{"push_id":3008085787,"size":32,"distinct_size":17,"ref":"refs/heads/feature/161508497-add-endpoint-for-latestExperiments-and-static-landingPage","head":"0f36d44582385094e4753b81d3db70ed8174056a","before":"1ab18d714c662c05cbd497f59770dfc55e7f26a9","commits":[{"sha":"b9b17e1ce735f83a27f5ee03e420b5d8eeb01cba","author":{"name":"Monica Jianu","email":"212cb88a4ff0dc9b471dfff577e1cfa83a9a8f2b@users.noreply.github.com"},"message":"Added CSS rules to fix Highcharts tooltip getting cut off. (#176)","distinct":false,"url":"https://api.github.com/repos/ebi-gene-expression-group/atlas/commits/b9b17e1ce735f83a27f5ee03e420b5d8eeb01cba"},{"sha":"97a8ddc04cc74fd10b994763680d9ce2e439091b","author":{"name":"Monica Jianu","email":"212cb88a4ff0dc9b471dfff577e1cfa83a9a8f2b@users.noreply.github.com"},"message":"Feature #160591849 - Add additional attributes to tooltip (#175)\n\n* Added additional attributes from the IDF to the experiment page JSON payload, such that they can be displayed in the colour by dropdown. Added tests.\r\n\r\n* Added retrieval of additional attributes from the idf to the cell metadata service. Removed unused method and associated test cases.","distinct":false,"url":"https://api.github.com/repos/ebi-gene-expression-group/atlas/commits/97a8ddc04cc74fd10b994763680d9ce2e439091b"},{"sha":"423c125de1f337b3286b9846bd36376bd87ad8a8","author":{"name":"Monica Jianu","email":"96d53734fc1bd54d848cd30f98069b90333b1bb3@ebi.ac.uk"},"message":"Fixed failing test.","distinct":false,"url":"https://api.github.com/repos/ebi-gene-expression-group/atlas/commits/423c125de1f337b3286b9846bd36376bd87ad8a8"},{"sha":"3168f8afd41744b4e84cff14bba739c1ea86a98f","author":{"name":"Monica Jianu","email":"212cb88a4ff0dc9b471dfff577e1cfa83a9a8f2b@users.noreply.github.com"},"message":"Feature #160591968 - Additional attributes in dropdown (#174)\n\n* Added additional attributes from the IDF to the experiment page JSON payload, such that they can be displayed in the colour by dropdown. Added tests.\r\n\r\n* Made test provider methods more isolated from idf parser implementation.","distinct":false,"url":"https://api.github.com/repos/ebi-gene-expression-group/atlas/commits/3168f8afd41744b4e84cff14bba739c1ea86a98f"},{"sha":"9da69698a54da74ece2bff1ae33ee7a2527d11dc","author":{"name":"Lingyun Zhao","email":"8ddcc5b128a9371b2eef7683f84adb9bbd02ed00@users.noreply.github.com"},"message":"Feature/160724655 show GitHub page release notes (#180)\n\n* Delete local images in release-notes\r\n\r\n* Show release notes from github page with iframe\r\n\r\n* Add iFrame-Resizer to expand the hosted iframe vertically based on contents","distinct":false,"url":"https://api.github.com/repos/ebi-gene-expression-group/atlas/commits/9da69698a54da74ece2bff1ae33ee7a2527d11dc"},{"sha":"779cc571e9696eb6d38bf73dc469377ef485d893","author":{"name":"Alfonso Muñoz-Pomer Fuentes","email":"9b22a3f218239d703e611023e2ad45fb3b8d9bdf@ebi.ac.uk"},"message":"Chore/160166795 split gxa test data (#171)\n\n* Delete all test data\r\n\r\n* Use private as it was ever intended, as a boolean\r\n\r\n* Fix incorrect depth column index, caught by randomized test! :O\r\n\r\n* Reorganize SQL migrations\r\n\r\n* Get rid off experiment_organism, the worst table ever\r\n\r\n* Simplify layout of files\r\n\r\n* Tweak test to adapt it to the new file format, without the term root\r\n\r\n* Rename method, it returns an instance of OntologyTerm\r\n\r\n* Randomize test\r\n\r\n* Migrate InterPro trader to use TsvStreamer\r\nWeirdly enough, CSVReader fails with IPR029684, but with the fantastic TsvStreamer it doesn’t!