Harvest for Smith et al 2011 Created 13 Oct 13:22

Harvesting Log

[INFO] [2023-10-13 13:22:25] Created harvest instance #4447
[STOP] [2023-10-13 13:22:25] create_harvest_instance
[START] [2023-10-13 13:22:25] fetch_files
[STOP] [2023-10-13 13:22:25] fetch_files
[START] [2023-10-13 13:22:25] validate_each_file
[INFO] [2023-10-13 13:22:25] Looping over 4 formats...
[INFO] [2023-10-13 13:22:25] ...refs (/app/public/data/smith_et_al_smit/references.txt)
[INFO] [2023-10-13 13:22:26] Valid: /app/public/data/smith_et_al_smit/converted_csv/smith_et_al_smit_refs_30783.csv (161 lines)
[INFO] [2023-10-13 13:22:26] ...nodes (/app/public/data/smith_et_al_smit/taxa.txt)
[INFO] [2023-10-13 13:22:26] Valid: /app/public/data/smith_et_al_smit/converted_csv/smith_et_al_smit_nodes_30784.csv (4862 lines)
[INFO] [2023-10-13 13:22:26] ...occurrences (/app/public/data/smith_et_al_smit/occurrences.txt)
[INFO] [2023-10-13 13:22:27] Valid: /app/public/data/smith_et_al_smit/converted_csv/smith_et_al_smit_occurrences_30785.csv (5703 lines)
[INFO] [2023-10-13 13:22:27] ...measurements (/app/public/data/smith_et_al_smit/measurements-or-facts.txt)
[INFO] [2023-10-13 13:22:27] Valid: /app/public/data/smith_et_al_smit/converted_csv/smith_et_al_smit_measurements_30786.csv (9735 lines)
[STOP] [2023-10-13 13:22:27] validate_each_file
[START] [2023-10-13 13:22:27] convert_to_csv
[INFO] [2023-10-13 13:22:27] Looping over 4 formats...
[INFO] [2023-10-13 13:22:27] ...refs (/app/public/data/smith_et_al_smit/references.txt)
[CMD] [2023-10-13 13:22:27] /usr/bin/sort /app/public/data/smith_et_al_smit/converted_csv/smith_et_al_smit_refs_30783.csv > /app/public/data/smith_et_al_smit/converted_csv/smith_et_al_smit_refs_30783.csv_sorted
[INFO] [2023-10-13 13:22:27] Converted: /app/public/data/smith_et_al_smit/converted_csv/smith_et_al_smit_refs_30783.csv (161 lines)
[INFO] [2023-10-13 13:22:27] ...nodes (/app/public/data/smith_et_al_smit/taxa.txt)
[CMD] [2023-10-13 13:22:27] /usr/bin/sort /app/public/data/smith_et_al_smit/converted_csv/smith_et_al_smit_nodes_30784.csv > /app/public/data/smith_et_al_smit/converted_csv/smith_et_al_smit_nodes_30784.csv_sorted
[INFO] [2023-10-13 13:22:28] Converted: /app/public/data/smith_et_al_smit/converted_csv/smith_et_al_smit_nodes_30784.csv (4862 lines)
[INFO] [2023-10-13 13:22:28] ...occurrences (/app/public/data/smith_et_al_smit/occurrences.txt)
[CMD] [2023-10-13 13:22:28] /usr/bin/sort /app/public/data/smith_et_al_smit/converted_csv/smith_et_al_smit_occurrences_30785.csv > /app/public/data/smith_et_al_smit/converted_csv/smith_et_al_smit_occurrences_30785.csv_sorted
[INFO] [2023-10-13 13:22:28] Converted: /app/public/data/smith_et_al_smit/converted_csv/smith_et_al_smit_occurrences_30785.csv (5703 lines)
[INFO] [2023-10-13 13:22:28] ...measurements (/app/public/data/smith_et_al_smit/measurements-or-facts.txt)
[CMD] [2023-10-13 13:22:28] /usr/bin/sort /app/public/data/smith_et_al_smit/converted_csv/smith_et_al_smit_measurements_30786.csv > /app/public/data/smith_et_al_smit/converted_csv/smith_et_al_smit_measurements_30786.csv_sorted
[INFO] [2023-10-13 13:22:28] Converted: /app/public/data/smith_et_al_smit/converted_csv/smith_et_al_smit_measurements_30786.csv (9735 lines)
[STOP] [2023-10-13 13:22:28] convert_to_csv
[START] [2023-10-13 13:22:28] calculate_delta
[INFO] [2023-10-13 13:22:28] Looping over 4 formats...
