Harvest for Cyprus Species List Created 12 Oct 12:36

Stage: completed
Fetched: 12 Oct 12:36
Validated: 12 Oct 12:36
Deltas Created 12 Oct 12:36
Units Normalized: 12 Oct 12:39
Ancestry Built: 12 Oct 12:37
Nodes Matched: 12 Oct 12:39
Names Parsed: 12 Oct 12:37
New Models Stored: 12 Oct 12:37
Indexed: 12 Oct 12:39
Completed: 12 Oct 12:41
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-12 12:36:45 -0400 by logger.rb/56815
[START] [2019-10-12 12:36:45] logged process
[START] [2019-10-12 12:36:45] create_harvest_instance
[STOP] [2019-10-12 12:36:45] create_harvest_instance
[START] [2019-10-12 12:36:45] fetch_files
[STOP] [2019-10-12 12:36:45] fetch_files
[START] [2019-10-12 12:36:45] validate_each_file
[STOP] [2019-10-12 12:36:46] validate_each_file
[START] [2019-10-12 12:36:46] convert_to_csv
[CMD] [2019-10-12 12:36:46] /usr/bin/sort /app/public/converted_csv/cyprus_sp_list_refs_15555.csv > /app/public/converted_csv/cyprus_sp_list_refs_15555.csv_sorted
[CMD] [2019-10-12 12:36:46] /usr/bin/sort /app/public/converted_csv/cyprus_sp_list_nodes_15556.csv > /app/public/converted_csv/cyprus_sp_list_nodes_15556.csv_sorted
[CMD] [2019-10-12 12:36:46] /usr/bin/sort /app/public/converted_csv/cyprus_sp_list_occurrences_15557.csv > /app/public/converted_csv/cyprus_sp_list_occurrences_15557.csv_sorted
[CMD] [2019-10-12 12:36:46] /usr/bin/sort /app/public/converted_csv/cyprus_sp_list_measurements_15558.csv > /app/public/converted_csv/cyprus_sp_list_measurements_15558.csv_sorted
[STOP] [2019-10-12 12:36:46] convert_to_csv
[START] [2019-10-12 12:36:46] calculate_delta
[CMD] [2019-10-12 12:36:46] echo "0a" > /app/public/diff/cyprus_sp_list_refs_15555.diff
[CMD] [2019-10-12 12:36:46] tail -n +1 /app/public/converted_csv/cyprus_sp_list_refs_15555.csv >> /app/public/diff/cyprus_sp_list_refs_15555.diff
[CMD] [2019-10-12 12:36:46] echo "." >> /app/public/diff/cyprus_sp_list_refs_15555.diff
[CMD] [2019-10-12 12:36:47] echo "0a" > /app/public/diff/cyprus_sp_list_nodes_15556.diff
[CMD] [2019-10-12 12:36:47] tail -n +1 /app/public/converted_csv/cyprus_sp_list_nodes_15556.csv >> /app/public/diff/cyprus_sp_list_nodes_15556.diff
[CMD] [2019-10-12 12:36:47] echo "." >> /app/public/diff/cyprus_sp_list_nodes_15556.diff
[CMD] [2019-10-12 12:36:47] echo "0a" > /app/public/diff/cyprus_sp_list_occurrences_15557.diff
[CMD] [2019-10-12 12:36:47] tail -n +1 /app/public/converted_csv/cyprus_sp_list_occurrences_15557.csv >> /app/public/diff/cyprus_sp_list_occurrences_15557.diff
[CMD] [2019-10-12 12:36:47] echo "." >> /app/public/diff/cyprus_sp_list_occurrences_15557.diff
[CMD] [2019-10-12 12:36:47] echo "0a" > /app/public/diff/cyprus_sp_list_measurements_15558.diff
[CMD] [2019-10-12 12:36:47] tail -n +1 /app/public/converted_csv/cyprus_sp_list_measurements_15558.csv >> /app/public/diff/cyprus_sp_list_measurements_15558.diff
[CMD] [2019-10-12 12:36:47] echo "." >> /app/public/diff/cyprus_sp_list_measurements_15558.diff
[STOP] [2019-10-12 12:36:47] calculate_delta
[START] [2019-10-12 12:36:47] parse_diff_and_store