\r\n\r\n* camelCase all the things\r\n\r\n* Add minimal, basic, sufficient test for ArrayDesign\r\n\r\n* Repackage array design-related classes\r\n\r\n* Flatten package structure (we have just one single “3rd party integration”)\r\n\r\n* Remove forsaken endpoint\r\n\r\n* Do not memoize results, just go to the database as needed; remove method only used in api/arraydesigns.txt endpoint\r\n\r\n* Add some good tests for ArrayDesignDao\r\n\r\n* Feature #160196467 – Expand icon mappings in landing pages (#154)\r\n\r\n* Add/remove more species icons based on EBI Icon Font v1.2\r\n\r\n* Refactor species icon logic\r\n\r\n(cherry picked from commit 739ace2)\r\n\r\n* Make pig warm-blooded instead of photosynthetic (#157)\r\n\r\nHotfix #160200562 – Pig icon should be red\r\n\r\n(cherry picked from commit e4193e3)\r\n\r\n* If Comment[AEExperimentDisplayName] is empty default to Investigation Title (#156)\r\n\r\nHotfix #160200567 – E-MTAB-5214 title is empty\r\n\r\n(cherry picked from commit e173573)\r\n\r\n* Reformat code; run all JS code after all is loaded; give some size values that work in Firefox *and* Chrome (#155)\r\n\r\nHotfix #160201398 – Tableau is cropped in Chrome\r\n\r\n(cherry picked from commit 71711c2)\r\n\r\n* Worms are cold-blooded\r\n\r\n* Another forgotten endpoint bites the dust\r\n\r\n* We don’t need DataFileHubFactory: just injecting the path bean and using DataFileHub’s constructor is enough\r\n\r\n* Rewrite methods so that the ontology terms multimap don’t rely on functions with side effects; be more functional all around\r\n\r\n* Rewrite EfoLookupService as a simpler single class and move it to the conditions package, the only place where it’s used\r\n\r\n* Remove unused method\r\n\r\n* Move out of AssayGroup a convenience constructor used in tests and refactor it into a tests package factory class\r\n\r\n* Add Guava flavour of AssertJ to the project\r\n\r\n* Refactor all uses of ThreadLocalRandom.current() into a private constant\r\n\r\n* Make two conditions equal if the metadata terms are the same, regardless of the order\r\n\r\n* Rename ConditionsLookupService to LegacyConditionsLookupService; refactor design of the class to two classes with only five methods and half the code, without any transient state (i.e. builders), just pure functions\r\n\r\n* Add tests:\r\n• Compare results of legacy service with current class\r\n• Good mocks that mirror our actual data model\r\n\r\n* Remove legacy conditions service\r\n\r\n* Remove all logic that inserts data to the DB from the web app\r\n\r\n* Change varargs to List to get rid of a compilation warning\r\n\r\n* Replace deprecated methods after the template of the SC suggestions without highlighting\r\n\r\n* Minor code clean up\r\n\r\n* Add repository atlas-schemas as a submodule in the test resources directory\r\n\r\n* Add Spring-profile-dependent configuration to use an embedded database when running integration tests (i.e. all tests that use TestConfig for their context configuration)\r\n\r\n* Use PostgreSQL unless other profile such as \"test\" is set\r\n\r\n* Move fixtures to a separate directory and load them in @BeforeAll for consistency with other ITs, as it’s a more general solution\r\n\r\n* Populate experiments table before running tests\r\n\r\n* Remove PostgreSQL-specific functions\r\nIt’s a shame because TABLESAMPLE was faster than random-sorting the results, but since we’ll be using fixtures from now on I don’t think it’s going to be even noticeable\r\n\r\n* Use the already-defined transaction manager bean from our JdbcConfig class\r\n\r\n* It’s not organism, but species!\r\n\r\n* Rewrite test suite to include: parameterized tests, embedded DB and SQL fixtures\r\n\r\n* Add H2 dependency and remove PostgreSQL connection parameters from the integration profile\r\n\r\n* Load all the test configuration from TestConfig instead of segregating beans in two files\r\nThis is really a workaround for the fact that @ActiveProfiles is skipped in configuration classes and only works for tests. For instance, you can have a base integration test class that includes this annotation and make all other ITs inherit it.