Harvest for Martins et al 2008 Created 19 Jan 14:51

Harvesting Log

[INFO] [2023-01-19 14:51:51] Created harvest instance #4262
[STOP] [2023-01-19 14:51:51] create_harvest_instance
[START] [2023-01-19 14:51:51] fetch_files
[STOP] [2023-01-19 14:51:51] fetch_files
[START] [2023-01-19 14:51:51] validate_each_file
[INFO] [2023-01-19 14:51:51] Looping over 3 formats...
[INFO] [2023-01-19 14:51:51] ...nodes (/app/public/data/martins_et_al_ma/taxa.txt)
[INFO] [2023-01-19 14:51:51] Valid: /app/public/data/martins_et_al_ma/converted_csv/martins_et_al_ma_nodes_30034.csv (92 lines)
[INFO] [2023-01-19 14:51:51] ...occurrences (/app/public/data/martins_et_al_ma/occurrences.txt)
[INFO] [2023-01-19 14:51:51] Valid: /app/public/data/martins_et_al_ma/converted_csv/martins_et_al_ma_occurrences_30035.csv (90 lines)
[INFO] [2023-01-19 14:51:51] ...measurements (/app/public/data/martins_et_al_ma/measurementsorfacts.txt)
[INFO] [2023-01-19 14:51:51] Valid: /app/public/data/martins_et_al_ma/converted_csv/martins_et_al_ma_measurements_30036.csv (270 lines)
[STOP] [2023-01-19 14:51:51] validate_each_file
[START] [2023-01-19 14:51:51] convert_to_csv
[INFO] [2023-01-19 14:51:51] Looping over 3 formats...
[INFO] [2023-01-19 14:51:51] ...nodes (/app/public/data/martins_et_al_ma/taxa.txt)
[CMD] [2023-01-19 14:51:51] /usr/bin/sort /app/public/data/martins_et_al_ma/converted_csv/martins_et_al_ma_nodes_30034.csv > /app/public/data/martins_et_al_ma/converted_csv/martins_et_al_ma_nodes_30034.csv_sorted
[INFO] [2023-01-19 14:51:51] Converted: /app/public/data/martins_et_al_ma/converted_csv/martins_et_al_ma_nodes_30034.csv (92 lines)
[INFO] [2023-01-19 14:51:51] ...occurrences (/app/public/data/martins_et_al_ma/occurrences.txt)
[CMD] [2023-01-19 14:51:51] /usr/bin/sort /app/public/data/martins_et_al_ma/converted_csv/martins_et_al_ma_occurrences_30035.csv > /app/public/data/martins_et_al_ma/converted_csv/martins_et_al_ma_occurrences_30035.csv_sorted
[INFO] [2023-01-19 14:51:52] Converted: /app/public/data/martins_et_al_ma/converted_csv/martins_et_al_ma_occurrences_30035.csv (90 lines)
[INFO] [2023-01-19 14:51:52] ...measurements (/app/public/data/martins_et_al_ma/measurementsorfacts.txt)
[CMD] [2023-01-19 14:51:52] /usr/bin/sort /app/public/data/martins_et_al_ma/converted_csv/martins_et_al_ma_measurements_30036.csv > /app/public/data/martins_et_al_ma/converted_csv/martins_et_al_ma_measurements_30036.csv_sorted
[INFO] [2023-01-19 14:51:52] Converted: /app/public/data/martins_et_al_ma/converted_csv/martins_et_al_ma_measurements_30036.csv (270 lines)
[STOP] [2023-01-19 14:51:52] convert_to_csv
[START] [2023-01-19 14:51:52] calculate_delta
[INFO] [2023-01-19 14:51:52] Looping over 3 formats...
