Harvest for Hone et al 2013 Created 17 May 14:23

Harvesting Log

[INFO] [2021-05-17 14:23:48] Created harvest instance #3866
[STOP] [2021-05-17 14:23:48] create_harvest_instance
[START] [2021-05-17 14:23:48] fetch_files
[STOP] [2021-05-17 14:23:48] fetch_files
[START] [2021-05-17 14:23:48] validate_each_file
[INFO] [2021-05-17 14:23:48] Looping over 3 formats...
[INFO] [2021-05-17 14:23:48] ...nodes (/app/public/data/hone_et_al_hone_/taxa.txt)
[INFO] [2021-05-17 14:23:48] Valid: /app/public/converted_csv/hone_et_al_hone__nodes_3866.csv (6196 lines)
[INFO] [2021-05-17 14:23:48] ...occurrences (/app/public/data/hone_et_al_hone_/occurrences.txt)
[INFO] [2021-05-17 14:23:49] Valid: /app/public/converted_csv/hone_et_al_hone__occurrences_3866.csv (6206 lines)
[INFO] [2021-05-17 14:23:49] ...measurements (/app/public/data/hone_et_al_hone_/measurements or facts.txt)
[INFO] [2021-05-17 14:23:49] Valid: /app/public/converted_csv/hone_et_al_hone__measurements_3866.csv (6206 lines)
[STOP] [2021-05-17 14:23:49] validate_each_file
[START] [2021-05-17 14:23:49] convert_to_csv
[INFO] [2021-05-17 14:23:49] Looping over 3 formats...
[INFO] [2021-05-17 14:23:49] ...nodes (/app/public/data/hone_et_al_hone_/taxa.txt)
[CMD] [2021-05-17 14:23:49] /usr/bin/sort /app/public/converted_csv/hone_et_al_hone__nodes_3866.csv > /app/public/converted_csv/hone_et_al_hone__nodes_3866.csv_sorted
[INFO] [2021-05-17 14:23:49] Converted: /app/public/converted_csv/hone_et_al_hone__nodes_3866.csv (6196 lines)
[INFO] [2021-05-17 14:23:49] ...occurrences (/app/public/data/hone_et_al_hone_/occurrences.txt)
[CMD] [2021-05-17 14:23:49] /usr/bin/sort /app/public/converted_csv/hone_et_al_hone__occurrences_3866.csv > /app/public/converted_csv/hone_et_al_hone__occurrences_3866.csv_sorted
[INFO] [2021-05-17 14:23:49] Converted: /app/public/converted_csv/hone_et_al_hone__occurrences_3866.csv (6206 lines)
[INFO] [2021-05-17 14:23:49] ...measurements (/app/public/data/hone_et_al_hone_/measurements or facts.txt)
[CMD] [2021-05-17 14:23:49] /usr/bin/sort /app/public/converted_csv/hone_et_al_hone__measurements_3866.csv > /app/public/converted_csv/hone_et_al_hone__measurements_3866.csv_sorted
[INFO] [2021-05-17 14:23:49] Converted: /app/public/converted_csv/hone_et_al_hone__measurements_3866.csv (6206 lines)
[STOP] [2021-05-17 14:23:49] convert_to_csv
[START] [2021-05-17 14:23:49] calculate_delta
[INFO] [2021-05-17 14:23:49] Looping over 3 formats...
