Harvest for marine ecology literature Created 02 Jan 11:28

Stage: completed
Fetched: 02 Jan 11:28
Validated: 02 Jan 11:28
Deltas Created 02 Jan 11:28
Units Normalized: 02 Jan 11:28
Ancestry Built: 02 Jan 11:28
Nodes Matched: 02 Jan 11:28
Names Parsed: 02 Jan 11:28
New Models Stored: 02 Jan 11:28
Indexed: 02 Jan 11:28
Completed: 02 Jan 11:30
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2020-01-02 11:28:12 -0500 by logger.rb/56815
[START] [2020-01-02 11:28:12] logged process
[START] [2020-01-02 11:28:12] create_harvest_instance
[STOP] [2020-01-02 11:28:13] create_harvest_instance
[START] [2020-01-02 11:28:13] fetch_files
[STOP] [2020-01-02 11:28:13] fetch_files
[START] [2020-01-02 11:28:13] validate_each_file
[STOP] [2020-01-02 11:28:13] validate_each_file
[START] [2020-01-02 11:28:13] convert_to_csv
[CMD] [2020-01-02 11:28:13] /usr/bin/sort /app/public/converted_csv/mar_eco_lit_v2_refs_19889.csv > /app/public/converted_csv/mar_eco_lit_v2_refs_19889.csv_sorted
[CMD] [2020-01-02 11:28:14] /usr/bin/sort /app/public/converted_csv/mar_eco_lit_v2_nodes_19890.csv > /app/public/converted_csv/mar_eco_lit_v2_nodes_19890.csv_sorted
[CMD] [2020-01-02 11:28:14] /usr/bin/sort /app/public/converted_csv/mar_eco_lit_v2_occurrences_19891.csv > /app/public/converted_csv/mar_eco_lit_v2_occurrences_19891.csv_sorted
[CMD] [2020-01-02 11:28:15] /usr/bin/sort /app/public/converted_csv/mar_eco_lit_v2_measurements_19892.csv > /app/public/converted_csv/mar_eco_lit_v2_measurements_19892.csv_sorted
[STOP] [2020-01-02 11:28:16] convert_to_csv
[START] [2020-01-02 11:28:16] calculate_delta
[CMD] [2020-01-02 11:28:16] echo "0a" > /app/public/diff/mar_eco_lit_v2_refs_19889.diff
[CMD] [2020-01-02 11:28:16] tail -n +1 /app/public/converted_csv/mar_eco_lit_v2_refs_19889.csv >> /app/public/diff/mar_eco_lit_v2_refs_19889.diff
[CMD] [2020-01-02 11:28:17] echo "." >> /app/public/diff/mar_eco_lit_v2_refs_19889.diff
[CMD] [2020-01-02 11:28:17] echo "0a" > /app/public/diff/mar_eco_lit_v2_nodes_19890.diff
[CMD] [2020-01-02 11:28:18] tail -n +1 /app/public/converted_csv/mar_eco_lit_v2_nodes_19890.csv >> /app/public/diff/mar_eco_lit_v2_nodes_19890.diff
[CMD] [2020-01-02 11:28:19] echo "." >> /app/public/diff/mar_eco_lit_v2_nodes_19890.diff
[CMD] [2020-01-02 11:28:19] echo "0a" > /app/public/diff/mar_eco_lit_v2_occurrences_19891.diff
[CMD] [2020-01-02 11:28:20] tail -n +1 /app/public/converted_csv/mar_eco_lit_v2_occurrences_19891.csv >> /app/public/diff/mar_eco_lit_v2_occurrences_19891.diff
[CMD] [2020-01-02 11:28:20] echo "." >> /app/public/diff/mar_eco_lit_v2_occurrences_19891.diff
[CMD] [2020-01-02 11:28:21] echo "0a" > /app/public/diff/mar_eco_lit_v2_measurements_19892.diff
[CMD] [2020-01-02 11:28:22] tail -n +1 /app/public/converted_csv/mar_eco_lit_v2_measurements_19892.csv >> /app/public/diff/mar_eco_lit_v2_measurements_19892.diff
[CMD] [2020-01-02 11:28:22] echo "." >> /app/public/diff/mar_eco_lit_v2_measurements_19892.diff
[STOP] [2020-01-02 11:28:23] calculate_delta
[START] [2020-01-02 11:28:23] parse_diff_and_store
[INFO] [2020-01-02 11:28:24] Loading refs diff file into memory (true lines)...
