8 @@ datasets: id: CL:0000010 name: cultured cell cross_references: - publications: 10.1101/2024.06.27.600657 - related_database_entries: EMD-44921, EMD-44909, EMD-44922 + publications: 10.1038/s41467-025-56045-z, 10.1101/2024.06.27.600657 + related_database_entries: EMD-44921, EMD-44909, EMD-44922, EMD-46973 dataset_description: Michalak, Sun, Sochacki et al. 2024 unroofing manuscript contains 10 grids. This is grid 5 of 10 and contains apical membranes of HEK293 Trex cells. The cell line is stably expressing Dynamin 1 (K44A)- GFP on a tetracycline diff --git a/ingestion_tools/dataset_configs/10431.yaml b/ingestion_tools/dataset_configs/10431.yaml index 51fb3706a..61d63d65a 100644 --- a/ingestion_tools/dataset_configs/10431.yaml +++ b/ingestion_tools/dataset_configs/10431.yaml @@ -39,8 +39,8 @@ datasets: id: CL:0000010 name: cultured cell cross_references: - publications: 10.1101/2024.06.27.600657 - related_database_entries: EMD-44921, EMD-44909, EMD-44922 + publications: 10.1038/s41467-025-56045-z, 10.1101/2024.06.27.600657 + related_database_entries: EMD-44921, EMD-44909, EMD-44922, EMD-46973 dataset_description: Michalak, Sun, Sochacki et al. 2024 unroofing manuscript contains 10 grids. This is grid 6 of 10 and contains apical membranes of HEK293 Trex cells. The cell line is stably expressing Dynamin 1 (K44A)- GFP on a tetracycline diff --git a/ingestion_tools/dataset_configs/10432.yaml b/ingestion_tools/dataset_configs/10432.yaml index 41e290a13..31c6616db 100644 --- a/ingestion_tools/dataset_configs/10432.yaml +++ b/ingestion_tools/dataset_configs/10432.yaml @@ -41,8 +41,8 @@ datasets: id: CL:0000010 name: cultured cell cross_references: - publications: 10.1101/2024.06.27.600657 - related_database_entries: EMD-44921, EMD-44909, EMD-44922 + publications: 10.1038/s41467-025-56045-z, 10.1101/2024.06.27.600657 + related_database_entries: EMD-44921, EMD-44909, EMD-44922, EMD-46973 dataset_description: Michalak, Sun, Sochacki et al. 2024 unroofing manuscript contains 10 grids. This is grid 7 of 10 and contains apical membranes of HEK293 cells. The cells are expressing FerriTag and GFP-FKBP-LCa (clathrin light chain) diff --git a/ingestion_tools/dataset_configs/10433.yaml b/ingestion_tools/dataset_configs/10433.yaml index a8520ac38..d5178e386 100644 --- a/ingestion_tools/dataset_configs/10433.yaml +++ b/ingestion_tools/dataset_configs/10433.yaml @@ -41,8 +41,8 @@ datasets: id: CL:0000010 name: cultured cell cross_references: - publications: 10.1101/2024.06.27.600657 - related_database_entries: EMD-44921, EMD-44909, EMD-44922 + publications: 10.1038/s41467-025-56045-z, 10.1101/2024.06.27.600657 + related_database_entries: EMD-44921, EMD-44909, EMD-44922, EMD-46973 dataset_description: Michalak, Sun, Sochacki et al. 2024 unroofing manuscript contains 10 grids. This is grid 8 of 10 and contains apical membranes of HEK293 cells. The cells are expressing FerriTag and GFP-FKBP-LCa (clathrin light chain) diff --git a/ingestion_tools/dataset_configs/10434.yaml b/ingestion_tools/dataset_configs/10434.yaml index 0507f9b25..a9cde6910 100644 --- a/ingestion_tools/dataset_configs/10434.yaml +++ b/ingestion_tools/dataset_configs/10434.yaml @@ -41,8 +41,8 @@ datasets: id: CL:0000010 name: cultured cell cross_references: - publications: 10.1101/2024.06.27.600657 - related_database_entries: EMD-44921, EMD-44909, EMD-44922 + publications: 10.1038/s41467-025-56045-z, 10.1101/2024.06.27.600657 + related_database_entries: EMD-44921, EMD-44909, EMD-44922, EMD-46973 