[INFO] [2023-01-19 14:51:52] ...nodes (/app/public/data/martins_et_al_ma/taxa.txt)
[CMD] [2023-01-19 14:51:52] echo "0a" > /app/public/data/martins_et_al_ma/diff/martins_et_al_ma_nodes_30034.diff
[CMD] [2023-01-19 14:51:52] tail -n +1 /app/public/data/martins_et_al_ma/converted_csv/martins_et_al_ma_nodes_30034.csv >> /app/public/data/martins_et_al_ma/diff/martins_et_al_ma_nodes_30034.diff
[CMD] [2023-01-19 14:51:52] echo "." >> /app/public/data/martins_et_al_ma/diff/martins_et_al_ma_nodes_30034.diff
[INFO] [2023-01-19 14:51:52] Created diff: /app/public/data/martins_et_al_ma/diff/martins_et_al_ma_nodes_30034.diff (94 lines)
[INFO] [2023-01-19 14:51:52] ...occurrences (/app/public/data/martins_et_al_ma/occurrences.txt)
[CMD] [2023-01-19 14:51:52] echo "0a" > /app/public/data/martins_et_al_ma/diff/martins_et_al_ma_occurrences_30035.diff
[CMD] [2023-01-19 14:51:52] tail -n +1 /app/public/data/martins_et_al_ma/converted_csv/martins_et_al_ma_occurrences_30035.csv >> /app/public/data/martins_et_al_ma/diff/martins_et_al_ma_occurrences_30035.diff
[CMD] [2023-01-19 14:51:52] echo "." >> /app/public/data/martins_et_al_ma/diff/martins_et_al_ma_occurrences_30035.diff
[INFO] [2023-01-19 14:51:52] Created diff: /app/public/data/martins_et_al_ma/diff/martins_et_al_ma_occurrences_30035.diff (92 lines)
[INFO] [2023-01-19 14:51:52] ...measurements (/app/public/data/martins_et_al_ma/measurementsorfacts.txt)
[CMD] [2023-01-19 14:51:52] echo "0a" > /app/public/data/martins_et_al_ma/diff/martins_et_al_ma_measurements_30036.diff
[CMD] [2023-01-19 14:51:52] tail -n +1 /app/public/data/martins_et_al_ma/converted_csv/martins_et_al_ma_measurements_30036.csv >> /app/public/data/martins_et_al_ma/diff/martins_et_al_ma_measurements_30036.diff
[CMD] [2023-01-19 14:51:52] echo "." >> /app/public/data/martins_et_al_ma/diff/martins_et_al_ma_measurements_30036.diff
[INFO] [2023-01-19 14:51:52] Created diff: /app/public/data/martins_et_al_ma/diff/martins_et_al_ma_measurements_30036.diff (272 lines)
[STOP] [2023-01-19 14:51:52] calculate_delta
[START] [2023-01-19 14:51:52] parse_diff_and_store
[INFO] [2023-01-19 14:51:52] Handling diff: /app/public/data/martins_et_al_ma/diff/martins_et_al_ma_nodes_30034.diff (94 lines)
[INFO] [2023-01-19 14:51:52] Loading nodes diff file into memory (94 lines)...
[WARN] [2023-01-19 14:51:52] Filtered Scientific Name `Liophis typhlus  (Manaus)` to `Liophis typhlus (Manaus)`
[INFO] [2023-01-19 14:51:52] Storing 96 ScientificNames (192/92/94)
[INFO] [2023-01-19 14:51:52] Storing 96 Nodes (192/92/94)
[INFO] [2023-01-19 14:51:52] Handling diff: /app/public/data/martins_et_al_ma/diff/martins_et_al_ma_occurrences_30035.diff (92 lines)
[INFO] [2023-01-19 14:51:52] Loading occurrences diff file into memory (92 lines)...
[INFO] [2023-01-19 14:51:52] Storing 90 Occurrences (90/90/92)
[INFO] [2023-01-19 14:51:52] Handling diff: /app/public/data/martins_et_al_ma/diff/martins_et_al_ma_measurements_30036.diff (272 lines)
[INFO] [2023-01-19 14:51:52] Loading measurements diff file into memory (272 lines)...
