Harvest for Pakistan Species List Created 15 Oct 05:52

Stage: completed
Fetched: 15 Oct 05:53
Validated: 15 Oct 05:53
Deltas Created 15 Oct 05:53
Units Normalized: 15 Oct 06:05
Ancestry Built: 15 Oct 05:55
Nodes Matched: 15 Oct 06:05
Names Parsed: 15 Oct 05:55
New Models Stored: 15 Oct 05:54
Indexed: 15 Oct 06:05
Completed: 15 Oct 06:09
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
# Logfile created on 2019-10-15 05:52:59 -0400 by logger.rb/56815
[START] [2019-10-15 05:52:59] logged process
[START] [2019-10-15 05:52:59] create_harvest_instance
[STOP] [2019-10-15 05:53:00] create_harvest_instance
[START] [2019-10-15 05:53:00] fetch_files
[STOP] [2019-10-15 05:53:00] fetch_files
[START] [2019-10-15 05:53:00] validate_each_file
[STOP] [2019-10-15 05:53:01] validate_each_file
[START] [2019-10-15 05:53:01] convert_to_csv
[CMD] [2019-10-15 05:53:01] /usr/bin/sort /app/public/converted_csv/pakistan_sp_list_refs_16845.csv > /app/public/converted_csv/pakistan_sp_list_refs_16845.csv_sorted
[CMD] [2019-10-15 05:53:01] /usr/bin/sort /app/public/converted_csv/pakistan_sp_list_nodes_16846.csv > /app/public/converted_csv/pakistan_sp_list_nodes_16846.csv_sorted
[CMD] [2019-10-15 05:53:02] /usr/bin/sort /app/public/converted_csv/pakistan_sp_list_occurrences_16847.csv > /app/public/converted_csv/pakistan_sp_list_occurrences_16847.csv_sorted
[CMD] [2019-10-15 05:53:02] /usr/bin/sort /app/public/converted_csv/pakistan_sp_list_measurements_16848.csv > /app/public/converted_csv/pakistan_sp_list_measurements_16848.csv_sorted
[STOP] [2019-10-15 05:53:02] convert_to_csv
[START] [2019-10-15 05:53:02] calculate_delta
[CMD] [2019-10-15 05:53:02] echo "0a" > /app/public/diff/pakistan_sp_list_refs_16845.diff
[CMD] [2019-10-15 05:53:02] tail -n +1 /app/public/converted_csv/pakistan_sp_list_refs_16845.csv >> /app/public/diff/pakistan_sp_list_refs_16845.diff
[CMD] [2019-10-15 05:53:03] echo "." >> /app/public/diff/pakistan_sp_list_refs_16845.diff
[CMD] [2019-10-15 05:53:03] echo "0a" > /app/public/diff/pakistan_sp_list_nodes_16846.diff
[CMD] [2019-10-15 05:53:03] tail -n +1 /app/public/converted_csv/pakistan_sp_list_nodes_16846.csv >> /app/public/diff/pakistan_sp_list_nodes_16846.diff
[CMD] [2019-10-15 05:53:03] echo "." >> /app/public/diff/pakistan_sp_list_nodes_16846.diff
[CMD] [2019-10-15 05:53:04] echo "0a" > /app/public/diff/pakistan_sp_list_occurrences_16847.diff
[CMD] [2019-10-15 05:53:04] tail -n +1 /app/public/converted_csv/pakistan_sp_list_occurrences_16847.csv >> /app/public/diff/pakistan_sp_list_occurrences_16847.diff
[CMD] [2019-10-15 05:53:04] echo "." >> /app/public/diff/pakistan_sp_list_occurrences_16847.diff
[CMD] [2019-10-15 05:53:05] echo "0a" > /app/public/diff/pakistan_sp_list_measurements_16848.diff
[CMD] [2019-10-15 05:53:05] tail -n +1 /app/public/converted_csv/pakistan_sp_list_measurements_16848.csv >> /app/public/diff/pakistan_sp_list_measurements_16848.diff
[CMD] [2019-10-15 05:53:05] echo "." >> /app/public/diff/pakistan_sp_list_measurements_16848.diff
[STOP] [2019-10-15 05:53:05] calculate_delta
[START] [2019-10-15 05:53:05] parse_diff_and_store
[INFO] [2019-10-15 05:53:06] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 05:53:06] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 05:53:10] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 05:53:11] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 05:53:50] Storing 2 References
[INFO] [2019-10-15 05:53:50] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 05:53:50] Average Time: 0.0