[INFO] [2021-05-17 14:23:49] ...nodes (/app/public/data/hone_et_al_hone_/taxa.txt)
[CMD] [2021-05-17 14:23:49] echo "0a" > /app/public/diff/hone_et_al_hone__nodes_3866.diff
[CMD] [2021-05-17 14:23:49] tail -n +1 /app/public/converted_csv/hone_et_al_hone__nodes_3866.csv >> /app/public/diff/hone_et_al_hone__nodes_3866.diff
[CMD] [2021-05-17 14:23:49] echo "." >> /app/public/diff/hone_et_al_hone__nodes_3866.diff
[INFO] [2021-05-17 14:23:49] Created diff: /app/public/diff/hone_et_al_hone__nodes_3866.diff (6198 lines)
[INFO] [2021-05-17 14:23:49] ...occurrences (/app/public/data/hone_et_al_hone_/occurrences.txt)
[CMD] [2021-05-17 14:23:49] echo "0a" > /app/public/diff/hone_et_al_hone__occurrences_3866.diff
[CMD] [2021-05-17 14:23:49] tail -n +1 /app/public/converted_csv/hone_et_al_hone__occurrences_3866.csv >> /app/public/diff/hone_et_al_hone__occurrences_3866.diff
[CMD] [2021-05-17 14:23:49] echo "." >> /app/public/diff/hone_et_al_hone__occurrences_3866.diff
[INFO] [2021-05-17 14:23:49] Created diff: /app/public/diff/hone_et_al_hone__occurrences_3866.diff (6208 lines)
[INFO] [2021-05-17 14:23:49] ...measurements (/app/public/data/hone_et_al_hone_/measurements or facts.txt)
[CMD] [2021-05-17 14:23:49] echo "0a" > /app/public/diff/hone_et_al_hone__measurements_3866.diff
[CMD] [2021-05-17 14:23:49] tail -n +1 /app/public/converted_csv/hone_et_al_hone__measurements_3866.csv >> /app/public/diff/hone_et_al_hone__measurements_3866.diff
[CMD] [2021-05-17 14:23:50] echo "." >> /app/public/diff/hone_et_al_hone__measurements_3866.diff
[INFO] [2021-05-17 14:23:50] Created diff: /app/public/diff/hone_et_al_hone__measurements_3866.diff (6208 lines)
[STOP] [2021-05-17 14:23:50] calculate_delta
[START] [2021-05-17 14:23:50] parse_diff_and_store
[INFO] [2021-05-17 14:23:50] Handling diff: /app/public/diff/hone_et_al_hone__nodes_3866.diff (6198 lines)
[INFO] [2021-05-17 14:23:50] Loading nodes diff file into memory (6198 /app/public/diff/hone_et_al_hone__nodes_3866.diff lines)...
[WARN] [2021-05-17 14:23:50] Filtered Scientific Name `Amphiesma  inas` to `Amphiesma inas`
[INFO] [2021-05-17 14:23:52] Handling diff: /app/public/diff/hone_et_al_hone__occurrences_3866.diff (6208 lines)
[INFO] [2021-05-17 14:23:52] Loading occurrences diff file into memory (6208 /app/public/diff/hone_et_al_hone__occurrences_3866.diff lines)...
[INFO] [2021-05-17 14:23:54] Handling diff: /app/public/diff/hone_et_al_hone__measurements_3866.diff (6208 lines)
[INFO] [2021-05-17 14:23:54] Loading measurements diff file into memory (6208 /app/public/diff/hone_et_al_hone__measurements_3866.diff lines)...
[INFO] [2021-05-17 14:23:56] Storing 7101 ScientificNames
[INFO] [2021-05-17 14:23:56] Processing group of 7101 in 8 groups of 1000
[INFO] [2021-05-17 14:23:59] Average Time: 0.268
[INFO] [2021-05-17 14:23:59] Total Time: 3s
[INFO] [2021-05-17 14:23:59] last 3 / first 3: 0.72
[INFO] [2021-05-17 14:23:59] Std.Dev: 0.1; Max: 0.36
[INFO] [2021-05-17 14:23:59] Storing 7101 Nodes
[INFO] [2021-05-17 14:23:59] Processing group of 7101 in 8 groups of 1000
[INFO] [2021-05-17 14:24:01] Average Time: 0.23
[INFO] [2021-05-17 14:24:01] Total Time: 2s
[INFO] [2021-05-17 14:24:01] last 3 / first 3: 0.84
[INFO] [2021-05-17 14:24:01] Std.Dev: 0.08366600265340755; Max: 0.33
[INFO] [2021-05-17 14:24:01] Storing 6206 Occurrences
[INFO] [2021-05-17 14:24:01] Processing group of 6206 in 7 groups of 1000
[INFO] [2021-05-17 14:24:01] Average Time: 0.089