\r\n\r\n* Split fixture files into data insertion and table clean up\r\nUnfortunately @Sql doesn’t work with @ParameterizedTest :(\r\n\r\n* Ditch Spring profiles and load/skip the necessary @Configuration with filters in @ComponentScan\r\nWe need to set the active profile at compile time (through environment or -D variables) so that the right @Configuration classes are loaded when @ComponentScan is found, but then we can’t set a profile when running Tomcat. In that case we’d need to activate a profile programmatically in AppConfig or similar. In summary: it’d be a mess.\r\n\r\n* Name returned columns explicitly and don’t rely on PostgreSQL-specifics\r\n\r\n* Add schemas submodule directory entry\r\n\r\n* Clean up tables after array design-related classes have been tested\r\n\r\n* Comment where the fixtures come from\r\n\r\n* Test PopularSpeciesDao with sensible-looking data\r\n\r\n* Wrap id-to-EFO map in a LazyReference to speed up application start up\r\nThis is how it was before, now it’s time to bring it back again now that everything seems to be working fine\r\n\r\n* A new beginning...\r\n\r\n* Remove commented out line\r\n\r\n* Add comment to clarify the difference between highlighted and non-highlighted suggestions\r\n\r\n* Be descriptive about what @BeforeAll and @AfterAll actually do\r\n\r\n* Don’t build the assay-to-conditions map every time we visit an assay, instead build it once and reuse it when building the stream elements\r\nTry to ANALYTICS_IMPORT GTEx without this... I did and it stalls for an indefinite amount of time until it starts to send documents to Solr. I waited for three hours until I decided something was wrong.\r\n\r\n* Resotre .gitignore file, it got lost somewhere along the way\r\n\r\n* Add additional external properties for ZK host and Solr port\r\n\r\n* Only strip descriptions with [Sourece:...], as there are other descriptions with interesting stuff in square brackets; parameterize tests, JUnit 5\r\n\r\n* Update comments to be truthful; remove unnecessary throw declaration\r\n\r\n* Remove unused constant\r\n\r\n* Rename generic type to be consistent across classes\r\n\r\n* Lower log level, it floods the logger when adding documents to the analytics index and performance really suffers\r\n\r\n* Add a public rawQuery method\r\nThis is a small defeat in our mini SorlCloud framework since by exposing this some type-safety is lost, but now we can write better tests. We can rethink the design if we move the framework to its own project.\r\n\r\n* Remove any mention of Spring profiles... ever\r\n\r\n* Add scxa-gene2experiment to the list of required collections\r\n\r\n* Modify some of the expected results to match our new test data\r\n\r\n* Add/modify settings for the new test data\r\n\r\n* Fix path of CI test data\r\n\r\n* Use version number with patch level\r\n\r\n* Remove redundant .gitignore file\r\nI think this one was accidentally moved in a previous commit (?)\r\n\r\n* Restructure app configuration classes to exclude Postgres-related beans in test classes; add new Solr/ZK port property\r\n\r\n* Change test configuration class to TestConfig instead of WebConfig\r\n\r\n* Add SQL fixtures to tests, migrate to JUnit 5 and parameterize\r\n\r\n* Inline JSON response in test\r\n\r\n* Fix RSE to work with the new schema that uses a BOOLEAN column instead of a VARCHAR\r\n\r\n* Use new suggestion field names\r\n\r\n* Wrap IOException in UncheckedIOException\r\n\r\n* Remove superfluous test cases\r\nImport operations just insert a row in the experiments test, there’s no longer a different behaviour depending on the experiment type, so we only need to test the operations regardless of the type\r\n\r\n* Move to JUnit 5 and leave the tables clean after testing\r\n\r\n* By default return public experiments\r\n\r\n* Restructure app configuration classes to exclude Postgres-related beans in test classes; 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