Harvest for Polytraits Created 14 Jan 16:05

Stage: completed
Fetched: 14 Jan 16:05
Validated: 14 Jan 16:05
Deltas Created 14 Jan 16:05
Units Normalized: 14 Jan 16:11
Ancestry Built: 14 Jan 16:08
Nodes Matched: 14 Jan 16:11
Names Parsed: 14 Jan 16:08
New Models Stored: 14 Jan 16:07
Indexed: 14 Jan 16:11
Completed: 14 Jan 16:13
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2020-01-14 16:05:07 -0500 by logger.rb/56815
[START] [2020-01-14 16:05:07] logged process
[START] [2020-01-14 16:05:07] create_harvest_instance
[STOP] [2020-01-14 16:05:10] create_harvest_instance
[START] [2020-01-14 16:05:10] fetch_files
[STOP] [2020-01-14 16:05:10] fetch_files
[START] [2020-01-14 16:05:10] validate_each_file
[STOP] [2020-01-14 16:05:13] validate_each_file
[START] [2020-01-14 16:05:13] convert_to_csv
[CMD] [2020-01-14 16:05:13] /usr/bin/sort /app/public/converted_csv/polytraits_agents_19921.csv > /app/public/converted_csv/polytraits_agents_19921.csv_sorted
[CMD] [2020-01-14 16:05:13] /usr/bin/sort /app/public/converted_csv/polytraits_refs_19922.csv > /app/public/converted_csv/polytraits_refs_19922.csv_sorted
[CMD] [2020-01-14 16:05:13] /usr/bin/sort /app/public/converted_csv/polytraits_nodes_19923.csv > /app/public/converted_csv/polytraits_nodes_19923.csv_sorted
[CMD] [2020-01-14 16:05:13] /usr/bin/sort /app/public/converted_csv/polytraits_media_19924.csv > /app/public/converted_csv/polytraits_media_19924.csv_sorted
[CMD] [2020-01-14 16:05:13] /usr/bin/sort /app/public/converted_csv/polytraits_vernaculars_19925.csv > /app/public/converted_csv/polytraits_vernaculars_19925.csv_sorted
[CMD] [2020-01-14 16:05:14] /usr/bin/sort /app/public/converted_csv/polytraits_occurrences_19926.csv > /app/public/converted_csv/polytraits_occurrences_19926.csv_sorted
[CMD] [2020-01-14 16:05:14] /usr/bin/sort /app/public/converted_csv/polytraits_measurements_19927.csv > /app/public/converted_csv/polytraits_measurements_19927.csv_sorted
[STOP] [2020-01-14 16:05:14] convert_to_csv
[START] [2020-01-14 16:05:14] calculate_delta
[CMD] [2020-01-14 16:05:14] echo "0a" > /app/public/diff/polytraits_agents_19921.diff
[CMD] [2020-01-14 16:05:14] tail -n +1 /app/public/converted_csv/polytraits_agents_19921.csv >> /app/public/diff/polytraits_agents_19921.diff
[CMD] [2020-01-14 16:05:14] echo "." >> /app/public/diff/polytraits_agents_19921.diff
[CMD] [2020-01-14 16:05:14] echo "0a" > /app/public/diff/polytraits_refs_19922.diff
[CMD] [2020-01-14 16:05:15] tail -n +1 /app/public/converted_csv/polytraits_refs_19922.csv >> /app/public/diff/polytraits_refs_19922.diff
[CMD] [2020-01-14 16:05:15] echo "." >> /app/public/diff/polytraits_refs_19922.diff
[CMD] [2020-01-14 16:05:15] echo "0a" > /app/public/diff/polytraits_nodes_19923.diff