[INFO] [2019-10-12 12:36:47] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 12:36:48] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 12:36:49] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 12:36:49] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 12:36:59] Storing 2 References
[INFO] [2019-10-12 12:36:59] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 12:36:59] Average Time: 0.0
[INFO] [2019-10-12 12:36:59] Total Time: 1s
[INFO] [2019-10-12 12:36:59] Storing 3115 ScientificNames
[INFO] [2019-10-12 12:36:59] Processing group of 3115 in 4 groups of 1000
[INFO] [2019-10-12 12:37:00] Average Time: 0.315
[INFO] [2019-10-12 12:37:00] Total Time: 2s
[INFO] [2019-10-12 12:37:00] Storing 3115 Nodes
[INFO] [2019-10-12 12:37:00] Processing group of 3115 in 4 groups of 1000
[INFO] [2019-10-12 12:37:01] Average Time: 0.235
[INFO] [2019-10-12 12:37:01] Total Time: 1s
[INFO] [2019-10-12 12:37:01] Storing 1446 Occurrences
[INFO] [2019-10-12 12:37:01] Processing group of 1446 in 2 groups of 1000
[INFO] [2019-10-12 12:37:01] Average Time: 0.08
[INFO] [2019-10-12 12:37:01] Total Time: 1s
[INFO] [2019-10-12 12:37:01] Storing 3192 TraitsReferences
[INFO] [2019-10-12 12:37:01] Processing group of 3192 in 4 groups of 1000
[INFO] [2019-10-12 12:37:01] Average Time: 0.075
[INFO] [2019-10-12 12:37:01] Total Time: 1s
[INFO] [2019-10-12 12:37:01] Storing 3191 Traits
[INFO] [2019-10-12 12:37:01] Processing group of 3191 in 4 groups of 1000
[INFO] [2019-10-12 12:37:02] Average Time: 0.275
[INFO] [2019-10-12 12:37:02] Total Time: 2s
[INFO] [2019-10-12 12:37:02] Storing 3191 MetaTraits
[INFO] [2019-10-12 12:37:02] Processing group of 3191 in 4 groups of 1000
[INFO] [2019-10-12 12:37:03] Average Time: 0.11
[INFO] [2019-10-12 12:37:03] Total Time: 1s
[STOP] [2019-10-12 12:37:03] parse_diff_and_store
[START] [2019-10-12 12:37:03] resolve_keys
[INFO] [2019-10-12 12:37:18] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 12:37:19] traits to occurrences...
[INFO] [2019-10-12 12:37:20] traits to nodes (through occurrences)...
[INFO] [2019-10-12 12:37:20] Traits to sex term...
[INFO] [2019-10-12 12:37:20] Traits to lifestage term...
[INFO] [2019-10-12 12:37:21] MetaTraits to traits...
[INFO] [2019-10-12 12:37:21] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 12:37:21] Assocs to occurrences...
[INFO] [2019-10-12 12:37:21] Assocs to nodes...
[INFO] [2019-10-12 12:37:21] Assoc to sex term...
[INFO] [2019-10-12 12:37:21] Assoc to lifestage term...
[STOP] [2019-10-12 12:37:21] resolve_keys
[START] [2019-10-12 12:37:21] hold_for_later_1
[STOP] [2019-10-12 12:37:21] hold_for_later_1
[START] [2019-10-12 12:37:21] hold_for_later_2
[STOP] [2019-10-12 12:37:21] hold_for_later_2
[START] [2019-10-12 12:37:21] resolve_missing_parents
[STOP] [2019-10-12 12:37:27] resolve_missing_parents
[START] [2019-10-12 12:37:27] rebuild_nodes
[START] [2019-10-12 12:37:27] Flattener#flatten
[START] [2019-10-12 12:37:27] Flattener#study_resource
[START] [2019-10-12 12:37:27] Flattener#build_ancestry
[STOP] [2019-10-12 12:37:27] Flattener#build_ancestry
[INFO] [2019-10-12 12:37:27] 3115 ancestry keys
[START] [2019-10-12 12:37:27] build_node_ancestors
[INFO] [2019-10-12 12:37:27] old ancestors deleted.