[INFO] [2023-10-13 13:22:28] ...refs (/app/public/data/smith_et_al_smit/references.txt)
[CMD] [2023-10-13 13:22:28] echo "0a" > /app/public/data/smith_et_al_smit/diff/smith_et_al_smit_refs_30783.diff
[CMD] [2023-10-13 13:22:28] tail -n +1 /app/public/data/smith_et_al_smit/converted_csv/smith_et_al_smit_refs_30783.csv >> /app/public/data/smith_et_al_smit/diff/smith_et_al_smit_refs_30783.diff
[CMD] [2023-10-13 13:22:28] echo "." >> /app/public/data/smith_et_al_smit/diff/smith_et_al_smit_refs_30783.diff
[INFO] [2023-10-13 13:22:28] Created diff: /app/public/data/smith_et_al_smit/diff/smith_et_al_smit_refs_30783.diff (163 lines)
[INFO] [2023-10-13 13:22:28] ...nodes (/app/public/data/smith_et_al_smit/taxa.txt)
[CMD] [2023-10-13 13:22:28] echo "0a" > /app/public/data/smith_et_al_smit/diff/smith_et_al_smit_nodes_30784.diff
[CMD] [2023-10-13 13:22:28] tail -n +1 /app/public/data/smith_et_al_smit/converted_csv/smith_et_al_smit_nodes_30784.csv >> /app/public/data/smith_et_al_smit/diff/smith_et_al_smit_nodes_30784.diff
[CMD] [2023-10-13 13:22:28] echo "." >> /app/public/data/smith_et_al_smit/diff/smith_et_al_smit_nodes_30784.diff
[INFO] [2023-10-13 13:22:28] Created diff: /app/public/data/smith_et_al_smit/diff/smith_et_al_smit_nodes_30784.diff (4864 lines)
[INFO] [2023-10-13 13:22:28] ...occurrences (/app/public/data/smith_et_al_smit/occurrences.txt)
[CMD] [2023-10-13 13:22:28] echo "0a" > /app/public/data/smith_et_al_smit/diff/smith_et_al_smit_occurrences_30785.diff
[CMD] [2023-10-13 13:22:28] tail -n +1 /app/public/data/smith_et_al_smit/converted_csv/smith_et_al_smit_occurrences_30785.csv >> /app/public/data/smith_et_al_smit/diff/smith_et_al_smit_occurrences_30785.diff
[CMD] [2023-10-13 13:22:29] echo "." >> /app/public/data/smith_et_al_smit/diff/smith_et_al_smit_occurrences_30785.diff
[INFO] [2023-10-13 13:22:29] Created diff: /app/public/data/smith_et_al_smit/diff/smith_et_al_smit_occurrences_30785.diff (5705 lines)
[INFO] [2023-10-13 13:22:29] ...measurements (/app/public/data/smith_et_al_smit/measurements-or-facts.txt)
[CMD] [2023-10-13 13:22:29] echo "0a" > /app/public/data/smith_et_al_smit/diff/smith_et_al_smit_measurements_30786.diff
[CMD] [2023-10-13 13:22:29] tail -n +1 /app/public/data/smith_et_al_smit/converted_csv/smith_et_al_smit_measurements_30786.csv >> /app/public/data/smith_et_al_smit/diff/smith_et_al_smit_measurements_30786.diff
[CMD] [2023-10-13 13:22:29] echo "." >> /app/public/data/smith_et_al_smit/diff/smith_et_al_smit_measurements_30786.diff
[INFO] [2023-10-13 13:22:29] Created diff: /app/public/data/smith_et_al_smit/diff/smith_et_al_smit_measurements_30786.diff (9737 lines)
[STOP] [2023-10-13 13:22:29] calculate_delta
[START] [2023-10-13 13:22:29] parse_diff_and_store
[INFO] [2023-10-13 13:22:29] Handling diff: /app/public/data/smith_et_al_smit/diff/smith_et_al_smit_refs_30783.diff (163 lines)
[INFO] [2023-10-13 13:22:29] Loading refs diff file into memory (163 lines)...
[INFO] [2023-10-13 13:22:29] Storing 161 References (161/161/163)
[INFO] [2023-10-13 13:22:29] Handling diff: /app/public/data/smith_et_al_smit/diff/smith_et_al_smit_nodes_30784.diff (4864 lines)
[INFO] [2023-10-13 13:22:29] Loading nodes diff file into memory (4864 lines)...
