Harvest for McDaniel et al 2012 Created 15 Jan 16:31

Stage: completed
Fetched: 15 Jan 16:31
Validated: 15 Jan 16:31
Deltas Created 15 Jan 16:31
Units Normalized: 15 Jan 16:32
Ancestry Built: 15 Jan 16:31
Nodes Matched: 15 Jan 16:32
Names Parsed: 15 Jan 16:31
New Models Stored: 15 Jan 16:31
Indexed: 15 Jan 16:32
Completed: 15 Jan 16:33
Time to Harvest: less than a minute
Harvesting Log

(126 lines)
# Logfile created on 2020-01-15 16:31:31 -0500 by logger.rb/56815
[START] [2020-01-15 16:31:31] logged process
[START] [2020-01-15 16:31:31] create_harvest_instance
[STOP] [2020-01-15 16:31:32] create_harvest_instance
[START] [2020-01-15 16:31:32] fetch_files
[STOP] [2020-01-15 16:31:32] fetch_files
[START] [2020-01-15 16:31:32] validate_each_file
[STOP] [2020-01-15 16:31:32] validate_each_file
[START] [2020-01-15 16:31:32] convert_to_csv
[CMD] [2020-01-15 16:31:32] /usr/bin/sort /app/public/converted_csv/mdeam_nodes_19957.csv > /app/public/converted_csv/mdeam_nodes_19957.csv_sorted
[CMD] [2020-01-15 16:31:32] /usr/bin/sort /app/public/converted_csv/mdeam_occurrences_19958.csv > /app/public/converted_csv/mdeam_occurrences_19958.csv_sorted
[CMD] [2020-01-15 16:31:32] /usr/bin/sort /app/public/converted_csv/mdeam_measurements_19959.csv > /app/public/converted_csv/mdeam_measurements_19959.csv_sorted
[STOP] [2020-01-15 16:31:32] convert_to_csv
[START] [2020-01-15 16:31:32] calculate_delta
[CMD] [2020-01-15 16:31:32] echo "0a" > /app/public/diff/mdeam_nodes_19957.diff
[CMD] [2020-01-15 16:31:33] tail -n +1 /app/public/converted_csv/mdeam_nodes_19957.csv >> /app/public/diff/mdeam_nodes_19957.diff
[CMD] [2020-01-15 16:31:33] echo "." >> /app/public/diff/mdeam_nodes_19957.diff
[CMD] [2020-01-15 16:31:33] echo "0a" > /app/public/diff/mdeam_occurrences_19958.diff
[CMD] [2020-01-15 16:31:33] tail -n +1 /app/public/converted_csv/mdeam_occurrences_19958.csv >> /app/public/diff/mdeam_occurrences_19958.diff
[CMD] [2020-01-15 16:31:33] echo "." >> /app/public/diff/mdeam_occurrences_19958.diff
[CMD] [2020-01-15 16:31:33] echo "0a" > /app/public/diff/mdeam_measurements_19959.diff
[CMD] [2020-01-15 16:31:34] tail -n +1 /app/public/converted_csv/mdeam_measurements_19959.csv >> /app/public/diff/mdeam_measurements_19959.diff
[CMD] [2020-01-15 16:31:34] echo "." >> /app/public/diff/mdeam_measurements_19959.diff
[STOP] [2020-01-15 16:31:34] calculate_delta
[START] [2020-01-15 16:31:34] parse_diff_and_store
[INFO] [2020-01-15 16:31:34] Loading nodes diff file into memory (true lines)...
[INFO] [2020-01-15 16:31:34] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-01-15 16:31:35] Loading measurements diff file into memory (true lines)...
[INFO] [2020-01-15 16:31:37] Storing 492 ScientificNames
[INFO] [2020-01-15 16:31:37] Processing group of 492 in 1 groups of 1000
[INFO] [2020-01-15 16:31:37] Average Time: 0.27
[INFO] [2020-01-15 16:31:37] Total Time: 1s
[INFO] [2020-01-15 16:31:37] Storing 492 Nodes
[INFO] [2020-01-15 16:31:37] Processing group of 492 in 1 groups of 1000
[INFO] [2020-01-15 16:31:37] Average Time: 0.17
[INFO] [2020-01-15 16:31:37] Total Time: 1s
[INFO] [2020-01-15 16:31:37] Storing 487 Occurrences
[INFO] [2020-01-15 16:31:37] Processing group of 487 in 1 groups of 1000
[INFO] [2020-01-15 16:31:37] Average Time: 0.05
[INFO] [2020-01-15 16:31:37] Total Time: 1s
[INFO] [2020-01-15 16:31:37] Storing 487 Traits
[INFO] [2020-01-15 16:31:37] Processing group of 487 in 1 groups of 1000
[INFO] [2020-01-15 16:31:38] Average Time: 0.29
[INFO] [2020-01-15 16:31:38] Total Time: 1s
[INFO] [2020-01-15 16:31:38] Storing 1157 MetaTraits
[INFO] [2020-01-15 16:31:38] Processing group of 1157 in 2 groups of 1000
[INFO] [2020-01-15 16:31:38] Average Time: 0.08
[INFO] [2020-01-15 16:31:38] Total Time: 1s
[STOP] [2020-01-15 16:31:38] parse_diff_and_store
[START] [2020-01-15 16:31:38] resolve_keys
[INFO] [2020-01-15 16:31:42] Occurrences to nodes (through scientific_names)...
[INFO] [2020-01-15 16:31:42] traits to occurrences...
[INFO] [2020-01-15 16:31:42] traits to nodes (through occurrences)...
[INFO] [2020-01-15 16:31:42] Traits to sex term...
[INFO] [2020-01-15 16:31:42] Traits to lifestage term...
[INFO] [2020-01-15 16:31:42] MetaTraits to traits...
[INFO] [2020-01-15 16:31:42] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-01-15 16:31:42] Assocs to occurrences...
[INFO] [2020-01-15 16:31:42] Assocs to nodes...
[INFO] [2020-01-15 16:31:42] Assoc to sex term...
[INFO] [2020-01-15 16:31:42] Assoc to lifestage term...
[STOP] [2020-01-15 16:31:42] resolve_keys
[START] [2020-01-15 16:31:42] hold_for_later_1
[STOP] [2020-01-15 16:31:42] hold_for_later_1
[START] [2020-01-15 16:31:42] hold_for_later_2
[STOP] [2020-01-15 16:31:42] hold_for_later_2
[START] [2020-01-15 16:31:42] resolve_missing_parents
[STOP] [2020-01-15 16:31:42] resolve_missing_parents
[START] [2020-01-15 16:31:42] rebuild_nodes
[START] [2020-01-15 16:31:42] Flattener#flatten
[START] [2020-01-15 16:31:42] Flattener#study_resource
[START] [2020-01-15 16:31:42] Flattener#build_ancestry
[STOP] [2020-01-15 16:31:42] Flattener#build_ancestry
[INFO] [2020-01-15 16:31:42] 492 ancestry keys
[START] [2020-01-15 16:31:42] build_node_ancestors
[INFO] [2020-01-15 16:31:42] old ancestors deleted.
[STOP] [2020-01-15 16:31:43] build_node_ancestors
[START] [2020-01-15 16:31:43] Flattener#propagate_ancestor_ids
[STOP] [2020-01-15 16:31:43] Flattener#propagate_ancestor_ids
[STOP] [2020-01-15 16:31:43] Flattener#flatten
[STOP] [2020-01-15 16:31:43] rebuild_nodes
[START] [2020-01-15 16:31:43] resolve_missing_media_owners
[STOP] [2020-01-15 16:31:43] resolve_missing_media_owners
[START] [2020-01-15 16:31:43] sanitize_media_verbatims
[STOP] [2020-01-15 16:31:43] sanitize_media_verbatims
[START] [2020-01-15 16:31:43] queue_downloads
[STOP] [2020-01-15 16:31:43] queue_downloads
[START] [2020-01-15 16:31:43] parse_names
[WARN] [2020-01-15 16:31:43] I see 492 names which still need to be parsed.
[STOP] [2020-01-15 16:31:44] parse_names
[START] [2020-01-15 16:31:44] denormalize_canonical_names_to_nodes
[STOP] [2020-01-15 16:31:44] denormalize_canonical_names_to_nodes
[START] [2020-01-15 16:31:44] match_nodes
[START] [2020-01-15 16:31:44] map_all_nodes_to_pages
[STOP] [2020-01-15 16:32:16] map_all_nodes_to_pages
[INFO] [2020-01-15 16:32:16] 15 Unmatched nodes (of 492)! That's too many to output. First 10: Aerolindigia cappilacea (#62804174); Benitotania wakatenokaii (#62804202); Cyrtohypnum schistocalyx (#62804285); Dolichomitriopsis diversiformi (#62804310); Forsstroemia trichomitra (#62804346); Indusiella thianshanicanica (#62804396); Kiaeria gracialis (#62804407); Leptopterigynandrum austroalpinum (#62804418); Microbryum dallavianum (#62804450); Myurium hockstetteri (#62804459)
[START] [2020-01-15 16:32:16] update_nodes
[STOP] [2020-01-15 16:32:17] update_nodes
[STOP] [2020-01-15 16:32:17] match_nodes
[START] [2020-01-15 16:32:17] reindex_search
[STOP] [2020-01-15 16:32:17] reindex_search
[START] [2020-01-15 16:32:17] normalize_units
[STOP] [2020-01-15 16:32:17] normalize_units
[START] [2020-01-15 16:32:17] calculate_statistics
[STOP] [2020-01-15 16:32:17] calculate_statistics
[START] [2020-01-15 16:32:17] complete_harvest_instance
[START] [2020-01-15 16:32:17] overall_tsv_creation
[INFO] [2020-01-15 16:32:17] Processing group of 492 in 1 batches of 10000
[INFO] [2020-01-15 16:33:05] 487 Traits (unfiltered)...
[INFO] [2020-01-15 16:33:18] 487 Traits (filtered)...
[INFO] [2020-01-15 16:33:18] 0 Associations (filtered)...
[INFO] [2020-01-15 16:33:56] 1157 metadata added.
[INFO] [2020-01-15 16:33:56] 0 metadata added.
[INFO] [2020-01-15 16:33:56] Average Time: 75.09
[INFO] [2020-01-15 16:33:56] Total Time: 1m39s
[STOP] [2020-01-15 16:33:56] overall_tsv_creation
[INFO] [2020-01-15 16:33:56] Done. Check your files:
[INFO] [2020-01-15 16:33:56] (492 lines) /app/public/data/mdeam/publish_nodes.tsv
[INFO] [2020-01-15 16:33:56] (2445 lines) /app/public/data/mdeam/publish_node_ancestors.tsv
[INFO] [2020-01-15 16:33:56] (492 lines) /app/public/data/mdeam/publish_scientific_names.tsv
[INFO] [2020-01-15 16:33:56] (488 lines) /app/public/data/mdeam/publish_traits.tsv
[INFO] [2020-01-15 16:33:56] (1158 lines) /app/public/data/mdeam/publish_metadata.tsv
[STOP] [2020-01-15 16:33:56] complete_harvest_instance
[START] [2020-01-15 16:33:56] completed
[STOP] [2020-01-15 16:33:56] completed
[STOP] [2020-01-15 16:33:56] logged process, took 145.06
Latest Process

15 Jan 16:31 EXITED currently processing 0