Harvest for Azerbaijan Species List Created 02 Oct 00:52

Stage: completed
Fetched: 02 Oct 00:52
Validated: 02 Oct 00:52
Deltas Created 02 Oct 00:53
Units Normalized: 02 Oct 00:57
Ancestry Built: 02 Oct 00:54
Nodes Matched: 02 Oct 00:56
Names Parsed: 02 Oct 00:54
New Models Stored: 02 Oct 00:53
Indexed: 02 Oct 00:57
Completed: 02 Oct 00:59
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-10-02 00:52:40 -0400 by logger.rb/56815
[START] [2019-10-02 00:52:40] logged process
[START] [2019-10-02 00:52:40] create_harvest_instance
[STOP] [2019-10-02 00:52:41] create_harvest_instance
[START] [2019-10-02 00:52:41] fetch_files
[STOP] [2019-10-02 00:52:41] fetch_files
[START] [2019-10-02 00:52:41] validate_each_file
[STOP] [2019-10-02 00:52:41] validate_each_file
[START] [2019-10-02 00:52:41] convert_to_csv
[CMD] [2019-10-02 00:52:41] /usr/bin/sort /app/public/converted_csv/azerbaijan_sp_li_refs_14858.csv > /app/public/converted_csv/azerbaijan_sp_li_refs_14858.csv_sorted
[CMD] [2019-10-02 00:52:43] /usr/bin/sort /app/public/converted_csv/azerbaijan_sp_li_nodes_14859.csv > /app/public/converted_csv/azerbaijan_sp_li_nodes_14859.csv_sorted
[CMD] [2019-10-02 00:52:44] /usr/bin/sort /app/public/converted_csv/azerbaijan_sp_li_occurrences_14860.csv > /app/public/converted_csv/azerbaijan_sp_li_occurrences_14860.csv_sorted
[CMD] [2019-10-02 00:52:46] /usr/bin/sort /app/public/converted_csv/azerbaijan_sp_li_measurements_14861.csv > /app/public/converted_csv/azerbaijan_sp_li_measurements_14861.csv_sorted
[STOP] [2019-10-02 00:52:47] convert_to_csv
[START] [2019-10-02 00:52:47] calculate_delta
[CMD] [2019-10-02 00:52:47] echo "0a" > /app/public/diff/azerbaijan_sp_li_refs_14858.diff
[CMD] [2019-10-02 00:52:49] tail -n +1 /app/public/converted_csv/azerbaijan_sp_li_refs_14858.csv >> /app/public/diff/azerbaijan_sp_li_refs_14858.diff
[CMD] [2019-10-02 00:52:50] echo "." >> /app/public/diff/azerbaijan_sp_li_refs_14858.diff
[CMD] [2019-10-02 00:52:52] echo "0a" > /app/public/diff/azerbaijan_sp_li_nodes_14859.diff
[CMD] [2019-10-02 00:52:53] tail -n +1 /app/public/converted_csv/azerbaijan_sp_li_nodes_14859.csv >> /app/public/diff/azerbaijan_sp_li_nodes_14859.diff
[CMD] [2019-10-02 00:52:55] echo "." >> /app/public/diff/azerbaijan_sp_li_nodes_14859.diff
[CMD] [2019-10-02 00:52:56] echo "0a" > /app/public/diff/azerbaijan_sp_li_occurrences_14860.diff
[CMD] [2019-10-02 00:52:58] tail -n +1 /app/public/converted_csv/azerbaijan_sp_li_occurrences_14860.csv >> /app/public/diff/azerbaijan_sp_li_occurrences_14860.diff
[CMD] [2019-10-02 00:52:59] echo "." >> /app/public/diff/azerbaijan_sp_li_occurrences_14860.diff
[CMD] [2019-10-02 00:53:01] echo "0a" > /app/public/diff/azerbaijan_sp_li_measurements_14861.diff
[CMD] [2019-10-02 00:53:02] tail -n +1 /app/public/converted_csv/azerbaijan_sp_li_measurements_14861.csv >> /app/public/diff/azerbaijan_sp_li_measurements_14861.diff
[CMD] [2019-10-02 00:53:04] echo "." >> /app/public/diff/azerbaijan_sp_li_measurements_14861.diff
[STOP] [2019-10-02 00:53:05] calculate_delta
[START] [2019-10-02 00:53:05] parse_diff_and_store