[WARN] [2023-10-13 13:22:29] Filtered Scientific Name `Brachyprotoma  obtusata` to `Brachyprotoma obtusata`
[WARN] [2023-10-13 13:22:30] Filtered Scientific Name `Holmesina  occidentalis` to `Holmesina occidentalis`
[WARN] [2023-10-13 13:22:30] Filtered Scientific Name `Holmesina  paulacoutoi` to `Holmesina paulacoutoi`
[WARN] [2023-10-13 13:22:30] Filtered Scientific Name `Holmesina  septentrionalis` to `Holmesina septentrionalis`
[INFO] [2023-10-13 13:22:31] Storing 6277 ScientificNames (12554/4862/4864)
[INFO] [2023-10-13 13:22:33] Storing 6277 Nodes (12554/4862/4864)
[INFO] [2023-10-13 13:22:35] Handling diff: /app/public/data/smith_et_al_smit/diff/smith_et_al_smit_occurrences_30785.diff (5705 lines)
[INFO] [2023-10-13 13:22:35] Loading occurrences diff file into memory (5705 lines)...
[INFO] [2023-10-13 13:22:36] Storing 5703 Occurrences (11406/5703/5705)
[INFO] [2023-10-13 13:22:37] Storing 5703 OccurrenceMetadata (11406/5703/5705)
[INFO] [2023-10-13 13:22:38] Handling diff: /app/public/data/smith_et_al_smit/diff/smith_et_al_smit_measurements_30786.diff (9737 lines)
[INFO] [2023-10-13 13:22:38] Loading measurements diff file into memory (9737 lines)...
[INFO] [2023-10-13 13:22:44] Storing 9735 Traits (39655/9735/9737)
[INFO] [2023-10-13 13:22:47] Storing 20752 MetaTraits (39655/9735/9737)
[INFO] [2023-10-13 13:22:50] Storing 9168 TraitsReferences (39655/9735/9737)
[STOP] [2023-10-13 13:22:50] parse_diff_and_store
[START] [2023-10-13 13:22:50] resolve_keys
[2023-10-13 13:22:52] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 13:22:59] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 13:23:00] traits to occurrences...
[INFO] [2023-10-13 13:23:00] traits to nodes (through occurrences)...
[INFO] [2023-10-13 13:23:00] Traits to sex term...
[INFO] [2023-10-13 13:23:01] Traits to lifestage term...
[INFO] [2023-10-13 13:23:01] MetaTraits to traits...
[INFO] [2023-10-13 13:23:01] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 13:23:02] Assocs to occurrences...
[INFO] [2023-10-13 13:23:02] Assocs to nodes...
[INFO] [2023-10-13 13:23:02] Assoc to sex term...
[INFO] [2023-10-13 13:23:02] Assoc to lifestage term...
[INFO] [2023-10-13 13:23:02] MetaAssoc to assocs...
[STOP] [2023-10-13 13:23:02] resolve_keys
[START] [2023-10-13 13:23:02] hold_for_later_1
[STOP] [2023-10-13 13:23:02] hold_for_later_1
[START] [2023-10-13 13:23:02] hold_for_later_2
[STOP] [2023-10-13 13:23:02] hold_for_later_2
[START] [2023-10-13 13:23:02] resolve_missing_parents
[STOP] [2023-10-13 13:23:02] resolve_missing_parents
[START] [2023-10-13 13:23:02] rebuild_nodes
[START] [2023-10-13 13:23:02] Flattener#flatten
[START] [2023-10-13 13:23:02] Flattener#study_resource
[START] [2023-10-13 13:23:02] Flattener#build_ancestry
[STOP] [2023-10-13 13:23:02] Flattener#build_ancestry
[INFO] [2023-10-13 13:23:02] 6277 ancestry keys
[START] [2023-10-13 13:23:02] build_node_ancestors
[INFO] [2023-10-13 13:23:02] old ancestors deleted.
[STOP] [2023-10-13 13:23:03] build_node_ancestors
[START] [2023-10-13 13:23:04] Flattener#propagate_ancestor_ids
[STOP] [2023-10-13 13:23:04] Flattener#propagate_ancestor_ids
[STOP] [2023-10-13 13:23:04] Flattener#flatten
[STOP] [2023-10-13 13:23:04] rebuild_nodes
[START] [2023-10-13 13:23:04] resolve_missing_media_owners
[STOP] [2023-10-13 13:23:04] resolve_missing_media_owners
[START] [2023-10-13 13:23:04] sanitize_media_verbatims
[STOP] [2023-10-13 13:23:04] sanitize_media_verbatims
[START] [2023-10-13 13:23:04] queue_downloads
[STOP] [2023-10-13 13:23:04] queue_downloads
[START] [2023-10-13 13:23:04] parse_names
[WARN] [2023-10-13 13:23:04] I see 6277 names which still need to be parsed.