[INFO] [2020-01-02 11:28:24] Loading nodes diff file into memory (true lines)...
[INFO] [2020-01-02 11:28:25] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-01-02 11:28:26] Loading measurements diff file into memory (true lines)...
[INFO] [2020-01-02 11:28:30] Storing 20 References
[INFO] [2020-01-02 11:28:30] Processing group of 20 in 1 groups of 1000
[INFO] [2020-01-02 11:28:30] Average Time: 0.01
[INFO] [2020-01-02 11:28:30] Total Time: 1s
[INFO] [2020-01-02 11:28:30] Storing 532 ScientificNames
[INFO] [2020-01-02 11:28:30] Processing group of 532 in 1 groups of 1000
[INFO] [2020-01-02 11:28:31] Average Time: 0.25
[INFO] [2020-01-02 11:28:31] Total Time: 1s
[INFO] [2020-01-02 11:28:31] Storing 532 Nodes
[INFO] [2020-01-02 11:28:31] Processing group of 532 in 1 groups of 1000
[INFO] [2020-01-02 11:28:31] Average Time: 0.2
[INFO] [2020-01-02 11:28:31] Total Time: 1s
[INFO] [2020-01-02 11:28:31] Storing 520 Occurrences
[INFO] [2020-01-02 11:28:31] Processing group of 520 in 1 groups of 1000
[INFO] [2020-01-02 11:28:31] Average Time: 0.09
[INFO] [2020-01-02 11:28:31] Total Time: 1s
[INFO] [2020-01-02 11:28:31] Storing 1772 Traits
[INFO] [2020-01-02 11:28:31] Processing group of 1772 in 2 groups of 1000
[INFO] [2020-01-02 11:28:32] Average Time: 0.375
[INFO] [2020-01-02 11:28:32] Total Time: 1s
[INFO] [2020-01-02 11:28:32] Storing 1963 MetaTraits
[INFO] [2020-01-02 11:28:32] Processing group of 1963 in 2 groups of 1000
[INFO] [2020-01-02 11:28:32] Average Time: 0.145
[INFO] [2020-01-02 11:28:32] Total Time: 1s
[INFO] [2020-01-02 11:28:32] Storing 45 TraitsReferences
[INFO] [2020-01-02 11:28:32] Processing group of 45 in 1 groups of 1000
[INFO] [2020-01-02 11:28:32] Average Time: 0.01
[INFO] [2020-01-02 11:28:32] Total Time: 1s
[STOP] [2020-01-02 11:28:32] parse_diff_and_store
[START] [2020-01-02 11:28:32] resolve_keys
[INFO] [2020-01-02 11:28:37] Occurrences to nodes (through scientific_names)...
[INFO] [2020-01-02 11:28:37] traits to occurrences...
[INFO] [2020-01-02 11:28:37] traits to nodes (through occurrences)...
[INFO] [2020-01-02 11:28:37] Traits to sex term...
[INFO] [2020-01-02 11:28:37] Traits to lifestage term...
[INFO] [2020-01-02 11:28:37] MetaTraits to traits...
[INFO] [2020-01-02 11:28:37] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-01-02 11:28:37] Assocs to occurrences...
[INFO] [2020-01-02 11:28:37] Assocs to nodes...
[INFO] [2020-01-02 11:28:37] Assoc to sex term...
[INFO] [2020-01-02 11:28:37] Assoc to lifestage term...
[STOP] [2020-01-02 11:28:37] resolve_keys
[START] [2020-01-02 11:28:37] hold_for_later_1
[STOP] [2020-01-02 11:28:37] hold_for_later_1
[START] [2020-01-02 11:28:37] hold_for_later_2
[STOP] [2020-01-02 11:28:37] hold_for_later_2
[START] [2020-01-02 11:28:37] resolve_missing_parents
[STOP] [2020-01-02 11:28:37] resolve_missing_parents
[START] [2020-01-02 11:28:37] rebuild_nodes
[START] [2020-01-02 11:28:37] Flattener#flatten
[START] [2020-01-02 11:28:37] Flattener#study_resource
[START] [2020-01-02 11:28:37] Flattener#build_ancestry
[STOP] [2020-01-02 11:28:37] Flattener#build_ancestry
[INFO] [2020-01-02 11:28:37] 532 ancestry keys
[START] [2020-01-02 11:28:37] build_node_ancestors
[INFO] [2020-01-02 11:28:37] old ancestors deleted.