[INFO] [2019-10-02 00:53:07] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-02 00:53:08] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-02 00:53:11] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-02 00:53:13] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-02 00:53:24] Storing 2 References
[INFO] [2019-10-02 00:53:24] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-02 00:53:24] Average Time: 0.0
[INFO] [2019-10-02 00:53:24] Total Time: 1s
[INFO] [2019-10-02 00:53:24] Storing 3445 ScientificNames
[INFO] [2019-10-02 00:53:24] Processing group of 3445 in 4 groups of 1000
[INFO] [2019-10-02 00:53:25] Average Time: 0.3
[INFO] [2019-10-02 00:53:25] Total Time: 2s
[INFO] [2019-10-02 00:53:25] Storing 3445 Nodes
[INFO] [2019-10-02 00:53:25] Processing group of 3445 in 4 groups of 1000
[INFO] [2019-10-02 00:53:26] Average Time: 0.24
[INFO] [2019-10-02 00:53:26] Total Time: 1s
[INFO] [2019-10-02 00:53:26] Storing 1928 Occurrences
[INFO] [2019-10-02 00:53:26] Processing group of 1928 in 2 groups of 1000
[INFO] [2019-10-02 00:53:27] Average Time: 0.095
[INFO] [2019-10-02 00:53:27] Total Time: 1s
[INFO] [2019-10-02 00:53:27] Storing 4140 TraitsReferences
[INFO] [2019-10-02 00:53:27] Processing group of 4140 in 5 groups of 1000
[INFO] [2019-10-02 00:53:27] Average Time: 0.056
[INFO] [2019-10-02 00:53:27] Total Time: 1s
[INFO] [2019-10-02 00:53:27] Storing 4139 Traits
[INFO] [2019-10-02 00:53:27] Processing group of 4139 in 5 groups of 1000
[INFO] [2019-10-02 00:53:28] Average Time: 0.288
[INFO] [2019-10-02 00:53:28] Total Time: 2s
[INFO] [2019-10-02 00:53:28] Storing 4140 MetaTraits
[INFO] [2019-10-02 00:53:28] Processing group of 4140 in 5 groups of 1000
[INFO] [2019-10-02 00:53:29] Average Time: 0.142
[INFO] [2019-10-02 00:53:29] Total Time: 1s
[STOP] [2019-10-02 00:53:29] parse_diff_and_store
[START] [2019-10-02 00:53:29] resolve_keys
[INFO] [2019-10-02 00:53:47] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-02 00:53:48] traits to occurrences...
[INFO] [2019-10-02 00:53:50] traits to nodes (through occurrences)...
[INFO] [2019-10-02 00:53:50] Traits to sex term...
[INFO] [2019-10-02 00:53:51] Traits to lifestage term...
[INFO] [2019-10-02 00:53:53] MetaTraits to traits...
[INFO] [2019-10-02 00:53:53] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-02 00:53:54] Assocs to occurrences...
[INFO] [2019-10-02 00:53:54] Assocs to nodes...
[INFO] [2019-10-02 00:53:54] Assoc to sex term...
[INFO] [2019-10-02 00:53:54] Assoc to lifestage term...
[STOP] [2019-10-02 00:53:54] resolve_keys
[START] [2019-10-02 00:53:54] hold_for_later_1
[STOP] [2019-10-02 00:53:54] hold_for_later_1
[START] [2019-10-02 00:53:54] hold_for_later_2
[STOP] [2019-10-02 00:53:54] hold_for_later_2
[START] [2019-10-02 00:53:54] resolve_missing_parents
[STOP] [2019-10-02 00:54:00] resolve_missing_parents
[START] [2019-10-02 00:54:00] rebuild_nodes
[START] [2019-10-02 00:54:00] Flattener#flatten
[START] [2019-10-02 00:54:00] Flattener#study_resource
[START] [2019-10-02 00:54:00] Flattener#build_ancestry
[STOP] [2019-10-02 00:54:00] Flattener#build_ancestry
[INFO] [2019-10-02 00:54:00] 3445 ancestry keys
[START] [2019-10-02 00:54:00] build_node_ancestors
[INFO] [2019-10-02 00:54:00] old ancestors deleted.