[WARN] [2023-10-13 13:23:05] Names to parse: 6277 formatted: 6277 learned: 6270 parsed: 6277
[STOP] [2023-10-13 13:23:09] parse_names
[START] [2023-10-13 13:23:09] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 13:23:10] denormalize_canonical_names_to_nodes
[START] [2023-10-13 13:23:10] match_nodes
[START] [2023-10-13 13:23:10] map_all_nodes_to_pages
[STOP] [2023-10-13 13:24:23] map_all_nodes_to_pages
[INFO] [2023-10-13 13:24:23] 225 Unmatched nodes (of 6277)! That's too many to output. Full list in /app/public/data/smith_et_al_smit/unmatched_nodes.txt ; First 10: Canonical: Akodon olivaceus; Node#137168302; ResourceID: Akodon_olivaceus; Canonical: Akodon xanthorhinus; Node#137168318; ResourceID: Akodon_xanthorhinus; Canonical: Alticola stracheyi; Node#137168375; ResourceID: Alticola_stracheyi; Canonical: Apodemus flavicollis; Node#137168491; ResourceID: Apodemus_flavicollis; Canonical: Apodemus hermonensis; Node#137168494; ResourceID: Apodemus_hermonensis; Canonical: Arvicanthis somalicus; Node#137168582; ResourceID: Arvicanthis_somalicus; Canonical: Bunomys heinrichi; Node#137168804; ResourceID: Bunomys_heinrichi; Canonical: Chrotomys; Node#137169210; ResourceID: Rodentia/Muridae/Chrotomys; Canonical: Clethrionomys sikotanensis; Node#137169234; ResourceID: Clethrionomys_sikotanensis; Canonical: Crunomys rabori; Node#137169475; ResourceID: Crunomys_rabori
[START] [2023-10-13 13:24:23] update_nodes
[STOP] [2023-10-13 13:24:26] update_nodes
[STOP] [2023-10-13 13:24:26] match_nodes
[START] [2023-10-13 13:24:26] reindex_search
[STOP] [2023-10-13 13:24:31] reindex_search
[START] [2023-10-13 13:24:31] normalize_units
[STOP] [2023-10-13 13:24:46] normalize_units
[START] [2023-10-13 13:24:46] calculate_statistics
[INFO] [2023-10-13 13:24:52] Duplicate page_id count: 0
[STOP] [2023-10-13 13:24:52] calculate_statistics
[START] [2023-10-13 13:24:52] complete_harvest_instance
[START] [2023-10-13 13:24:52] overall_tsv_creation
[INFO] [2023-10-13 13:24:52] Exporting 6277 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 13:24:52] Processing group of 6277 in 1 batches of 10000
[INFO] [2023-10-13 13:25:03] 9735 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 13:25:03] Building Traits map for 6277 nodes (this can take a while)...
[INFO] [2023-10-13 13:25:09] Mapped 9735 traits (20752 meta) for 6277 nodes.
[INFO] [2023-10-13 13:25:09] Building Associations map (this can take a while)...
[INFO] [2023-10-13 13:25:12] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 13:25:12] Adding 9735 traits...
[INFO] [2023-10-13 13:25:15] 18900 metadata added.
[INFO] [2023-10-13 13:25:15] Adding 0 assocs...
[INFO] [2023-10-13 13:25:15] 0 metadata added.
[INFO] [2023-10-13 13:26:00] Processed 6277/6277 nodes
[INFO] [2023-10-13 13:26:00] Average Time: 65.42
[INFO] [2023-10-13 13:26:00] Total Time: 1m9s
[STOP] [2023-10-13 13:26:00] overall_tsv_creation
[INFO] [2023-10-13 13:26:00] Done. Check your files:
[INFO] [2023-10-13 13:26:00] (6277 lines) /app/public/data/smith_et_al_smit/publish_nodes.tsv
[INFO] [2023-10-13 13:26:00] (17201 lines) /app/public/data/smith_et_al_smit/publish_node_ancestors.tsv
[INFO] [2023-10-13 13:26:00] (6277 lines) /app/public/data/smith_et_al_smit/publish_scientific_names.tsv
[INFO] [2023-10-13 13:26:00] (9736 lines) /app/public/data/smith_et_al_smit/publish_traits.tsv
[INFO] [2023-10-13 13:26:00] (18901 lines) /app/public/data/smith_et_al_smit/publish_metadata.tsv
[STOP] [2023-10-13 13:26:01] complete_harvest_instance
[START] [2023-10-13 13:26:01] completed
[STOP] [2023-10-13 13:26:01] completed
[STOP] [2023-10-13 13:26:01] logged process, took 215.24

Latest Process

13 Oct 13:22 EXITED currently processing 0