djtfmartin’s gists

djtfmartin / gist:551e632d75679b574bdc037abaa79208

Created June 29, 2023 15:52

species list clean up

	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 / export_of_raw_db_fields_2018-06-13.txt

Created June 13, 2018 22:29

export_of_raw_db_fields_2018-06-13.txt

	_class
	abcdIdentificationQualifier
	abcdIdentificationQualifierInsertionPoint
	abcdTypeStatus
	acceptedNameUsage
	associatedMedia
	associatedOccurrences
	associatedReferences
	associatedSequences
	associatedTaxa

djtfmartin / export_of_db_fields_2018-06-13.txt

Created June 13, 2018 22:26

export_of_db_fields_2018-06-13.txt

	_class
	_qa
	abcdIdentificationQualifier
	abcdIdentificationQualifier_p
	abcdIdentificationQualifierInsertionPoint
	abcdTypeStatus
	acceptedNameUsage
	associatedMedia
	associatedOccurrences
	associatedOccurrences_p

djtfmartin / gist:5064a77eeb7533e2d23d26c446ca51a0

Created November 16, 2017 11:45

Index sync script


	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 / gist:3a98a0f4339adea3444cf1ff761b18a1

Created November 16, 2017 11:31

FixDatePrecision.scala

	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 / gist:4a639e601ba4f156a8953c69cfbafef7

Created September 19, 2017 19:22

	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 / loading_nvc_table.sql

Created August 1, 2017 10:36

	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 / NVC SQL

Last active July 31, 2017 18:33

	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 / gist:4395dd91d377d35f1a5e61e806e6b791

Created March 28, 2017 11:42

subgroups.json

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

djtfmartin / gist:8977528215f949d10557f259314656d5

Created March 27, 2017 14:09

This file has been truncated, but you can view the full file.


	<?xml version="1.0" encoding="UTF-8"?>
	<response>

	<lst name="responseHeader">
	<int name="status">0</int>
	<int name="QTime">62</int>
	<lst name="params">
	<str name="qt">standard</str>
	<str name="_stateVer_">biocache:222</str>

Dave Martin djtfmartin