Harvest for Turbellarian Taxonomic Database Created 09 Dec 16:20

Harvesting Log

# Logfile created on 2019-12-09 16:20:12 -0500 by logger.rb/56815
[START] [2019-12-09 16:20:12] logged process
[START] [2019-12-09 16:20:12] create_harvest_instance
[STOP] [2019-12-09 16:20:13] create_harvest_instance
[START] [2019-12-09 16:20:13] fetch_files
[STOP] [2019-12-09 16:20:13] fetch_files
[START] [2019-12-09 16:20:13] validate_each_file
[STOP] [2019-12-09 16:20:15] validate_each_file
[START] [2019-12-09 16:20:15] convert_to_csv
[CMD] [2019-12-09 16:20:15] /usr/bin/sort /app/public/converted_csv/turbellarian_tax_agents_18864.csv > /app/public/converted_csv/turbellarian_tax_agents_18864.csv_sorted
[CMD] [2019-12-09 16:20:17] /usr/bin/sort /app/public/converted_csv/turbellarian_tax_refs_18865.csv > /app/public/converted_csv/turbellarian_tax_refs_18865.csv_sorted
[CMD] [2019-12-09 16:20:18] /usr/bin/sort /app/public/converted_csv/turbellarian_tax_nodes_18866.csv > /app/public/converted_csv/turbellarian_tax_nodes_18866.csv_sorted
[CMD] [2019-12-09 16:20:20] /usr/bin/sort /app/public/converted_csv/turbellarian_tax_media_18867.csv > /app/public/converted_csv/turbellarian_tax_media_18867.csv_sorted
[CMD] [2019-12-09 16:20:22] /usr/bin/sort /app/public/converted_csv/turbellarian_tax_occurrences_18868.csv > /app/public/converted_csv/turbellarian_tax_occurrences_18868.csv_sorted
[CMD] [2019-12-09 16:20:24] /usr/bin/sort /app/public/converted_csv/turbellarian_tax_measurements_18869.csv > /app/public/converted_csv/turbellarian_tax_measurements_18869.csv_sorted
[STOP] [2019-12-09 16:20:25] convert_to_csv
[START] [2019-12-09 16:20:25] calculate_delta
[CMD] [2019-12-09 16:20:25] echo "0a" > /app/public/diff/turbellarian_tax_agents_18864.diff
[CMD] [2019-12-09 16:20:27] tail -n +1 /app/public/converted_csv/turbellarian_tax_agents_18864.csv >> /app/public/diff/turbellarian_tax_agents_18864.diff
[CMD] [2019-12-09 16:20:29] echo "." >> /app/public/diff/turbellarian_tax_agents_18864.diff
[CMD] [2019-12-09 16:20:30] echo "0a" > /app/public/diff/turbellarian_tax_refs_18865.diff
[CMD] [2019-12-09 16:20:32] tail -n +1 /app/public/converted_csv/turbellarian_tax_refs_18865.csv >> /app/public/diff/turbellarian_tax_refs_18865.diff
[CMD] [2019-12-09 16:20:34] echo "." >> /app/public/diff/turbellarian_tax_refs_18865.diff
[CMD] [2019-12-09 16:20:35] echo "0a" > /app/public/diff/turbellarian_tax_nodes_18866.diff
[CMD] [2019-12-09 16:20:37] tail -n +1 /app/public/converted_csv/turbellarian_tax_nodes_18866.csv >> /app/public/diff/turbellarian_tax_nodes_18866.diff
[CMD] [2019-12-09 16:20:39] echo "." >> /app/public/diff/turbellarian_tax_nodes_18866.diff
[CMD] [2019-12-09 16:20:40] echo "0a" > /app/public/diff/turbellarian_tax_media_18867.diff
[CMD] [2019-12-09 16:20:42] tail -n +1 /app/public/converted_csv/turbellarian_tax_media_18867.csv >> /app/public/diff/turbellarian_tax_media_18867.diff
[CMD] [2019-12-09 16:20:44] echo "." >> /app/public/diff/turbellarian_tax_media_18867.diff
[CMD] [2019-12-09 16:20:45] echo "0a" > /app/public/diff/turbellarian_tax_occurrences_18868.diff
[CMD] [2019-12-09 16:20:47] tail -n +1 /app/public/converted_csv/turbellarian_tax_occurrences_18868.csv >> /app/public/diff/turbellarian_tax_occurrences_18868.diff
[CMD] [2019-12-09 16:20:49] echo "." >> /app/public/diff/turbellarian_tax_occurrences_18868.diff
[CMD] [2019-12-09 16:20:50] echo "0a" > /app/public/diff/turbellarian_tax_measurements_18869.diff
[CMD] [2019-12-09 16:20:52] tail -n +1 /app/public/converted_csv/turbellarian_tax_measurements_18869.csv >> /app/public/diff/turbellarian_tax_measurements_18869.diff
[CMD] [2019-12-09 16:20:54] echo "." >> /app/public/diff/turbellarian_tax_measurements_18869.diff
[STOP] [2019-12-09 16:20:55] calculate_delta
[START] [2019-12-09 16:20:55] parse_diff_and_store
[INFO] [2019-12-09 16:20:57] Loading agents diff file into memory (true lines)...
[INFO] [2019-12-09 16:20:59] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-09 16:21:01] Loading nodes diff file into memory (true lines)...
[WARN] [2019-12-09 16:21:04] Filtered Scientific Name `Syndesmis echinorum  (2)` to `Syndesmis echinorum (2)`
[WARN] [2019-12-09 16:21:04] Filtered Scientific Name `Temnocephala chilensis  (1)` to `Temnocephala chilensis (1)`
[WARN] [2019-12-09 16:21:05] Filtered Scientific Name `Acelis (part) "species"` to `Acelis (part) species`
[INFO] [2019-12-09 16:21:07] Loading media diff file into memory (true lines)...
[WARN] [2019-12-09 16:21:07] Could not find a media subtype (format) of "image/png"
[INFO] [2019-12-09 16:21:11] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-09 16:21:14] Loading measurements diff file into memory (true lines)...
[WARN] [2019-12-09 16:22:02] Created value term for https://marineregions.org/mrgid/4365!
[INFO] [2019-12-09 16:22:06] Storing 4 Attributions
[INFO] [2019-12-09 16:22:06] Processing group of 4 in 1 groups of 1000
[INFO] [2019-12-09 16:22:06] Average Time: 0.01
[INFO] [2019-12-09 16:22:06] Total Time: 1s
[INFO] [2019-12-09 16:22:06] Storing 2296 References
[INFO] [2019-12-09 16:22:06] Processing group of 2296 in 3 groups of 1000
[INFO] [2019-12-09 16:22:06] Average Time: 0.167
[INFO] [2019-12-09 16:22:06] Total Time: 1s
[INFO] [2019-12-09 16:22:06] Storing 11249 ScientificNames
[INFO] [2019-12-09 16:22:06] Processing group of 11249 in 12 groups of 1000
[INFO] [2019-12-09 16:22:11] Average Time: 0.38
[INFO] [2019-12-09 16:22:11] Total Time: 5s
[INFO] [2019-12-09 16:22:11] last 3 / first 3: 0.92
[INFO] [2019-12-09 16:22:11] Std.Dev: 0.1341640786499874; Max: 0.65
[INFO] [2019-12-09 16:22:11] Storing 6961 Nodes
[INFO] [2019-12-09 16:22:11] Processing group of 6961 in 7 groups of 1000
[INFO] [2019-12-09 16:22:13] Average Time: 0.304
[INFO] [2019-12-09 16:22:13] Total Time: 3s
[INFO] [2019-12-09 16:22:13] last 3 / first 3: 0.94
[INFO] [2019-12-09 16:22:13] Std.Dev: 0.0; Max: 0.34
[INFO] [2019-12-09 16:22:13] Storing 13140 ContentAttributions
[INFO] [2019-12-09 16:22:13] Processing group of 13140 in 14 groups of 1000
[INFO] [2019-12-09 16:22:15] Average Time: 0.104
[INFO] [2019-12-09 16:22:15] Total Time: 2s
[INFO] [2019-12-09 16:22:15] last 3 / first 3: 0.47
[INFO] [2019-12-09 16:22:15] Std.Dev: 0.044721359549995794; Max: 0.22
[INFO] [2019-12-09 16:22:15] Storing 3285 Media
[INFO] [2019-12-09 16:22:15] Processing group of 3285 in 4 groups of 1000
[INFO] [2019-12-09 16:22:16] Average Time: 0.358
[INFO] [2019-12-09 16:22:16] Total Time: 2s
[INFO] [2019-12-09 16:22:16] Storing 4961 Occurrences
[INFO] [2019-12-09 16:22:16] Processing group of 4961 in 5 groups of 1000
[INFO] [2019-12-09 16:22:17] Average Time: 0.112
[INFO] [2019-12-09 16:22:17] Total Time: 1s
[INFO] [2019-12-09 16:22:17] Storing 13398 TraitsReferences
[INFO] [2019-12-09 16:22:17] Processing group of 13398 in 14 groups of 1000
[INFO] [2019-12-09 16:22:18] Average Time: 0.077
[INFO] [2019-12-09 16:22:18] Total Time: 2s