[INFO] [2021-05-17 14:24:01] Total Time: 1s
[INFO] [2021-05-17 14:24:01] last 3 / first 3: 0.73
[INFO] [2021-05-17 14:24:01] Std.Dev: 0.03162277660168379; Max: 0.1
[INFO] [2021-05-17 14:24:01] Storing 6206 OccurrenceMetadata
[INFO] [2021-05-17 14:24:01] Processing group of 6206 in 7 groups of 1000
[INFO] [2021-05-17 14:24:02] Average Time: 0.097
[INFO] [2021-05-17 14:24:02] Total Time: 1s
[INFO] [2021-05-17 14:24:02] last 3 / first 3: 0.73
[INFO] [2021-05-17 14:24:02] Std.Dev: 0.03162277660168379; Max: 0.11
[INFO] [2021-05-17 14:24:02] Storing 6206 Traits
[INFO] [2021-05-17 14:24:02] Processing group of 6206 in 7 groups of 1000
[INFO] [2021-05-17 14:24:04] Average Time: 0.253
[INFO] [2021-05-17 14:24:04] Total Time: 2s
[INFO] [2021-05-17 14:24:04] last 3 / first 3: 0.63
[INFO] [2021-05-17 14:24:04] Std.Dev: 0.09486832980505137; Max: 0.38
[INFO] [2021-05-17 14:24:04] Storing 6206 MetaTraits
[INFO] [2021-05-17 14:24:04] Processing group of 6206 in 7 groups of 1000
[INFO] [2021-05-17 14:24:05] Average Time: 0.117
[INFO] [2021-05-17 14:24:05] Total Time: 1s
[INFO] [2021-05-17 14:24:05] last 3 / first 3: 0.56
[INFO] [2021-05-17 14:24:05] Std.Dev: 0.05477225575051661; Max: 0.22
[STOP] [2021-05-17 14:24:05] parse_diff_and_store
[START] [2021-05-17 14:24:05] resolve_keys
[INFO] [2021-05-17 14:24:11] Occurrences to nodes (through scientific_names)...
[INFO] [2021-05-17 14:24:12] traits to occurrences...
[INFO] [2021-05-17 14:24:12] traits to nodes (through occurrences)...
[INFO] [2021-05-17 14:24:12] Traits to sex term...
[INFO] [2021-05-17 14:24:12] Traits to lifestage term...
[INFO] [2021-05-17 14:24:12] MetaTraits to traits...
[INFO] [2021-05-17 14:24:12] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-05-17 14:24:12] Assocs to occurrences...
[INFO] [2021-05-17 14:24:12] Assocs to nodes...
[INFO] [2021-05-17 14:24:12] Assoc to sex term...
[INFO] [2021-05-17 14:24:12] Assoc to lifestage term...
[INFO] [2021-05-17 14:24:12] MetaAssoc to assocs...
[STOP] [2021-05-17 14:24:12] resolve_keys
[START] [2021-05-17 14:24:12] hold_for_later_1
[STOP] [2021-05-17 14:24:12] hold_for_later_1
[START] [2021-05-17 14:24:12] hold_for_later_2
[STOP] [2021-05-17 14:24:12] hold_for_later_2
[START] [2021-05-17 14:24:12] resolve_missing_parents
[STOP] [2021-05-17 14:24:13] resolve_missing_parents
[START] [2021-05-17 14:24:13] rebuild_nodes
[START] [2021-05-17 14:24:13] Flattener#flatten
[START] [2021-05-17 14:24:13] Flattener#study_resource
[START] [2021-05-17 14:24:13] Flattener#build_ancestry
[STOP] [2021-05-17 14:24:13] Flattener#build_ancestry
[INFO] [2021-05-17 14:24:13] 7101 ancestry keys
[START] [2021-05-17 14:24:13] build_node_ancestors
[INFO] [2021-05-17 14:24:13] old ancestors deleted.
[STOP] [2021-05-17 14:24:13] build_node_ancestors
[START] [2021-05-17 14:24:14] Flattener#propagate_ancestor_ids
[STOP] [2021-05-17 14:24:14] Flattener#propagate_ancestor_ids
[STOP] [2021-05-17 14:24:14] Flattener#flatten
[STOP] [2021-05-17 14:24:14] rebuild_nodes
[START] [2021-05-17 14:24:14] resolve_missing_media_owners
[STOP] [2021-05-17 14:24:14] resolve_missing_media_owners
[START] [2021-05-17 14:24:14] sanitize_media_verbatims
[STOP] [2021-05-17 14:24:14] sanitize_media_verbatims
[START] [2021-05-17 14:24:14] queue_downloads
[STOP] [2021-05-17 14:24:14] queue_downloads
[START] [2021-05-17 14:24:14] parse_names
[WARN] [2021-05-17 14:24:14] I see 7101 names which still need to be parsed.
