djtfmartin

SELECT 
    SUM(CASE WHEN requestpath LIKE '/v1/species/match%' THEN 1 ELSE 0 END) AS match,
    SUM(CASE WHEN requestpath LIKE '/v1/species/%/vernacularNames' THEN 1 ELSE 0 END) AS vernacularNames,
    SUM(CASE WHEN requestpath LIKE '/v1/species/%/verbatim' THEN 1 ELSE 0 END) AS verbatim,
    SUM(CASE WHEN requestpath LIKE '/v1/species/%/typeSpecimens' THEN 1 ELSE 0 END) AS typeSpecimens,
    SUM(CASE WHEN requestpath LIKE '/v1/species/%/toc' THEN 1 ELSE 0 END) AS toc_count,
    SUM(CASE WHEN requestpath LIKE '/v1/species/%/synonyms' THEN 1 ELSE 0 END) AS synonyms_count,
    SUM(CASE WHEN requestpath LIKE '/v1/species/%/speciesProfiles' THEN 1 ELSE 0 END) AS speciesProfiles,
    SUM(CASE WHEN requestpath LIKE '/v1/species/%/related' THEN 1 ELSE 0 END) AS related,
    SUM(CASE WHEN requestpath LIKE '/v1/species/%/references' THEN 1 ELSE 0 END) AS species_references,

djtfmartin

update species_list set is_private=true WHERE list_name REGEXP '^[0-9]' and list_type='OTHER' and is_authoritative is null;
update species_list set is_private=true WHERE list_name REGEXP '^[0-9]' and list_type='SPATIAL_PORTAL' and is_authoritative is null;
update species_list set is_private=true WHERE list_name like 'My species list%' and list_type='OTHER' and is_authoritative is null;
update species_list set is_private=true WHERE list_name = 'My species list' and list_type='SPATIAL_PORTAL' and is_authoritative is null;
update species_list set is_private=true WHERE list_name like 'My species list%' and list_type='SPATIAL_PORTAL' and is_authoritative is null;
update species_list set is_private=true WHERE list_name = 'My species list' and is_authoritative is null;
update species_list set is_private=true 
WHERE 
( list_name like 'My species list%' 
  OR list_name = 'My species list'

djtfmartin

_class
abcdIdentificationQualifier
abcdIdentificationQualifierInsertionPoint
abcdTypeStatus
acceptedNameUsage
associatedMedia
associatedOccurrences
associatedReferences
associatedSequences
associatedTaxa

djtfmartin

_class
_qa
abcdIdentificationQualifier
abcdIdentificationQualifier_p
abcdIdentificationQualifierInsertionPoint
abcdTypeStatus
acceptedNameUsage
associatedMedia
associatedOccurrences
associatedOccurrences_p

djtfmartin

import groovy.json.JsonSlurper
statusUrl = new URL("http://XXXXXXXX:8983/solr/admin/collections?action=clusterstatus&wt=json")
slurper = new JsonSlurper()
json = slurper.parseText(statusUrl.text)

collectionName = "biocache"

println("Parsing")

djtfmartin

package au.org.ala.biocache.tool

import au.org.ala.biocache.Config
import org.slf4j.LoggerFactory

object FixDatePrecision extends au.org.ala.biocache.cmd.Tool {

  def cmd = "fix-date-precision"

  def desc = "Cleanup old date precision values."

djtfmartin

2017-09-20 02:07:07,477 INFO  [GbifRegistryService] Updating GBIF organisation dp46: 8dda5e56-c4b4-4af2-90f9-170d9d22f2c1
2017-09-20 02:07:08,179 INFO  [GbifRegistryService] Setting GBIF country of attribution to AU
2017-09-20 02:07:09,030 INFO  [GbifRegistryService] Successfully updated provider in GBIF: 8dda5e56-c4b4-4af2-90f9-170d9d22f2c1
2017-09-20 02:07:09,839 INFO  [GbifRegistryService] Removing contacts
2017-09-20 02:07:10,670 INFO  [GbifRegistryService] Removed contact 615477
2017-09-20 02:07:10,671 INFO  [GbifRegistryService] Successfully synced contacts: 8dda5e56-c4b4-4af2-90f9-170d9d22f2c1
2017-09-20 02:07:10,674 INFO  [GbifRegistryService] Creating GBIF resource for dr797
2017-09-20 02:07:10,674 INFO  [GbifRegistryService] Creating dataset in GBIF: null
2017-09-20 02:07:10,674 WARN  [GbifRegistryService] Unable to register dataset - please check license: dr797 :  Whicher Scarp Flora Survey :  other
2017-09-20 02:07:10,674 INFO  [GbifRegistryService] Registry key not set for resource: dr797. Not sy

djtfmartin

create table nvc_scotland (pid integer, name varchar(255), the_geom geometry, the_geom_4326 geometry);

insert into nvc_scotland(pid, name, the_geom)
SELECT nextval('objects_id_seq'::regclass), commun_cat, ST_UNION(the_geom) FROM "65" where commun_cat='A, Aquatic Communities' GROUP BY commun_cat;

insert into nvc_scotland(pid, name, the_geom)
SELECT nextval('objects_id_seq'::regclass), commun_cat, ST_UNION(the_geom) FROM "65" where commun_cat='W, Woodlands' GROUP BY commun_cat;

# Doesnt return.....
insert into nvc_scotland(pid, name, the_geom)

djtfmartin

delete from "65" where COMMUN_CAT IS NULL;
update "65" set COMMUN_CAT = 'A, Aquatic Communities' where COMMUN_CAT='A';
update "65" set COMMUN_CAT = 'CG, Calciolous Grassland' where COMMUN_CAT='CG';
update "65" set COMMUN_CAT = 'H, Heathland' where COMMUN_CAT='H';
update "65" set COMMUN_CAT = 'M, Mires' where COMMUN_CAT='M';
update "65" set COMMUN_CAT = 'MC, Maritime Cliff Communities' where COMMUN_CAT='MC';
update "65" set COMMUN_CAT = 'MG, Mesotrophic Grassland' where COMMUN_CAT='MG';
update "65" set COMMUN_CAT = 'N/A, Non-standard code' where COMMUN_CAT='N/A';
update "65" set COMMUN_CAT = 'S, Swamps and tall-herb fens' where COMMUN_CAT='S';
update "65" set COMMUN_CAT = 'OW, Open Water' where COMMUN_CAT='OW';

djtfmartin

[
    {
        "speciesGroup": "Mammals",
        "taxonRank": "order",
        "taxa": [
            {
                "name": "DASYUROMORPHIA",
                "common": "Carnivorous Marsupials"
            },
            {