[STOP] [2019-10-12 12:37:27] build_node_ancestors
[START] [2019-10-12 12:37:28] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 12:37:28] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 12:37:28] Flattener#flatten
[STOP] [2019-10-12 12:37:28] rebuild_nodes
[START] [2019-10-12 12:37:28] resolve_missing_media_owners
[STOP] [2019-10-12 12:37:28] resolve_missing_media_owners
[START] [2019-10-12 12:37:28] sanitize_media_verbatims
[STOP] [2019-10-12 12:37:28] sanitize_media_verbatims
[START] [2019-10-12 12:37:28] queue_downloads
[STOP] [2019-10-12 12:37:28] queue_downloads
[START] [2019-10-12 12:37:28] parse_names
[WARN] [2019-10-12 12:37:28] I see 3115 names which still need to be parsed.
[STOP] [2019-10-12 12:37:32] parse_names
[START] [2019-10-12 12:37:32] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 12:37:32] denormalize_canonical_names_to_nodes
[START] [2019-10-12 12:37:32] match_nodes
[START] [2019-10-12 12:37:32] map_all_nodes_to_pages
[STOP] [2019-10-12 12:39:46] map_all_nodes_to_pages
[INFO] [2019-10-12 12:39:46] 212 Unmatched nodes (of 3115)! That's too many to output. First 10: Corvus monedula (#49380559); Erythropygia (#49382933); Erythropygia galactotes (#49382932); Hirundo rupestris (#49381242); Delichon urbica (#49380849); Sylvia rueppelli (#49380665); Phylloscopus sibillatrix (#49380759); Hippolais pallida (#49381026); Parus ater (#49380928); Carduelis cannabina (#49380539)
[START] [2019-10-12 12:39:46] update_nodes
[STOP] [2019-10-12 12:39:47] update_nodes
[STOP] [2019-10-12 12:39:47] match_nodes
[START] [2019-10-12 12:39:47] reindex_search
[STOP] [2019-10-12 12:39:52] reindex_search
[START] [2019-10-12 12:39:52] normalize_units
[STOP] [2019-10-12 12:39:52] normalize_units
[START] [2019-10-12 12:39:52] calculate_statistics
[STOP] [2019-10-12 12:39:52] calculate_statistics
[START] [2019-10-12 12:39:52] complete_harvest_instance
[START] [2019-10-12 12:39:52] overall_tsv_creation
[INFO] [2019-10-12 12:39:52] Processing group of 3115 in 1 batches of 10000
[INFO] [2019-10-12 12:40:51] 1446 Traits (unfiltered)...
[INFO] [2019-10-12 12:41:05] 1446 Traits (filtered)...
[INFO] [2019-10-12 12:41:05] 0 Associations (filtered)...
[INFO] [2019-10-12 12:41:45] 7229 metadata added.
[INFO] [2019-10-12 12:41:45] 0 metadata added.
[INFO] [2019-10-12 12:41:45] Average Time: 89.57
[INFO] [2019-10-12 12:41:45] Total Time: 1m53s
[STOP] [2019-10-12 12:41:45] overall_tsv_creation
[INFO] [2019-10-12 12:41:45] Done. Check your files:
[INFO] [2019-10-12 12:41:45] (3115 lines) /app/public/data/cyprus_sp_list/publish_nodes.tsv
[INFO] [2019-10-12 12:41:45] (7011 lines) /app/public/data/cyprus_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-12 12:41:45] (3115 lines) /app/public/data/cyprus_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-12 12:41:45] (1447 lines) /app/public/data/cyprus_sp_list/publish_traits.tsv
[INFO] [2019-10-12 12:41:45] (7230 lines) /app/public/data/cyprus_sp_list/publish_metadata.tsv
[STOP] [2019-10-12 12:41:45] complete_harvest_instance
[START] [2019-10-12 12:41:45] completed
[STOP] [2019-10-12 12:41:45] completed
[STOP] [2019-10-12 12:41:45] logged process, took 300.5
Latest Process

12 Oct 12:36 EXITED currently processing 0