Merge branch 'develop'

.travis.yml

@@ -1,12 +1,16 @@
-dist: precise
+dist: trusty
+sudo: required
 
 language: php
 
 php:
-  - '5.6'
   - '7.0'
   - '7.1'
-#  - hhvm
+  - '7.2'
+
+env:
+  - POSTGRESQL_VERSION=postgresql-9.3-postgis-2.1
+  - POSTGRESQL_VERSION=postgresql-10-postgis-2.4
 
 services:
   - postgresql
@@ -23,25 +27,38 @@ before_install:
   # Reinstall PostgreSQL - see https://github.com/travis-ci/travis-ci/issues/7048#issuecomment-267731971
   - sudo apt-get autoremove postgis*
   - sudo apt-get autoremove postgresql*
-  - sudo apt-get install postgresql-9.3-postgis-2.1
+  - sudo apt-get install $POSTGRESQL_VERSION
   # Install Apache.
   - sudo apt-get install apache2 libapache2-mod-fastcgi
-  # Enable php-fpm.
-  - sudo cp ~/.phpenv/versions/$(phpenv version-name)/etc/php-fpm.conf.default ~/.phpenv/versions/$(phpenv version-name)/etc/php-fpm.conf
+  # See https://www.marcus-povey.co.uk/2016/02/16/travisci-with-php-7-on-apache-php-fpm/
   - if [[ ${TRAVIS_PHP_VERSION:0:2} == "7." ]]; then sudo cp ~/.phpenv/versions/$(phpenv version-name)/etc/php-fpm.d/www.conf.default ~/.phpenv/versions/$(phpenv version-name)/etc/php-fpm.d/www.conf; fi
+  # enable php-fpm
+  - sudo cp ~/.phpenv/versions/$(phpenv version-name)/etc/php-fpm.conf.default ~/.phpenv/versions/$(phpenv version-name)/etc/php-fpm.conf
   - sudo a2enmod rewrite actions fastcgi alias
   - echo "cgi.fix_pathinfo = 1" >> ~/.phpenv/versions/$(phpenv version-name)/etc/php.ini
+  - sudo sed -i -e "s,www-data,travis,g" /etc/apache2/envvars
+  - sudo chown -R travis:travis /var/lib/apache2/fastcgi
   - ~/.phpenv/versions/$(phpenv version-name)/sbin/php-fpm
-  # Configure apache virtual hosts.
-  - sudo cp -f .travis/travis-ci-apache /etc/apache2/sites-available/default
-  - sudo sed -e "s?%TRAVIS_BUILD_DIR%?$(pwd)?g" --in-place /etc/apache2/sites-available/default
+  # configure apache virtual hosts
+  - sudo cp -f .travis/travis-ci-apache /etc/apache2/sites-available/000-default.conf
+  - sudo sed -e "s?%TRAVIS_BUILD_DIR%?$(pwd)?g" --in-place /etc/apache2/sites-available/000-default.conf
   - sudo service apache2 restart
 
 install:
   # Grant execute on scripts
   - chmod +x .travis/postgres_setup.sh
 
 before_script:
+    # Special configuration required for PostgreSQL 10.
+  - |
+    if [ ${POSTGRESQL_VERSION:10:4} == "-10-" ]; then
+      # Use default port
+      sudo sed -i 's/port = 5433/port = 5432/' /etc/postgresql/10/main/postgresql.conf
+      # Use 9.6 auth config:
+      sudo cp /etc/postgresql/{9.6,10}/main/pg_hba.conf
+    fi
+  - sudo service postgresql restart
+  # Create database
   - psql -c 'create database indicia;' -U postgres -d postgres
   # Add extension for PostGIS
   - psql -U postgres -d indicia -c "create extension postgis"
@@ -58,12 +75,12 @@ before_script:
   - sudo mv phpunit-5.7.phar /usr/local/bin/phpunit
 
 script:
-  - /usr/local/bin/phpunit --configuration phpunit-config-test.xml
-  - /usr/local/bin/phpunit --configuration phpunit-setup-check-test.xml
-  - /usr/local/bin/phpunit --configuration phpunit-home-test.xml
+  - /usr/local/bin/phpunit --stderr --configuration phpunit-config-test.xml
+  - /usr/local/bin/phpunit --stderr --configuration phpunit-setup-check-test.xml
+  - /usr/local/bin/phpunit --stderr --configuration phpunit-home-test.xml
   # Repeat to upgrade modules
-  - /usr/local/bin/phpunit --configuration phpunit-home-test.xml
-  - /usr/local/bin/phpunit --configuration phpunit-tests.xml
+  - /usr/local/bin/phpunit --stderr --configuration phpunit-home-test.xml
+  - /usr/local/bin/phpunit --stderr --configuration phpunit-tests.xml
 
 after_script:
   - cat application/logs/*

.travis/travis-ci-apache

@@ -2,11 +2,10 @@
 
   DocumentRoot %TRAVIS_BUILD_DIR%
 
-  <Directory "%TRAVIS_BUILD_DIR%">
+  <Directory "%TRAVIS_BUILD_DIR%/">
     Options FollowSymLinks MultiViews ExecCGI
     AllowOverride All
-    Order deny,allow
-    Allow from all
+    Require all granted
   </Directory>
 
