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https://github.com/abbe98/catalogue_of_life
https://github.com/abbe98/catalogue_of_life
Last synced: 7 days ago
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- Host: GitHub
- URL: https://github.com/abbe98/catalogue_of_life
- Owner: Abbe98
- Created: 2016-02-04T18:54:18.000Z (almost 9 years ago)
- Default Branch: master
- Last Pushed: 2016-02-03T10:05:50.000Z (almost 9 years ago)
- Last Synced: 2024-10-10T18:54:27.629Z (28 days ago)
- Language: Ruby
- Size: 129 KB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# catalogue_of_life
## prerequisites
Install Vagrant and VirtualBox.
## install
$ git clone https://github.com/Biocaching/catalogue_of_life.git
$ cd catalogue_of_life
$ vagrant up
After this, Catalogue of Life: 2015 Annual Checklist will be installed and available at http://192.168.33.8/col2015ac/
## database
To browse the database:
$ vagrant ssh
$ cd /vagrant/sql
[vagrant@localhost ~]$ mysql -u root col2015ac
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A
Welcome to the MariaDB monitor. Commands end with ; or \g.
Your MariaDB connection id is 31
Server version: 10.1.9-MariaDB MariaDB Server
Copyright (c) 2000, 2015, Oracle, MariaDB Corporation Ab and others.
Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.
MariaDB [col2015ac]> show tables;
+---------------------------------------+
| Tables_in_col2015ac |
+---------------------------------------+
| _natural_keys |
| _search_all |
| _search_distribution |
| _search_family |
| _search_scientific |
| _source_database_details |
| _source_database_to_taxon_tree_branch |
| _species_details |
| _taxon_tree |
| _totals |
| author_string |
| common_name |
| common_name_element |
| country |
| distribution |
| distribution_free_text |
| distribution_status |
| hybrid |
| language |
| lifezone |
| lifezone_to_taxon_detail |
| reference |
| reference_to_common_name |
| reference_to_synonym |
| reference_to_taxon |
| reference_type |
| region |
| region_free_text |
| region_standard |
| scientific_name_element |
| scientific_name_status |
| scrutiny |
| source_database |
| specialist |
| synonym |
| synonym_name_element |
| taxon |
| taxon_detail |
| taxon_name_element |
| taxonomic_coverage |
| taxonomic_rank |
| uri |
| uri_scheme |
| uri_to_source_database |
| uri_to_taxon |
+---------------------------------------+
45 rows in set (0.00 sec)
MariaDB [col2015ac]> source top_level.sql
+--------------+
| name_element |
+--------------+
| animalia |
| plantae |
| fungi |
| viruses |
| bacteria |
| chromista |
| protozoa |
| archaea |
+--------------+
8 rows in set (0.00 sec)
MariaDB [col2015ac]>
Alle i dyreriket:
MariaDB [col2015ac]> source animalia.sql
Alle i chordata:
MariaDB [col2015ac]> source chordata.sql
Alle i chordata:
MariaDB [col2015ac]> source chordata.sql
Alle pattedyr:
MariaDB [col2015ac]> source mammalia.sql
Alle rodyr (kjøttetere):
MariaDB [col2015ac]> source carnivora.sql
Alle arter i bjørnefamilien:
MariaDB [col2015ac]> source ursus.sql
Alle underarter av nordamerikansk bjørn:
MariaDB [col2015ac]> source americanus.sql
### Finne navn på art:
MariaDB [col2015ac]> select * from common_name cn, common_name_element cne where cn.taxon_id = 21936335 and cn.common_name_element_id = cne.id;
+------+----------+------------------------+--------------+-------------+---------------------+------+------------+-----------------+
| id | taxon_id | common_name_element_id | language_iso | country_iso | region_free_text_id | id | name | transliteration |
+------+----------+------------------------+--------------+-------------+---------------------+------+------------+-----------------+
| 1866 | 21936335 | 1864 | fra | NULL | NULL | 1864 | ours blanc | NULL |
| 1867 | 21936335 | 1865 | eng | NULL | NULL | 1865 | Polar Bear | NULL |
+------+----------+------------------------+--------------+-------------+---------------------+------+------------+-----------------+
2 rows in set (0.00 sec)
Gorilla:
select * from common_name, common_name_element, taxon, taxonomic_rank, scientific_name_element, taxon_name_element
where name like '%gorilla%'
and common_name.common_name_element_id = common_name_element.id
and taxon.id = common_name.taxon_id
and scientific_name_element.id = taxon_name_element.scientific_name_element_id
and taxonomic_rank.id = taxon.taxonomic_rank_id
and taxon_name_element.taxon_id = taxon.id;
Arter i løvetannfamilien:
select s.name_element, tne.taxon_id, tr.rank from scientific_name_element s, taxon_name_element tne, taxon t, taxonomic_rank tr where s.id = tne.scientific_name_element_id and t.id = tne.taxon_id and tr.id = t.taxonomic_rank_id and tne.parent_id = 22102505 order by s.name_element;
Funker ikke:
select s.name_element, tne.taxon_id, tr.rank
from scientific_name_element s, taxon_name_element tne, taxon t, taxonomic_rank tr, common_name cn, common_name_element cne
where s.id = tne.scientific_name_element_id and t.id = tne.taxon_id and tr.id = t.taxonomic_rank_id
and tne.parent_id = 22102505 and cn.taxon_id = tne.taxon_id and cn.common_name_element_id = cne.id
order by s.name_element;
Finne hvor mange arter som er i COL:
select count(*) from taxon t, taxonomic_rank tr
where tr.id = t.taxonomic_rank_id and tr.rank = 'species';
# Rails app
Lager en Ruby on Rails app for å bygge Biocaching artsdatabase.
$ vagrant ssh
$ cd /vagrant/
$ mkdir rails
$ cd rails
$ rails new speciesdb -d mysql
$ cd speciesdb
Databasebruker for rails (speciesdb) skal ha blitt opprettet i MariaDB.
Installerer gems:
$ bundle install
Kjører kommando for å opprette databaser:
$ rake db:create
Kjører migreringer og seed:
$ rake db:migrate && rake db:seed
Evt slette databasen og opprette på nytt:
$ rake db:rollback STEP=6
$ rake db:migrate && rake db:seed
Opprette Elasticsearch indeks:
$ ./scripts/re_create_es_index.sh
Importere data fra COL (alle kingdoms og så animalia og chordata):
$ rake col:import_top_levels && rake col:import[22032961] && rake col:import[22032976]
Importere (rekursivt) alle pattedyr, reptiler og fugler fra COL:
$ rake col:import[22032977,true]
$ rake col:import[22033651,true]
$ rake col:import[22033189,true]
Indeksere ett artsnavn i Elasticsearch:
$ rake es:import_one
Indeksere alle genus, species og div infraspecific i Elasticsearch:
$ rake es:import
## Starte Rails
Kan starte rails slik:
$ cd /vagrant/rails/
$ rails s -b 0.0.0.0
Og åpne railsapplikasjonen på denne adressen http://localhost:3000