[WARN] [2021-05-17 14:24:20] I see 25 names which still need to be parsed.
[WARN] [2021-05-17 14:24:21] I see 1 names which still need to be parsed.
[STOP] [2021-05-17 14:24:22] parse_names
[START] [2021-05-17 14:24:22] denormalize_canonical_names_to_nodes
[STOP] [2021-05-17 14:24:22] denormalize_canonical_names_to_nodes
[START] [2021-05-17 14:24:22] match_nodes
[START] [2021-05-17 14:24:22] map_all_nodes_to_pages
[STOP] [2021-05-17 14:25:32] map_all_nodes_to_pages
[INFO] [2021-05-17 14:25:32] 268 Unmatched nodes (of 7101)! That's too many to output. Full list in /app/public/data/hone_et_al_hone_/unmatched_nodes.txt ; First 10: Canonical: Acontias brevipes; Node#94024857; ResourceID: Acontias_brevipes; Canonical: Acontophiops; Node#94024863; ResourceID: Acontophiops; Canonical: Afroablepharus; Node#94024885; ResourceID: Afroablepharus; Canonical: Afroablepharus duruarum; Node#94024886; ResourceID: Afroablepharus_duruarum; Canonical: Afroablepharus seydeli; Node#94024887; ResourceID: Afroablepharus_seydeli; Canonical: Afroablepharus wilsoni; Node#94024889; ResourceID: Afroablepharus_wilsoni; Canonical: Androngo; Node#94025098; ResourceID: Androngo; Canonical: Anomalopus verreauxii; Node#94025334; ResourceID: Anomalopus_verreauxii; Canonical: Apterygodon; Node#94025372; ResourceID: Apterygodon; Canonical: Bartleia; Node#94025491; ResourceID: Bartleia
[START] [2021-05-17 14:25:32] update_nodes
[STOP] [2021-05-17 14:25:35] update_nodes
[STOP] [2021-05-17 14:25:35] match_nodes
[START] [2021-05-17 14:25:35] reindex_search
[STOP] [2021-05-17 14:25:40] reindex_search
[START] [2021-05-17 14:25:40] normalize_units
[STOP] [2021-05-17 14:26:01] normalize_units
[START] [2021-05-17 14:26:01] calculate_statistics
[STOP] [2021-05-17 14:26:02] calculate_statistics
[START] [2021-05-17 14:26:02] complete_harvest_instance
[START] [2021-05-17 14:26:02] overall_tsv_creation
[INFO] [2021-05-17 14:26:02] Processing group of 7101 in 1 batches of 10000
[INFO] [2021-05-17 14:26:59] 6206 Traits (unfiltered)...
[INFO] [2021-05-17 14:28:09] 6206 Traits (filtered)...
[INFO] [2021-05-17 14:28:11] 0 Associations (filtered)...
[INFO] [2021-05-17 14:28:11] 0 metadata added.
[INFO] [2021-05-17 14:28:11] 0 metadata added.
[INFO] [2021-05-17 14:28:39] Average Time: 129.24
[INFO] [2021-05-17 14:28:39] Total Time: 2m38s
[STOP] [2021-05-17 14:28:39] overall_tsv_creation
[INFO] [2021-05-17 14:28:39] Done. Check your files:
[INFO] [2021-05-17 14:28:39] (7101 lines) /app/public/data/hone_et_al_hone_/publish_nodes.tsv
[INFO] [2021-05-17 14:28:39] (13252 lines) /app/public/data/hone_et_al_hone_/publish_node_ancestors.tsv
[INFO] [2021-05-17 14:28:39] (7101 lines) /app/public/data/hone_et_al_hone_/publish_scientific_names.tsv
[INFO] [2021-05-17 14:28:39] (6207 lines) /app/public/data/hone_et_al_hone_/publish_traits.tsv
[INFO] [2021-05-17 14:28:39] (1 lines) /app/public/data/hone_et_al_hone_/publish_metadata.tsv
[STOP] [2021-05-17 14:28:40] complete_harvest_instance
[START] [2021-05-17 14:28:40] completed
[STOP] [2021-05-17 14:28:40] completed
[STOP] [2021-05-17 14:28:40] logged process, took 292.04

Latest Process

17 May 14:23 EXITED currently processing 0