dataset_description: Michalak, Sun, Sochacki et al. 2024 unroofing manuscript contains 10 grids. This is grid 9 of 10 and contains apical membranes of HEK293 cells. The cells are expressing FerriTag and Hip1R-GFP-FKBP off of plasmids. The diff --git a/ingestion_tools/dataset_configs/10435.yaml b/ingestion_tools/dataset_configs/10435.yaml index a12bf230b..ff92e6818 100644 --- a/ingestion_tools/dataset_configs/10435.yaml +++ b/ingestion_tools/dataset_configs/10435.yaml @@ -41,8 +41,8 @@ datasets: id: CL:0000010 name: cultured cell cross_references: - publications: 10.1101/2024.06.27.600657 - related_database_entries: EMD-44921, EMD-44909, EMD-44922 + publications: 10.1038/s41467-025-56045-z, 10.1101/2024.06.27.600657 + related_database_entries: EMD-44921, EMD-44909, EMD-44922, EMD-46973 dataset_description: Michalak, Sun, Sochacki et al. 2024 unroofing manuscript contains 10 grids. This is grid 10 of 10 and contains apical membranes of HEK293 cells. The cells are expressing FerriTag and Hip1R-GFP-FKBP off of plasmids. The From 6d24b8203cebc18ec8d57439ab998b03e8ab7fb9 Mon Sep 17 00:00:00 2001 From: uermel Date: Tue, 14 Jan 2025 08:42:12 -0800 Subject: [PATCH 08/10] add deposition keyphotos --- ingestion_tools/dataset_configs/10426.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ingestion_tools/dataset_configs/10426.yaml b/ingestion_tools/dataset_configs/10426.yaml index 556bfd52b..4c9d8a973 100644 --- a/ingestion_tools/dataset_configs/10426.yaml +++ b/ingestion_tools/dataset_configs/10426.yaml @@ -99,8 +99,8 @@ deposition_keyphotos: - sources: - literal: value: - snapshot: null #"cryoetportal-rawdatasets-dev/deposition_key_photos/deposition_10306_snapshot.png" - thumbnail: null #"cryoetportal-rawdatasets-dev/deposition_key_photos/deposition_10306_thumbnail.png" + snapshot: "cryoetportal-rawdatasets-dev/deposition_key_photos/deposition_10306_snapshot.png" + thumbnail: "cryoetportal-rawdatasets-dev/deposition_key_photos/deposition_10306_thumbnail.png" frames: - sources: From 1480cb148bad8edeba8c996cb049ec15bcfda33c Mon Sep 17 00:00:00 2001 From: uermel Date: Wed, 22 Jan 2025 18:26:24 -0800 Subject: [PATCH 09/10] fix ts pattern for 10429 --- ingestion_tools/dataset_configs/10429.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ingestion_tools/dataset_configs/10429.yaml b/ingestion_tools/dataset_configs/10429.yaml index 30a422c09..ccb940b2e 100644 --- a/ingestion_tools/dataset_configs/10429.yaml +++ b/ingestion_tools/dataset_configs/10429.yaml @@ -143,7 +143,7 @@ tiltseries: total_flux: float {tilt_series_total_flux} sources: - source_glob: - list_glob: 'tilt_series/{run_name}_bin8_align.st' + list_glob: 'tilt_series/{mdoc_name}_bin8_align.st' match_regex: ^.*\.st$ tomograms: From b04a93b308a49527260da7626002e4c26b9589aa Mon Sep 17 00:00:00 2001 From: uermel Date: Wed, 22 Jan 2025 18:49:32 -0800 Subject: [PATCH 10/10] actually fix ts pattern for 10429 by introducing new field in tsv --- ingestion_tools/dataset_configs/10429.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ingestion_tools/dataset_configs/10429.yaml b/ingestion_tools/dataset_configs/10429.yaml index ccb940b2e..84fdf82ae 100644 --- a/ingestion_tools/dataset_configs/10429.yaml +++ b/ingestion_tools/dataset_configs/10429.yaml @@ -143,7 +143,7 @@ tiltseries: total_flux: float {tilt_series_total_flux} sources: - source_glob: - list_glob: 'tilt_series/{mdoc_name}_bin8_align.st' + list_glob: 'tilt_series/{ts_prefix}_bin8_align.st' match_regex: ^.*\.st$ tomograms: