Stage:
completed
Fetched:
25 Dec 13:43
Validated:
25 Dec 13:43
Deltas Created
25 Dec 13:44
Units Normalized:
25 Dec 13:52
Ancestry Built:
25 Dec 13:44
Nodes Matched:
25 Dec 13:52
Names Parsed:
25 Dec 13:45
New Models Stored:
25 Dec 13:44
Indexed:
25 Dec 13:52
Completed:
25 Dec 13:54
Time to Harvest:
less than a minute
Harvesting Log
(139 lines)
# Logfile created on 2019-12-25 13:43:57 -0500 by logger.rb/56815
[START] [2019-12-25 13:43:57] logged process
[START] [2019-12-25 13:43:57] create_harvest_instance
[STOP] [2019-12-25 13:43:57] create_harvest_instance
[START] [2019-12-25 13:43:57] fetch_files
[STOP] [2019-12-25 13:43:57] fetch_files
[START] [2019-12-25 13:43:57] validate_each_file
[STOP] [2019-12-25 13:43:58] validate_each_file
[START] [2019-12-25 13:43:58] convert_to_csv
[CMD] [2019-12-25 13:43:58] /usr/bin/sort /app/public/converted_csv/sissl_refs_19650.csv > /app/public/converted_csv/sissl_refs_19650.csv_sorted
[CMD] [2019-12-25 13:43:58] /usr/bin/sort /app/public/converted_csv/sissl_nodes_19651.csv > /app/public/converted_csv/sissl_nodes_19651.csv_sorted
[CMD] [2019-12-25 13:43:58] /usr/bin/sort /app/public/converted_csv/sissl_occurrences_19652.csv > /app/public/converted_csv/sissl_occurrences_19652.csv_sorted
[CMD] [2019-12-25 13:43:58] /usr/bin/sort /app/public/converted_csv/sissl_measurements_19653.csv > /app/public/converted_csv/sissl_measurements_19653.csv_sorted
[STOP] [2019-12-25 13:43:59] convert_to_csv
[START] [2019-12-25 13:43:59] calculate_delta
[CMD] [2019-12-25 13:43:59] echo "0a" > /app/public/diff/sissl_refs_19650.diff
[CMD] [2019-12-25 13:43:59] tail -n +1 /app/public/converted_csv/sissl_refs_19650.csv >> /app/public/diff/sissl_refs_19650.diff
[CMD] [2019-12-25 13:43:59] echo "." >> /app/public/diff/sissl_refs_19650.diff
[CMD] [2019-12-25 13:43:59] echo "0a" > /app/public/diff/sissl_nodes_19651.diff
[CMD] [2019-12-25 13:43:59] tail -n +1 /app/public/converted_csv/sissl_nodes_19651.csv >> /app/public/diff/sissl_nodes_19651.diff
[CMD] [2019-12-25 13:43:59] echo "." >> /app/public/diff/sissl_nodes_19651.diff
[CMD] [2019-12-25 13:44:00] echo "0a" > /app/public/diff/sissl_occurrences_19652.diff
[CMD] [2019-12-25 13:44:00] tail -n +1 /app/public/converted_csv/sissl_occurrences_19652.csv >> /app/public/diff/sissl_occurrences_19652.diff
[CMD] [2019-12-25 13:44:00] echo "." >> /app/public/diff/sissl_occurrences_19652.diff
[CMD] [2019-12-25 13:44:00] echo "0a" > /app/public/diff/sissl_measurements_19653.diff
[CMD] [2019-12-25 13:44:00] tail -n +1 /app/public/converted_csv/sissl_measurements_19653.csv >> /app/public/diff/sissl_measurements_19653.diff
[CMD] [2019-12-25 13:44:01] echo "." >> /app/public/diff/sissl_measurements_19653.diff
[STOP] [2019-12-25 13:44:01] calculate_delta
[START] [2019-12-25 13:44:01] parse_diff_and_store
[INFO] [2019-12-25 13:44:01] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-25 13:44:01] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-25 13:44:03] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-25 13:44:03] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-25 13:44:13] Storing 2 References
[INFO] [2019-12-25 13:44:13] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-25 13:44:13] Average Time: 0.0
[INFO] [2019-12-25 13:44:13] Total Time: 1s
[INFO] [2019-12-25 13:44:13] Storing 3802 ScientificNames
[INFO] [2019-12-25 13:44:13] Processing group of 3802 in 4 groups of 1000
[INFO] [2019-12-25 13:44:15] Average Time: 0.39
[INFO] [2019-12-25 13:44:15] Total Time: 2s
[INFO] [2019-12-25 13:44:15] Storing 3802 Nodes
[INFO] [2019-12-25 13:44:15] Processing group of 3802 in 4 groups of 1000
[INFO] [2019-12-25 13:44:16] Average Time: 0.315
[INFO] [2019-12-25 13:44:16] Total Time: 2s
[INFO] [2019-12-25 13:44:16] Storing 1712 Occurrences
[INFO] [2019-12-25 13:44:16] Processing group of 1712 in 2 groups of 1000
[INFO] [2019-12-25 13:44:16] Average Time: 0.105
[INFO] [2019-12-25 13:44:16] Total Time: 1s
[INFO] [2019-12-25 13:44:16] Storing 3424 TraitsReferences
[INFO] [2019-12-25 13:44:16] Processing group of 3424 in 4 groups of 1000
[INFO] [2019-12-25 13:44:17] Average Time: 0.08
[INFO] [2019-12-25 13:44:17] Total Time: 1s
[INFO] [2019-12-25 13:44:17] Storing 3424 Traits
[INFO] [2019-12-25 13:44:17] Processing group of 3424 in 4 groups of 1000
[INFO] [2019-12-25 13:44:18] Average Time: 0.365
[INFO] [2019-12-25 13:44:18] Total Time: 2s
[INFO] [2019-12-25 13:44:18] Storing 3418 MetaTraits
[INFO] [2019-12-25 13:44:18] Processing group of 3418 in 4 groups of 1000
[INFO] [2019-12-25 13:44:19] Average Time: 0.215
[INFO] [2019-12-25 13:44:19] Total Time: 1s
[STOP] [2019-12-25 13:44:19] parse_diff_and_store
[START] [2019-12-25 13:44:19] resolve_keys
[INFO] [2019-12-25 13:44:36] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-25 13:44:38] traits to occurrences...
[INFO] [2019-12-25 13:44:40] traits to nodes (through occurrences)...
[INFO] [2019-12-25 13:44:40] Traits to sex term...
[INFO] [2019-12-25 13:44:41] Traits to lifestage term...
[INFO] [2019-12-25 13:44:43] MetaTraits to traits...
[INFO] [2019-12-25 13:44:44] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-25 13:44:44] Assocs to occurrences...
[INFO] [2019-12-25 13:44:44] Assocs to nodes...
[INFO] [2019-12-25 13:44:44] Assoc to sex term...
[INFO] [2019-12-25 13:44:44] Assoc to lifestage term...
[STOP] [2019-12-25 13:44:44] resolve_keys
[START] [2019-12-25 13:44:44] hold_for_later_1
[STOP] [2019-12-25 13:44:44] hold_for_later_1
[START] [2019-12-25 13:44:44] hold_for_later_2
[STOP] [2019-12-25 13:44:44] hold_for_later_2
[START] [2019-12-25 13:44:44] resolve_missing_parents
[STOP] [2019-12-25 13:44:51] resolve_missing_parents
[START] [2019-12-25 13:44:51] rebuild_nodes
[START] [2019-12-25 13:44:51] Flattener#flatten
[START] [2019-12-25 13:44:51] Flattener#study_resource
[START] [2019-12-25 13:44:51] Flattener#build_ancestry
[STOP] [2019-12-25 13:44:51] Flattener#build_ancestry
[INFO] [2019-12-25 13:44:51] 3802 ancestry keys
[START] [2019-12-25 13:44:51] build_node_ancestors
[INFO] [2019-12-25 13:44:51] old ancestors deleted.
[STOP] [2019-12-25 13:44:52] build_node_ancestors
[START] [2019-12-25 13:44:56] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 13:44:57] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 13:44:57] Flattener#flatten
[STOP] [2019-12-25 13:44:57] rebuild_nodes
[START] [2019-12-25 13:44:57] resolve_missing_media_owners
[STOP] [2019-12-25 13:44:57] resolve_missing_media_owners
[START] [2019-12-25 13:44:57] sanitize_media_verbatims
[STOP] [2019-12-25 13:44:57] sanitize_media_verbatims
[START] [2019-12-25 13:44:57] queue_downloads
[STOP] [2019-12-25 13:44:57] queue_downloads
[START] [2019-12-25 13:44:57] parse_names
[WARN] [2019-12-25 13:44:57] I see 3802 names which still need to be parsed.
[STOP] [2019-12-25 13:45:01] parse_names
[START] [2019-12-25 13:45:01] denormalize_canonical_names_to_nodes
[STOP] [2019-12-25 13:45:01] denormalize_canonical_names_to_nodes
[START] [2019-12-25 13:45:01] match_nodes
[START] [2019-12-25 13:45:01] map_all_nodes_to_pages
[STOP] [2019-12-25 13:52:37] map_all_nodes_to_pages
[INFO] [2019-12-25 13:52:37] 197 Unmatched nodes (of 3802)! That's too many to output. First 10: Skeletonemaceae (#62442452); Thallassiosiraceae (#62442577); Thalassiosira binata (#62445040); Leptocylindrus mediterraneus (#62442721); Nitzschia lanceolata (#62443604); Thalassionematales (#62442506); Guinardia cylindrus (#62443653); Rhizosolenia clevei (#62445856); Dactyliosolen antarcticus (#62445327); Podosira stelliger (#62443093)
[START] [2019-12-25 13:52:37] update_nodes
[STOP] [2019-12-25 13:52:38] update_nodes
[STOP] [2019-12-25 13:52:38] match_nodes
[START] [2019-12-25 13:52:38] reindex_search
[STOP] [2019-12-25 13:52:45] reindex_search
[START] [2019-12-25 13:52:45] normalize_units
[STOP] [2019-12-25 13:52:45] normalize_units
[START] [2019-12-25 13:52:45] calculate_statistics
[STOP] [2019-12-25 13:52:45] calculate_statistics
[START] [2019-12-25 13:52:45] complete_harvest_instance
[START] [2019-12-25 13:52:45] overall_tsv_creation
[INFO] [2019-12-25 13:52:45] Processing group of 3802 in 1 batches of 10000
[INFO] [2019-12-25 13:53:49] 1712 Traits (unfiltered)...
[INFO] [2019-12-25 13:54:02] 1712 Traits (filtered)...
[INFO] [2019-12-25 13:54:03] 0 Associations (filtered)...
[INFO] [2019-12-25 13:54:43] 8554 metadata added.
[INFO] [2019-12-25 13:54:43] 0 metadata added.
[INFO] [2019-12-25 13:54:44] Average Time: 92.44
[INFO] [2019-12-25 13:54:44] Total Time: 1m59s
[STOP] [2019-12-25 13:54:44] overall_tsv_creation
[INFO] [2019-12-25 13:54:44] Done. Check your files:
[INFO] [2019-12-25 13:54:44] (3802 lines) /app/public/data/sissl/publish_nodes.tsv
[INFO] [2019-12-25 13:54:44] (18365 lines) /app/public/data/sissl/publish_node_ancestors.tsv
[INFO] [2019-12-25 13:54:44] (3802 lines) /app/public/data/sissl/publish_scientific_names.tsv
[INFO] [2019-12-25 13:54:44] (1713 lines) /app/public/data/sissl/publish_traits.tsv
[INFO] [2019-12-25 13:54:44] (8555 lines) /app/public/data/sissl/publish_metadata.tsv
[STOP] [2019-12-25 13:54:45] complete_harvest_instance
[START] [2019-12-25 13:54:45] completed
[STOP] [2019-12-25 13:54:45] completed
[STOP] [2019-12-25 13:54:45] logged process, took 647.8
Latest Process