[CMD] [2020-01-14 16:05:15] tail -n +1 /app/public/converted_csv/polytraits_nodes_19923.csv >> /app/public/diff/polytraits_nodes_19923.diff
[CMD] [2020-01-14 16:05:15] echo "." >> /app/public/diff/polytraits_nodes_19923.diff
[CMD] [2020-01-14 16:05:15] echo "0a" > /app/public/diff/polytraits_media_19924.diff
[CMD] [2020-01-14 16:05:16] tail -n +1 /app/public/converted_csv/polytraits_media_19924.csv >> /app/public/diff/polytraits_media_19924.diff
[CMD] [2020-01-14 16:05:16] echo "." >> /app/public/diff/polytraits_media_19924.diff
[CMD] [2020-01-14 16:05:16] echo "0a" > /app/public/diff/polytraits_vernaculars_19925.diff
[CMD] [2020-01-14 16:05:16] tail -n +1 /app/public/converted_csv/polytraits_vernaculars_19925.csv >> /app/public/diff/polytraits_vernaculars_19925.diff
[CMD] [2020-01-14 16:05:16] echo "." >> /app/public/diff/polytraits_vernaculars_19925.diff
[CMD] [2020-01-14 16:05:16] echo "0a" > /app/public/diff/polytraits_occurrences_19926.diff
[CMD] [2020-01-14 16:05:17] tail -n +1 /app/public/converted_csv/polytraits_occurrences_19926.csv >> /app/public/diff/polytraits_occurrences_19926.diff
[CMD] [2020-01-14 16:05:17] echo "." >> /app/public/diff/polytraits_occurrences_19926.diff
[CMD] [2020-01-14 16:05:17] echo "0a" > /app/public/diff/polytraits_measurements_19927.diff
[CMD] [2020-01-14 16:05:17] tail -n +1 /app/public/converted_csv/polytraits_measurements_19927.csv >> /app/public/diff/polytraits_measurements_19927.diff
[CMD] [2020-01-14 16:05:17] echo "." >> /app/public/diff/polytraits_measurements_19927.diff
[STOP] [2020-01-14 16:05:17] calculate_delta
[START] [2020-01-14 16:05:17] parse_diff_and_store
[INFO] [2020-01-14 16:05:18] Loading agents diff file into memory (true lines)...
[INFO] [2020-01-14 16:05:18] Loading refs diff file into memory (true lines)...
[INFO] [2020-01-14 16:05:18] Loading nodes diff file into memory (true lines)...
[INFO] [2020-01-14 16:05:19] Loading media diff file into memory (true lines)...
[INFO] [2020-01-14 16:05:19] Loading vernaculars diff file into memory (true lines)...
[INFO] [2020-01-14 16:05:19] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-01-14 16:05:20] Loading measurements diff file into memory (true lines)...
[START] [2020-01-14 16:05:25] logged process
[INFO] [2020-01-14 16:07:26] Storing 1019 References
[INFO] [2020-01-14 16:07:26] Processing group of 1019 in 2 groups of 1000
[INFO] [2020-01-14 16:07:26] Average Time: 0.125
[INFO] [2020-01-14 16:07:26] Total Time: 1s
[INFO] [2020-01-14 16:07:26] Storing 1262 ScientificNames
[INFO] [2020-01-14 16:07:26] Processing group of 1262 in 2 groups of 1000
[INFO] [2020-01-14 16:07:26] Average Time: 0.29
[INFO] [2020-01-14 16:07:26] Total Time: 1s
[INFO] [2020-01-14 16:07:26] Storing 1262 Nodes
[INFO] [2020-01-14 16:07:26] Processing group of 1262 in 2 groups of 1000
[INFO] [2020-01-14 16:07:27] Average Time: 0.205