[STOP] [2019-10-02 00:54:01] build_node_ancestors
[START] [2019-10-02 00:54:02] Flattener#propagate_ancestor_ids
[STOP] [2019-10-02 00:54:02] Flattener#propagate_ancestor_ids
[STOP] [2019-10-02 00:54:02] Flattener#flatten
[STOP] [2019-10-02 00:54:02] rebuild_nodes
[START] [2019-10-02 00:54:02] resolve_missing_media_owners
[STOP] [2019-10-02 00:54:02] resolve_missing_media_owners
[START] [2019-10-02 00:54:02] sanitize_media_verbatims
[STOP] [2019-10-02 00:54:02] sanitize_media_verbatims
[START] [2019-10-02 00:54:02] queue_downloads
[STOP] [2019-10-02 00:54:02] queue_downloads
[START] [2019-10-02 00:54:02] parse_names
[WARN] [2019-10-02 00:54:02] I see 3445 names which still need to be parsed.
[STOP] [2019-10-02 00:54:07] parse_names
[START] [2019-10-02 00:54:07] denormalize_canonical_names_to_nodes
[STOP] [2019-10-02 00:54:07] denormalize_canonical_names_to_nodes
[START] [2019-10-02 00:54:07] match_nodes
[START] [2019-10-02 00:54:07] map_all_nodes_to_pages
[STOP] [2019-10-02 00:56:55] map_all_nodes_to_pages
[INFO] [2019-10-02 00:56:55] 267 Unmatched nodes (of 3445)! That's too many to output. First 10: Hordeum violaceum (#47664977); Aegilops squarrosum (#47664604); Aegilops triaristatum (#47666804); Festuca pratensis (#47666916); Aeluropus litoralis (#47667001); Elymus caespitosa (#47665034); Elymus elongata (#47665682); Elymus elongatum (#47667075); Phleum bulbosa (#47667152); Thinopyrum hispidus (#47666986)
[START] [2019-10-02 00:56:55] update_nodes
[STOP] [2019-10-02 00:56:56] update_nodes
[STOP] [2019-10-02 00:56:56] match_nodes
[START] [2019-10-02 00:56:56] reindex_search
[STOP] [2019-10-02 00:57:04] reindex_search
[START] [2019-10-02 00:57:04] normalize_units
[STOP] [2019-10-02 00:57:04] normalize_units
[START] [2019-10-02 00:57:04] calculate_statistics
[STOP] [2019-10-02 00:57:04] calculate_statistics
[START] [2019-10-02 00:57:04] complete_harvest_instance
[START] [2019-10-02 00:57:04] overall_tsv_creation
[INFO] [2019-10-02 00:57:04] Processing group of 3445 in 1 batches of 10000
[INFO] [2019-10-02 00:58:02] 1928 Traits (unfiltered)...
[INFO] [2019-10-02 00:58:15] 1928 Traits (filtered)...
[INFO] [2019-10-02 00:58:15] 0 Associations (filtered)...
[INFO] [2019-10-02 00:58:53] 9640 metadata added.
[INFO] [2019-10-02 00:58:53] 0 metadata added.
[INFO] [2019-10-02 00:58:53] Average Time: 85.8
[INFO] [2019-10-02 00:58:53] Total Time: 1m50s
[STOP] [2019-10-02 00:58:53] overall_tsv_creation
[INFO] [2019-10-02 00:58:53] Done. Check your files:
[INFO] [2019-10-02 00:58:55] (3445 lines) /app/public/data/azerbaijan_sp_li/publish_nodes.tsv
[INFO] [2019-10-02 00:58:56] (8312 lines) /app/public/data/azerbaijan_sp_li/publish_node_ancestors.tsv
[INFO] [2019-10-02 00:58:58] (3445 lines) /app/public/data/azerbaijan_sp_li/publish_scientific_names.tsv
[INFO] [2019-10-02 00:58:59] (1929 lines) /app/public/data/azerbaijan_sp_li/publish_traits.tsv
[INFO] [2019-10-02 00:59:01] (9641 lines) /app/public/data/azerbaijan_sp_li/publish_metadata.tsv
[STOP] [2019-10-02 00:59:01] complete_harvest_instance
[START] [2019-10-02 00:59:01] completed
[STOP] [2019-10-02 00:59:01] completed
[STOP] [2019-10-02 00:59:01] logged process, took 381.02

Latest Process