[INFO] [2019-12-09 16:22:18] last 3 / first 3: 0.55
[INFO] [2019-12-09 16:22:18] Std.Dev: 0.03162277660168379; Max: 0.16
[INFO] [2019-12-09 16:22:18] Storing 9352 Traits
[INFO] [2019-12-09 16:22:18] Processing group of 9352 in 10 groups of 1000
[INFO] [2019-12-09 16:22:21] Average Time: 0.294
[INFO] [2019-12-09 16:22:21] Total Time: 3s
[INFO] [2019-12-09 16:22:21] last 3 / first 3: 0.72
[INFO] [2019-12-09 16:22:21] Std.Dev: 0.07071067811865475; Max: 0.36
[INFO] [2019-12-09 16:22:21] Storing 28056 MetaTraits
[INFO] [2019-12-09 16:22:21] Processing group of 28056 in 29 groups of 1000
[INFO] [2019-12-09 16:22:24] Average Time: 0.112
[INFO] [2019-12-09 16:22:24] Total Time: 4s
[INFO] [2019-12-09 16:22:24] last 3 / first 3: 0.64
[INFO] [2019-12-09 16:22:24] Std.Dev: 0.0; Max: 0.14
[STOP] [2019-12-09 16:22:24] parse_diff_and_store
[START] [2019-12-09 16:22:24] resolve_keys
[INFO] [2019-12-09 16:22:41] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-09 16:22:43] traits to occurrences...
[INFO] [2019-12-09 16:22:44] traits to nodes (through occurrences)...
[INFO] [2019-12-09 16:22:44] Traits to sex term...
[INFO] [2019-12-09 16:22:44] Traits to lifestage term...
[INFO] [2019-12-09 16:22:44] MetaTraits to traits...
[INFO] [2019-12-09 16:22:46] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-09 16:22:49] Assocs to occurrences...
[INFO] [2019-12-09 16:22:49] Assocs to nodes...
[INFO] [2019-12-09 16:22:49] Assoc to sex term...
[INFO] [2019-12-09 16:22:49] Assoc to lifestage term...
[STOP] [2019-12-09 16:22:50] resolve_keys
[START] [2019-12-09 16:22:50] hold_for_later_1
[STOP] [2019-12-09 16:22:50] hold_for_later_1
[START] [2019-12-09 16:22:50] hold_for_later_2
[STOP] [2019-12-09 16:22:50] hold_for_later_2
[START] [2019-12-09 16:22:50] resolve_missing_parents
[STOP] [2019-12-09 16:22:50] resolve_missing_parents
[START] [2019-12-09 16:22:50] rebuild_nodes
[START] [2019-12-09 16:22:50] Flattener#flatten
[START] [2019-12-09 16:22:50] Flattener#study_resource
[START] [2019-12-09 16:22:50] Flattener#build_ancestry
[STOP] [2019-12-09 16:22:51] Flattener#build_ancestry
[INFO] [2019-12-09 16:22:51] 6961 ancestry keys
[START] [2019-12-09 16:22:51] build_node_ancestors
[INFO] [2019-12-09 16:22:51] old ancestors deleted.
[STOP] [2019-12-09 16:22:57] build_node_ancestors
[START] [2019-12-09 16:23:02] Flattener#propagate_ancestor_ids
[STOP] [2019-12-09 16:23:04] Flattener#propagate_ancestor_ids
[STOP] [2019-12-09 16:23:04] Flattener#flatten
[STOP] [2019-12-09 16:23:04] rebuild_nodes
[START] [2019-12-09 16:23:04] resolve_missing_media_owners
[STOP] [2019-12-09 16:23:04] resolve_missing_media_owners
[START] [2019-12-09 16:23:04] sanitize_media_verbatims
[STOP] [2019-12-09 16:23:04] sanitize_media_verbatims
[START] [2019-12-09 16:23:04] queue_downloads
[STOP] [2019-12-09 16:23:04] queue_downloads
[START] [2019-12-09 16:23:05] parse_names
[WARN] [2019-12-09 16:23:05] I see 11249 names which still need to be parsed.
[WARN] [2019-12-09 16:23:15] I see 765 names which still need to be parsed.