   # Wire up Apache to use Travis CI's php-fpm.
@@ -15,6 +14,10 @@
     Action php5-fcgi /php5-fcgi
     Alias /php5-fcgi /usr/lib/cgi-bin/php5-fcgi
     FastCgiExternalServer /usr/lib/cgi-bin/php5-fcgi -host 127.0.0.1:9000 -pass-header Authorization
+
+    <Directory /usr/lib/cgi-bin>
+        Require all granted
+    </Directory>
   </IfModule>
 
 </VirtualHost>

CHANGELOG.md

@@ -0,0 +1,69 @@
+# Version 2.0.0
+
+Please see [upgrading to version 2.0.0](UPGRADE-v2.md).
+
+## Warehouse user interface changes
+
+* Warehouse client helper and media code libraries updated to use jQuery 3.2.1
+  and jQuery UI 1.12.
+* Overhaul the warehouse UI with a new Bootstrap 3 based theme and more logical menu
+  structure.
+* Warehouse home page now has additional help for getting started and diagnosing
+  problems.
+
+## Back-end changes
+
+* Support for PostgreSQL version 10.
+* Support for PHP 7.2.
+* Support for prioritised load aware background task scheduling via a work queue module.
+
+## Database schema changes
+
+* Removed the following:
+  * index_locations_samples table
+  * fields named location_id_* from cache_occurrences_functional
+  * fields named location_id_* from cache_samples_functional
+  Replaced the above with cache_occurrences_functional.location_ids (integer[]) and
+  cache_samples_functional.location_ids (integer[]). This means there is no need to
+  distinguish between uniquely indexed location types (linked via the locaiton_id_*
+  fields) and non-uniquely indexed location types (linked in the index_locations_samples
+  table). Removes the need for additional join to index_locations_samples so will improve
+  performance in many cases.
+* Attribute values for taxa, samples and occurrences are now stored in the relevant
+  reporting cache tables in a JSON document (attrs_json field). This means that reports
+  can output custom attribute values for a record without additional joins for each
+  attribute. To enable this functionality, the report needs a parameter of type taxattrs,
+  smpattrs or occattrs (allowing attributes to include to be dynamically declared in a
+  parameter). Then provide a parameter useJsonAttributes set to a value of '1' to enable
+  the new method of accessing attribute values. This has the potential to improve
+  performance significantly for reports which include many different attribute values in
+  the output.
+* New cache_taxon_paths which provides a hierarchical link between taxa and all their
+  taxonomic parents.
+* Cache_occurrences_functional now has a taxon_path field which links to the parent taxa
+  for the record, as defined by the main taxon list configured on the warehouse.
+* Reports no longer need to join via users to check the sharing/privacy settings of a
+  user. Any sharing task codes which are not available for the user are listed in
+  cache_*_functional.blocked_sharing_tasks.
+* Support for dynamic attributes, i.e custom sample or occurrence attributes which are
+  linked to a taxon. They can then be included on a recording form only when entering a
+  taxon that is, or is a descendant of, the linked taxon.
+
+## Report updates
+
+* Updated reports which used the location_id_* fields to output a location for a record
+  to now update a list of overlapping locations rather than being limited to a single
+  location. For example, if a record is added which overlaps 2 country boundaries then
+  the report may include both country names in the output field rather than just one.
+* Removed the following unused verification reports. Existing verification
+  implementations on client websites should be updated to use the verification_5 prebuilt
+  form and its reports:
+  * reports/library/occurrences/verification_list.xml
+  * reports/library/occurrences/verification_list_2.xml
+  * reports/library/occurrences/verification_list_3.xml
+  * reports/library/occurrences/verification_list_3_mapping.xml
+  * reports/library/occurrences/verification_list_3_mapping_using_spatial_index_builder.xml
+  * reports/library/occurrences/verification_list_3_using_spatial_index_builder.xml
+* Other unused reports removed:
+  * reports/library/locations/filterable_occurrence_counts_mappable_2.xml
+  * reports/library/locations/filterable_species_counts_mappable_2.xml