[STOP] [2020-01-02 11:28:37] build_node_ancestors
[START] [2020-01-02 11:28:37] Flattener#propagate_ancestor_ids
[STOP] [2020-01-02 11:28:37] Flattener#propagate_ancestor_ids
[STOP] [2020-01-02 11:28:37] Flattener#flatten
[STOP] [2020-01-02 11:28:37] rebuild_nodes
[START] [2020-01-02 11:28:37] resolve_missing_media_owners
[STOP] [2020-01-02 11:28:37] resolve_missing_media_owners
[START] [2020-01-02 11:28:37] sanitize_media_verbatims
[STOP] [2020-01-02 11:28:37] sanitize_media_verbatims
[START] [2020-01-02 11:28:37] queue_downloads
[STOP] [2020-01-02 11:28:37] queue_downloads
[START] [2020-01-02 11:28:37] parse_names
[WARN] [2020-01-02 11:28:37] I see 532 names which still need to be parsed.
[WARN] [2020-01-02 11:28:39] I see 13 names which still need to be parsed.
[WARN] [2020-01-02 11:28:40] I see 1 names which still need to be parsed.
[STOP] [2020-01-02 11:28:41] parse_names
[START] [2020-01-02 11:28:41] denormalize_canonical_names_to_nodes
[STOP] [2020-01-02 11:28:41] denormalize_canonical_names_to_nodes
[START] [2020-01-02 11:28:41] match_nodes
[START] [2020-01-02 11:28:41] map_all_nodes_to_pages
[STOP] [2020-01-02 11:28:57] map_all_nodes_to_pages
[INFO] [2020-01-02 11:28:57] Unmatched nodes (9 of 532): Stilbonematidae (#62791642); Astomonema (#62791748); Parastomonema (#62791837); Spelaeogriphacea (#62791726); Branchinecta raptor (#62791836); Kiwa puravida (#62791966); Typhlocybinae (#62792058); Antipathipolyeunoa nuttingi (#62791819); Calamyzinae (#62791841)
[START] [2020-01-02 11:28:57] update_nodes
[STOP] [2020-01-02 11:28:57] update_nodes
[STOP] [2020-01-02 11:28:57] match_nodes
[START] [2020-01-02 11:28:57] reindex_search
[STOP] [2020-01-02 11:28:58] reindex_search
[START] [2020-01-02 11:28:58] normalize_units
[STOP] [2020-01-02 11:28:58] normalize_units
[START] [2020-01-02 11:28:58] calculate_statistics
[STOP] [2020-01-02 11:28:58] calculate_statistics
[START] [2020-01-02 11:28:58] complete_harvest_instance
[START] [2020-01-02 11:28:58] overall_tsv_creation
[INFO] [2020-01-02 11:28:58] Processing group of 532 in 1 batches of 10000
[INFO] [2020-01-02 11:30:04] 749 Traits (unfiltered)...
[INFO] [2020-01-02 11:30:17] 749 Traits (filtered)...
[INFO] [2020-01-02 11:30:17] 0 Associations (filtered)...
[INFO] [2020-01-02 11:30:56] 2997 metadata added.
[INFO] [2020-01-02 11:30:56] 0 metadata added.
[INFO] [2020-01-02 11:30:56] Average Time: 76.89
[INFO] [2020-01-02 11:30:56] Total Time: 1m59s
[STOP] [2020-01-02 11:30:56] overall_tsv_creation
[INFO] [2020-01-02 11:30:56] Done. Check your files:
[INFO] [2020-01-02 11:30:57] (521 lines) /app/public/data/mar_eco_lit_v2/publish_nodes.tsv
[INFO] [2020-01-02 11:30:57] (10 lines) /app/public/data/mar_eco_lit_v2/publish_node_ancestors.tsv
[INFO] [2020-01-02 11:30:58] (532 lines) /app/public/data/mar_eco_lit_v2/publish_scientific_names.tsv
[INFO] [2020-01-02 11:30:59] (750 lines) /app/public/data/mar_eco_lit_v2/publish_traits.tsv
[INFO] [2020-01-02 11:30:59] (2998 lines) /app/public/data/mar_eco_lit_v2/publish_metadata.tsv
[STOP] [2020-01-02 11:30:59] complete_harvest_instance
[START] [2020-01-02 11:30:59] completed
[STOP] [2020-01-02 11:30:59] completed
[STOP] [2020-01-02 11:30:59] logged process, took 167.17

Latest Process