[INFO] [2020-01-14 16:07:27] Total Time: 1s
[INFO] [2020-01-14 16:07:27] Storing 1259 Occurrences
[INFO] [2020-01-14 16:07:27] Processing group of 1259 in 2 groups of 1000
[INFO] [2020-01-14 16:07:27] Average Time: 0.07
[INFO] [2020-01-14 16:07:27] Total Time: 1s
[INFO] [2020-01-14 16:07:27] Storing 17321 TraitsReferences
[INFO] [2020-01-14 16:07:27] Processing group of 17321 in 18 groups of 1000
[INFO] [2020-01-14 16:07:29] Average Time: 0.077
[INFO] [2020-01-14 16:07:29] Total Time: 2s
[INFO] [2020-01-14 16:07:29] last 3 / first 3: 0.47
[INFO] [2020-01-14 16:07:29] Std.Dev: 0.03162277660168379; Max: 0.17
[INFO] [2020-01-14 16:07:29] Storing 17321 Traits
[INFO] [2020-01-14 16:07:29] Processing group of 17321 in 18 groups of 1000
[INFO] [2020-01-14 16:07:34] Average Time: 0.302
[INFO] [2020-01-14 16:07:34] Total Time: 6s
[INFO] [2020-01-14 16:07:34] last 3 / first 3: 0.72
[INFO] [2020-01-14 16:07:34] Std.Dev: 0.05477225575051661; Max: 0.42
[INFO] [2020-01-14 16:07:34] Storing 83189 MetaTraits
[INFO] [2020-01-14 16:07:34] Processing group of 83189 in 84 groups of 1000
[INFO] [2020-01-14 16:07:44] Average Time: 0.118
[INFO] [2020-01-14 16:07:44] Total Time: 11s
[INFO] [2020-01-14 16:07:44] last 3 / first 3: 0.69
[INFO] [2020-01-14 16:07:44] Std.Dev: 0.044721359549995794; Max: 0.31
[STOP] [2020-01-14 16:07:44] parse_diff_and_store
[START] [2020-01-14 16:07:44] resolve_keys
[INFO] [2020-01-14 16:07:55] Occurrences to nodes (through scientific_names)...
[INFO] [2020-01-14 16:07:59] traits to occurrences...
[INFO] [2020-01-14 16:07:59] traits to nodes (through occurrences)...
[INFO] [2020-01-14 16:08:00] Traits to sex term...
[INFO] [2020-01-14 16:08:00] Traits to lifestage term...
[INFO] [2020-01-14 16:08:00] MetaTraits to traits...
[INFO] [2020-01-14 16:08:02] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-01-14 16:08:04] Assocs to occurrences...
[INFO] [2020-01-14 16:08:04] Assocs to nodes...
[INFO] [2020-01-14 16:08:04] Assoc to sex term...
[INFO] [2020-01-14 16:08:04] Assoc to lifestage term...
[STOP] [2020-01-14 16:08:04] resolve_keys
[START] [2020-01-14 16:08:04] hold_for_later_1
[STOP] [2020-01-14 16:08:04] hold_for_later_1
[START] [2020-01-14 16:08:04] hold_for_later_2
[STOP] [2020-01-14 16:08:04] hold_for_later_2
[START] [2020-01-14 16:08:04] resolve_missing_parents
[STOP] [2020-01-14 16:08:04] resolve_missing_parents
[START] [2020-01-14 16:08:04] rebuild_nodes
[START] [2020-01-14 16:08:04] Flattener#flatten
[START] [2020-01-14 16:08:04] Flattener#study_resource
[START] [2020-01-14 16:08:04] Flattener#build_ancestry
[STOP] [2020-01-14 16:08:04] Flattener#build_ancestry
[INFO] [2020-01-14 16:08:04] 1262 ancestry keys
[START] [2020-01-14 16:08:04] build_node_ancestors
[INFO] [2020-01-14 16:08:04] old ancestors deleted.