[INFO] [2023-01-19 14:51:52] Storing 270 Traits (540/270/272)
[INFO] [2023-01-19 14:51:52] Storing 270 MetaTraits (540/270/272)
[STOP] [2023-01-19 14:51:52] parse_diff_and_store
[START] [2023-01-19 14:51:52] resolve_keys
[2023-01-19 14:51:52] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-01-19 14:51:59] Occurrences to nodes (through scientific_names)...
[INFO] [2023-01-19 14:51:59] traits to occurrences...
[INFO] [2023-01-19 14:52:00] traits to nodes (through occurrences)...
[INFO] [2023-01-19 14:52:00] Traits to sex term...
[INFO] [2023-01-19 14:52:00] Traits to lifestage term...
[INFO] [2023-01-19 14:52:00] MetaTraits to traits...
[INFO] [2023-01-19 14:52:00] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-01-19 14:52:00] Assocs to occurrences...
[INFO] [2023-01-19 14:52:00] Assocs to nodes...
[INFO] [2023-01-19 14:52:00] Assoc to sex term...
[INFO] [2023-01-19 14:52:00] Assoc to lifestage term...
[INFO] [2023-01-19 14:52:00] MetaAssoc to assocs...
[STOP] [2023-01-19 14:52:00] resolve_keys
[START] [2023-01-19 14:52:00] hold_for_later_1
[STOP] [2023-01-19 14:52:00] hold_for_later_1
[START] [2023-01-19 14:52:00] hold_for_later_2
[STOP] [2023-01-19 14:52:00] hold_for_later_2
[START] [2023-01-19 14:52:00] resolve_missing_parents
[STOP] [2023-01-19 14:52:00] resolve_missing_parents
[START] [2023-01-19 14:52:00] rebuild_nodes
[START] [2023-01-19 14:52:00] Flattener#flatten
[START] [2023-01-19 14:52:00] Flattener#study_resource
[START] [2023-01-19 14:52:00] Flattener#build_ancestry
[STOP] [2023-01-19 14:52:00] Flattener#build_ancestry
[INFO] [2023-01-19 14:52:00] 96 ancestry keys
[START] [2023-01-19 14:52:00] build_node_ancestors
[INFO] [2023-01-19 14:52:00] old ancestors deleted.
[STOP] [2023-01-19 14:52:00] build_node_ancestors
[START] [2023-01-19 14:52:00] Flattener#propagate_ancestor_ids
[STOP] [2023-01-19 14:52:00] Flattener#propagate_ancestor_ids
[STOP] [2023-01-19 14:52:00] Flattener#flatten
[STOP] [2023-01-19 14:52:00] rebuild_nodes
[START] [2023-01-19 14:52:00] resolve_missing_media_owners
[STOP] [2023-01-19 14:52:00] resolve_missing_media_owners
[START] [2023-01-19 14:52:00] sanitize_media_verbatims
[STOP] [2023-01-19 14:52:00] sanitize_media_verbatims
[START] [2023-01-19 14:52:01] queue_downloads
[STOP] [2023-01-19 14:52:01] queue_downloads
[START] [2023-01-19 14:52:01] parse_names
[WARN] [2023-01-19 14:52:01] I see 96 names which still need to be parsed.