[WARN] [2019-12-09 16:23:17] I see 13 names which still need to be parsed.
[WARN] [2019-12-09 16:23:18] I see 4 names which still need to be parsed.
[WARN] [2019-12-09 16:23:19] I see 1 names which still need to be parsed.
[STOP] [2019-12-09 16:23:20] parse_names
[START] [2019-12-09 16:23:20] denormalize_canonical_names_to_nodes
[STOP] [2019-12-09 16:23:20] denormalize_canonical_names_to_nodes
[START] [2019-12-09 16:23:20] match_nodes
[START] [2019-12-09 16:23:20] map_all_nodes_to_pages
[ERR] [2019-12-09 16:24:22][hdls] download_and_prep FAILED for Medium.find(10316145): 404 Not Found
[ERR] [2019-12-09 16:26:00][hdls] download_and_prep FAILED for Medium.find(10316731): 404 Not Found
[ERR] [2019-12-09 16:27:38][hdls] download_and_prep FAILED for Medium.find(10317783): undefined method `[]' for #<MediumPrepper::ResizableImage:0x000055a2f0b76ab8>
[STOP] [2019-12-09 16:30:27] map_all_nodes_to_pages
[INFO] [2019-12-09 16:30:27] 398 Unmatched nodes (of 6961)! That's too many to output. First 10: Acoelomorpha (#60088157); Pseudaphanostoma opisthorchis (#60091035); Waminoa (#60089214); Oligochoerus (#60088583); Xenoturbellida (#60089508); Macrostomorpha (#60088159); Myozonariinae (#60089482); Austromacrostomum (#60088900); Microstomum artoisi (#60089722); Microstomum tchaikovskyi (#60089723)
[START] [2019-12-09 16:30:27] update_nodes
[STOP] [2019-12-09 16:30:29] update_nodes
[STOP] [2019-12-09 16:30:29] match_nodes
[START] [2019-12-09 16:30:29] reindex_search
[STOP] [2019-12-09 16:30:45] reindex_search
[START] [2019-12-09 16:30:45] normalize_units
[STOP] [2019-12-09 16:30:45] normalize_units
[START] [2019-12-09 16:30:45] calculate_statistics
[STOP] [2019-12-09 16:30:45] calculate_statistics
[START] [2019-12-09 16:30:45] complete_harvest_instance
[START] [2019-12-09 16:30:45] overall_tsv_creation
[INFO] [2019-12-09 16:30:46] Processing group of 6961 in 1 batches of 10000
[INFO] [2019-12-09 16:32:19] 9352 Traits (unfiltered)...
[INFO] [2019-12-09 16:32:32] 9352 Traits (filtered)...
[INFO] [2019-12-09 16:32:33] 0 Associations (filtered)...
[INFO] [2019-12-09 16:33:27] 41454 metadata added.
[INFO] [2019-12-09 16:33:27] 0 metadata added.
[INFO] [2019-12-09 16:33:27] Average Time: 131.03
[INFO] [2019-12-09 16:33:27] Total Time: 2m42s
[STOP] [2019-12-09 16:33:27] overall_tsv_creation
[INFO] [2019-12-09 16:33:27] Done. Check your files:
[INFO] [2019-12-09 16:33:29] (6961 lines) /app/public/data/turbellarian_tax/publish_nodes.tsv
[INFO] [2019-12-09 16:33:30] (80079 lines) /app/public/data/turbellarian_tax/publish_node_ancestors.tsv
[INFO] [2019-12-09 16:33:32] (11249 lines) /app/public/data/turbellarian_tax/publish_scientific_names.tsv
[INFO] [2019-12-09 16:33:34] (3285 lines) /app/public/data/turbellarian_tax/publish_media.tsv
[INFO] [2019-12-09 16:33:35] (3282 lines) /app/public/data/turbellarian_tax/publish_image_info.tsv
[INFO] [2019-12-09 16:33:37] (13140 lines) /app/public/data/turbellarian_tax/publish_attributions.tsv
[INFO] [2019-12-09 16:33:39] (9353 lines) /app/public/data/turbellarian_tax/publish_traits.tsv
[INFO] [2019-12-09 16:33:40] (41455 lines) /app/public/data/turbellarian_tax/publish_metadata.tsv
[STOP] [2019-12-09 16:33:40] complete_harvest_instance
[START] [2019-12-09 16:33:40] completed
[STOP] [2019-12-09 16:33:40] completed
[STOP] [2019-12-09 16:33:41] logged process, took 808.14

Latest Process

09 Dec 16:20 EXITED currently processing 0