[INFO] [2019-10-15 05:53:50] Total Time: 1s
[INFO] [2019-10-15 05:53:50] Storing 10485 ScientificNames
[INFO] [2019-10-15 05:53:50] Processing group of 10485 in 11 groups of 1000
[INFO] [2019-10-15 05:53:54] Average Time: 0.364
[INFO] [2019-10-15 05:53:54] Total Time: 5s
[INFO] [2019-10-15 05:53:54] last 3 / first 3: 0.76
[INFO] [2019-10-15 05:53:54] Std.Dev: 0.07745966692414834; Max: 0.47
[INFO] [2019-10-15 05:53:54] Storing 10485 Nodes
[INFO] [2019-10-15 05:53:54] Processing group of 10485 in 11 groups of 1000
[INFO] [2019-10-15 05:53:57] Average Time: 0.289
[INFO] [2019-10-15 05:53:57] Total Time: 4s
[INFO] [2019-10-15 05:53:57] last 3 / first 3: 0.83
[INFO] [2019-10-15 05:53:57] Std.Dev: 0.05477225575051661; Max: 0.37
[INFO] [2019-10-15 05:53:57] Storing 6266 Occurrences
[INFO] [2019-10-15 05:53:57] Processing group of 6266 in 7 groups of 1000
[INFO] [2019-10-15 05:53:58] Average Time: 0.093
[INFO] [2019-10-15 05:53:58] Total Time: 1s
[INFO] [2019-10-15 05:53:58] last 3 / first 3: 0.77
[INFO] [2019-10-15 05:53:58] Std.Dev: 0.03162277660168379; Max: 0.11
[INFO] [2019-10-15 05:53:58] Storing 13130 TraitsReferences
[INFO] [2019-10-15 05:53:58] Processing group of 13130 in 14 groups of 1000
[INFO] [2019-10-15 05:53:59] Average Time: 0.078
[INFO] [2019-10-15 05:53:59] Total Time: 2s
[INFO] [2019-10-15 05:53:59] last 3 / first 3: 0.5
[INFO] [2019-10-15 05:53:59] Std.Dev: 0.03162277660168379; Max: 0.16
[INFO] [2019-10-15 05:53:59] Storing 13129 Traits
[INFO] [2019-10-15 05:53:59] Processing group of 13129 in 14 groups of 1000
[INFO] [2019-10-15 05:54:03] Average Time: 0.282
[INFO] [2019-10-15 05:54:03] Total Time: 5s
[INFO] [2019-10-15 05:54:03] last 3 / first 3: 0.64
[INFO] [2019-10-15 05:54:03] Std.Dev: 0.07745966692414834; Max: 0.38
[INFO] [2019-10-15 05:54:03] Storing 13120 MetaTraits
[INFO] [2019-10-15 05:54:03] Processing group of 13120 in 14 groups of 1000
[INFO] [2019-10-15 05:54:05] Average Time: 0.111
[INFO] [2019-10-15 05:54:05] Total Time: 2s
[INFO] [2019-10-15 05:54:05] last 3 / first 3: 0.64
[INFO] [2019-10-15 05:54:05] Std.Dev: 0.03162277660168379; Max: 0.18
[STOP] [2019-10-15 05:54:05] parse_diff_and_store
[START] [2019-10-15 05:54:05] resolve_keys
[INFO] [2019-10-15 05:54:44] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 05:54:47] traits to occurrences...
[INFO] [2019-10-15 05:54:52] traits to nodes (through occurrences)...
[INFO] [2019-10-15 05:54:53] Traits to sex term...
[INFO] [2019-10-15 05:54:57] Traits to lifestage term...
[INFO] [2019-10-15 05:55:01] MetaTraits to traits...
[INFO] [2019-10-15 05:55:02] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 05:55:04] Assocs to occurrences...
[INFO] [2019-10-15 05:55:04] Assocs to nodes...
[INFO] [2019-10-15 05:55:04] Assoc to sex term...
[INFO] [2019-10-15 05:55:04] Assoc to lifestage term...
[STOP] [2019-10-15 05:55:04] resolve_keys
[START] [2019-10-15 05:55:04] hold_for_later_1
[STOP] [2019-10-15 05:55:04] hold_for_later_1
[START] [2019-10-15 05:55:04] hold_for_later_2
[STOP] [2019-10-15 05:55:04] hold_for_later_2
[START] [2019-10-15 05:55:04] resolve_missing_parents
[STOP] [2019-10-15 05:55:23] resolve_missing_parents
[START] [2019-10-15 05:55:23] rebuild_nodes
[START] [2019-10-15 05:55:23] Flattener#flatten
[START] [2019-10-15 05:55:23] Flattener#study_resource
[START] [2019-10-15 05:55:23] Flattener#build_ancestry
[STOP] [2019-10-15 05:55:25] Flattener#build_ancestry
[INFO] [2019-10-15 05:55:25] 10485 ancestry keys
[START] [2019-10-15 05:55:25] build_node_ancestors
[INFO] [2019-10-15 05:55:25] old ancestors deleted.