[WARN] [2023-01-19 14:52:01] Names to parse: 96 formatted: 96 learned: 95 parsed: 96
[STOP] [2023-01-19 14:52:02] parse_names
[START] [2023-01-19 14:52:02] denormalize_canonical_names_to_nodes
[STOP] [2023-01-19 14:52:02] denormalize_canonical_names_to_nodes
[START] [2023-01-19 14:52:02] match_nodes
[START] [2023-01-19 14:52:02] map_all_nodes_to_pages
[STOP] [2023-01-19 14:52:08] map_all_nodes_to_pages
[INFO] [2023-01-19 14:52:08] Unmatched nodes (7 of 96): Canonical: Liophis schotti; Node#122416771; ResourceID: Liophis schotti; Canonical: Liophis typhlus; Node#122416773; ResourceID: Liophis typhlus  (Manaus); Canonical: Liophis typhlus; Node#122416774; ResourceID: Liophis typhlus (Atlantic); Canonical: Liophis typhlus; Node#122416775; ResourceID: Liophis typhlus (Atlantic); Canonical: Pseudoboa neuwiedi; Node#122416789; ResourceID: Pseudoboa neuwiedi; Canonical: Taeniophallus breviceps; Node#122416799; ResourceID: Taeniophallus breviceps; Canonical: Xenoxybelis argenteus; Node#122416813; ResourceID: Xenoxybelis argenteus
[START] [2023-01-19 14:52:08] update_nodes
[STOP] [2023-01-19 14:52:08] update_nodes
[STOP] [2023-01-19 14:52:08] match_nodes
[START] [2023-01-19 14:52:08] reindex_search
[STOP] [2023-01-19 14:52:08] reindex_search
[START] [2023-01-19 14:52:08] normalize_units
[STOP] [2023-01-19 14:52:08] normalize_units
[START] [2023-01-19 14:52:08] calculate_statistics
[INFO] [2023-01-19 14:52:08] Duplicate page_id count: 0
[STOP] [2023-01-19 14:52:08] calculate_statistics
[START] [2023-01-19 14:52:08] complete_harvest_instance
[START] [2023-01-19 14:52:08] overall_tsv_creation
[INFO] [2023-01-19 14:52:08] Exporting 96 nodes as TSV in batches of 10000...
[INFO] [2023-01-19 14:52:08] Processing group of 96 in 1 batches of 10000
[INFO] [2023-01-19 14:52:08] 270 Traits (unfiltered) and 0 associations...
[INFO] [2023-01-19 14:52:08] Building Traits map for 96 nodes (this can take a while)...
[INFO] [2023-01-19 14:52:08] Mapped 270 traits (270 meta) for 96 nodes.
[INFO] [2023-01-19 14:52:08] Building Associations map (this can take a while)...
[INFO] [2023-01-19 14:52:08] Done. 0 assocs mapped (0 meta).
[INFO] [2023-01-19 14:52:08] Adding 270 traits...
[INFO] [2023-01-19 14:52:08] 0 metadata added.
[INFO] [2023-01-19 14:52:08] Adding 0 assocs...
[INFO] [2023-01-19 14:52:08] 0 metadata added.
[INFO] [2023-01-19 14:52:52] Processed 96/96 nodes
[INFO] [2023-01-19 14:52:52] Average Time: 44.13
[INFO] [2023-01-19 14:52:52] Total Time: 45s
[STOP] [2023-01-19 14:52:52] overall_tsv_creation
[INFO] [2023-01-19 14:52:52] Done. Check your files:
[INFO] [2023-01-19 14:52:52] (94 lines) /app/public/data/martins_et_al_ma/publish_nodes.tsv
[INFO] [2023-01-19 14:52:52] (366 lines) /app/public/data/martins_et_al_ma/publish_node_ancestors.tsv
[INFO] [2023-01-19 14:52:52] (96 lines) /app/public/data/martins_et_al_ma/publish_scientific_names.tsv
[INFO] [2023-01-19 14:52:52] (271 lines) /app/public/data/martins_et_al_ma/publish_traits.tsv
[INFO] [2023-01-19 14:52:52] (1 lines) /app/public/data/martins_et_al_ma/publish_metadata.tsv
[STOP] [2023-01-19 14:52:52] complete_harvest_instance
[START] [2023-01-19 14:52:52] completed
[STOP] [2023-01-19 14:52:52] completed
[STOP] [2023-01-19 14:52:52] logged process, took 60.91

Latest Process

19 Jan 14:50 EXITED currently processing 0