[STOP] [2020-01-14 16:08:04] build_node_ancestors
[START] [2020-01-14 16:08:05] Flattener#propagate_ancestor_ids
[STOP] [2020-01-14 16:08:05] Flattener#propagate_ancestor_ids
[STOP] [2020-01-14 16:08:05] Flattener#flatten
[STOP] [2020-01-14 16:08:05] rebuild_nodes
[START] [2020-01-14 16:08:05] resolve_missing_media_owners
[STOP] [2020-01-14 16:08:05] resolve_missing_media_owners
[START] [2020-01-14 16:08:05] sanitize_media_verbatims
[STOP] [2020-01-14 16:08:05] sanitize_media_verbatims
[START] [2020-01-14 16:08:05] queue_downloads
[STOP] [2020-01-14 16:08:05] queue_downloads
[START] [2020-01-14 16:08:05] parse_names
[WARN] [2020-01-14 16:08:05] I see 1262 names which still need to be parsed.
[WARN] [2020-01-14 16:08:07] I see 3 names which still need to be parsed.
[STOP] [2020-01-14 16:08:08] parse_names
[START] [2020-01-14 16:08:08] denormalize_canonical_names_to_nodes
[STOP] [2020-01-14 16:08:08] denormalize_canonical_names_to_nodes
[START] [2020-01-14 16:08:08] match_nodes
[START] [2020-01-14 16:08:08] map_all_nodes_to_pages
[STOP] [2020-01-14 16:11:09] map_all_nodes_to_pages
[INFO] [2020-01-14 16:11:09] 98 Unmatched nodes (of 1262)! That's too many to output. First 10: Capitella capitata capitata (#62799653); Nainereis (#62799724); Pirakia (#62799746); Glycera rouxi (#62799768); Sabella aspera (#62799813); Spirorbis borealis (#62799887); Melinantipoda quatredentata (#62799895); Melinnexis (#62799906); Demonax brachychona (#62799939); Demonax branchyona (#62799940)
[START] [2020-01-14 16:11:09] update_nodes
[STOP] [2020-01-14 16:11:09] update_nodes
[STOP] [2020-01-14 16:11:09] match_nodes
[START] [2020-01-14 16:11:09] reindex_search
[STOP] [2020-01-14 16:11:11] reindex_search
[START] [2020-01-14 16:11:11] normalize_units
[STOP] [2020-01-14 16:11:11] normalize_units
[START] [2020-01-14 16:11:11] calculate_statistics
[STOP] [2020-01-14 16:11:11] calculate_statistics
[START] [2020-01-14 16:11:11] complete_harvest_instance
[START] [2020-01-14 16:11:11] overall_tsv_creation
[INFO] [2020-01-14 16:11:11] Processing group of 1262 in 1 batches of 10000
[INFO] [2020-01-14 16:12:02] 17321 Traits (unfiltered)...
[INFO] [2020-01-14 16:12:15] 17321 Traits (filtered)...
[INFO] [2020-01-14 16:12:15] 0 Associations (filtered)...
[INFO] [2020-01-14 16:13:23] 100510 metadata added.
[INFO] [2020-01-14 16:13:23] 0 metadata added.
[INFO] [2020-01-14 16:13:23] Average Time: 107.99
[INFO] [2020-01-14 16:13:23] Total Time: 2m12s
[STOP] [2020-01-14 16:13:23] overall_tsv_creation
[INFO] [2020-01-14 16:13:23] Done. Check your files:
[INFO] [2020-01-14 16:13:23] (1262 lines) /app/public/data/polytraits/publish_nodes.tsv
[INFO] [2020-01-14 16:13:23] (2501 lines) /app/public/data/polytraits/publish_node_ancestors.tsv
[INFO] [2020-01-14 16:13:23] (1262 lines) /app/public/data/polytraits/publish_scientific_names.tsv
[INFO] [2020-01-14 16:13:23] (17322 lines) /app/public/data/polytraits/publish_traits.tsv
[INFO] [2020-01-14 16:13:23] (100511 lines) /app/public/data/polytraits/publish_metadata.tsv
[STOP] [2020-01-14 16:13:23] complete_harvest_instance
[START] [2020-01-14 16:13:23] completed
[STOP] [2020-01-14 16:13:23] completed
[STOP] [2020-01-14 16:13:23] logged process, took 496.39

Latest Process