[STOP] [2019-10-15 05:55:26] build_node_ancestors
[START] [2019-10-15 05:55:28] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 05:55:29] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 05:55:29] Flattener#flatten
[STOP] [2019-10-15 05:55:29] rebuild_nodes
[START] [2019-10-15 05:55:29] resolve_missing_media_owners
[STOP] [2019-10-15 05:55:29] resolve_missing_media_owners
[START] [2019-10-15 05:55:29] sanitize_media_verbatims
[STOP] [2019-10-15 05:55:29] sanitize_media_verbatims
[START] [2019-10-15 05:55:29] queue_downloads
[STOP] [2019-10-15 05:55:29] queue_downloads
[START] [2019-10-15 05:55:29] parse_names
[WARN] [2019-10-15 05:55:29] I see 10485 names which still need to be parsed.
[STOP] [2019-10-15 05:55:37] parse_names
[START] [2019-10-15 05:55:37] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 05:55:37] denormalize_canonical_names_to_nodes
[START] [2019-10-15 05:55:37] match_nodes
[START] [2019-10-15 05:55:37] map_all_nodes_to_pages
[STOP] [2019-10-15 06:05:15] map_all_nodes_to_pages
[INFO] [2019-10-15 06:05:15] 1001 Unmatched nodes (of 10485)! That's too many to output. First 10: Pollenia aurifrons (#51410355); Poa albertii (#51406295); Koeleria cristata (#51400526); Oryzopsis gracile (#51400551); Oryzopsis aequiglume (#51404045); Oryzopsis laterale (#51405810); Pennisetum glauca (#51408539); Aegilops squarrosum (#51403125); Aegilops triunciale (#51405415); Leymus thomsonii (#51406745)
[START] [2019-10-15 06:05:15] update_nodes
[STOP] [2019-10-15 06:05:19] update_nodes
[STOP] [2019-10-15 06:05:19] match_nodes
[START] [2019-10-15 06:05:19] reindex_search
[STOP] [2019-10-15 06:05:42] reindex_search
[START] [2019-10-15 06:05:42] normalize_units
[STOP] [2019-10-15 06:05:42] normalize_units
[START] [2019-10-15 06:05:42] calculate_statistics
[STOP] [2019-10-15 06:05:42] calculate_statistics
[START] [2019-10-15 06:05:42] complete_harvest_instance
[START] [2019-10-15 06:05:42] overall_tsv_creation
[INFO] [2019-10-15 06:05:42] Processing group of 10485 in 2 batches of 10000
[INFO] [2019-10-15 06:07:11] 6231 Traits (unfiltered)...
[INFO] [2019-10-15 06:07:25] 6231 Traits (filtered)...
[INFO] [2019-10-15 06:07:25] 0 Associations (filtered)...
[INFO] [2019-10-15 06:08:15] 31147 metadata added.
[INFO] [2019-10-15 06:08:15] 0 metadata added.
[INFO] [2019-10-15 06:09:01] 35 Traits (unfiltered)...
[INFO] [2019-10-15 06:09:15] 35 Traits (filtered)...
[INFO] [2019-10-15 06:09:15] 0 Associations (filtered)...
[INFO] [2019-10-15 06:09:51] 175 metadata added.
[INFO] [2019-10-15 06:09:51] 0 metadata added.
[INFO] [2019-10-15 06:09:51] Average Time: 100.815
[INFO] [2019-10-15 06:09:51] Total Time: 4m10s
[STOP] [2019-10-15 06:09:51] overall_tsv_creation
[INFO] [2019-10-15 06:09:51] Done. Check your files:
[INFO] [2019-10-15 06:09:52] (10485 lines) /app/public/data/pakistan_sp_list/publish_nodes.tsv
[INFO] [2019-10-15 06:09:52] (25060 lines) /app/public/data/pakistan_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-15 06:09:52] (10485 lines) /app/public/data/pakistan_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-15 06:09:53] (6267 lines) /app/public/data/pakistan_sp_list/publish_traits.tsv
[INFO] [2019-10-15 06:09:53] (31323 lines) /app/public/data/pakistan_sp_list/publish_metadata.tsv
[STOP] [2019-10-15 06:09:53] complete_harvest_instance
[START] [2019-10-15 06:09:53] completed
[STOP] [2019-10-15 06:09:53] completed
[STOP] [2019-10-15 06:09:53] logged process, took 1013.94
Latest Process

15 Oct 05:52 EXITED currently processing 0