CHANGELOG.rst

SODAR Changelog

Changelog for the SODAR project. Loosely follows the Keep a Changelog guidelines.

v0.15.1 (2024-09-12)

Changed

• Samplesheets

  • Upgrade Vue app dependencies (#1986)

Fixed

• Landingzones

  • Invalid CSS classes set by zone status update (#1995)

• Samplesheets

  • generic assay plugin inline links pointing to ResultsReports (#1982)
  • generic assay plugin cache update crash with row path built from ontology column (#1984)

v0.15.0 (2024-08-08)

Added

• General

  • Cyberduck documentation (#1931)

• Isatemplates

  • isatemplates app for custom ISA-Tab template management (#1961)
  • isatemplates_backend plugin for template retrieval (#1961)

• Samplesheets

  • template_output_dir_display user setting (#1960)
  • Display BAM/CRAM/VCF omit patterns in study shortcut modal (#1963)
  • Row links display override using assay comment (#1968)
  • generic assay app plugin (#1946)

• Taskflowbackend

  • BatchCalculateChecksumTask retrying in case of timeouts (#1941)

Changed

• General

  • Upgrade critical Python dependencies (#1930)
  • Upgrade to black v24.3.0 (#1930)
  • Reformat with black (#1930)

• Irodsbackend

  • Remove Bootstrap tooltips from iRODS buttons (#1949)

• Landingzones

  • Remove Bootstrap tooltip updating for iRODS buttons (#1949)

• Samplesheets

  • Upgrade Vue app dependencies (#1930, #1971, #1972)
  • Sanitize iRODS paths in get_row_path() calls (#1947)
  • index arg in SampleSheetAssayPluginPoint.update_row() (#1957)
  • Hide template output dir field by default (#1960)
  • Improve StudyLinksAjaxView return data (#1963, #1966)
  • Optimize irodsbackend API retrieval in plugins (#1952)

• Taskflowbackend

  • Increase default for TASKFLOW_IRODS_CONN_TIMEOUT (#1900)
  • Disable lock requirement for role and project update flows (#1948)

Fixed

• General

  • README.rst badge rendering (#1938)

• Landingzones

  • Bootstrap tooltips preventing zone button clicking with certain conditions (#1949)
  • Zone with NOT CREATED status displayed as active in project list (#1962)

• Samplesheets

  • Invalid assay measurement type in i_minimal* test data (#1954)
  • Error message handling in StudyShortcutModal (#1965)
  • Overwrite warning displayed in OntologyEditModal with empty initial value (#1973)
  • ColumnToggleModal "toggle all" button misaligned with filtering enabled (#1975)

• Taskflowbackend

  • Malformed exception message in BatchValidateChecksumsTask (#1943)
  • Exceeded zone status info char limit in _raise_flow_exception() (#1953)
  • Uncaught exception in BatchCreateCollectionsTask (#1958)

v0.14.2 (2024-03-15)

Added

• General

  • Django settings for reverse proxy setup (#1917)

• Irodsbackend

  • Sanitize and validate IRODS_ROOT_PATH in get_root_path() (#1891)

• Landingzones

  • Create assay plugin shortcut collections for zones (#1869)
  • Zone statistics for siteinfo (#1898)
  • UI tests for project details card (#1902)

• Samplesheets

  • IrodsDataRequest timeline event extra data (#1912)
  • CRAM file support in study apps (#1908)
  • check_igv_file_suffix() helper in studyapps.utils (#1908)
  • Path checking for IGV omit settings (#1923)
  • Glob pattern support for IGV omit settings (#1923)

• Taskflowbackend

  • Django settings in siteinfo (#1901)
  • BatchSetAccessTask in iRODS tasks (#1905)
  • IrodsAccessMixin task helper mixin (#1905)

Changed

• General

  • Upgrade to Django v3.2.25 (#1854)
  • Upgrade to django-sodar-core v0.13.4 (#1899)
  • Upgrade critical Vue app dependencies (#1854)
  • Upgrade to cubi-isa-templates v0.1.2 (#1854)
  • Update installation documentation (#1871)

• Irodsbackend

  • Reduce redundant object queries (#1883)
  • Change method logic in get_objects() and get_objs_recursively() (#1883)
  • Use get_root_path() within IrodsAPI (#1890)
  • Refactor IrodsStatisticsAjaxView and related JQuery (#1903)

• Samplesheets

  • Improve Django messages for IrodsDataRequest exceptions (#1858)
  • Change IrodsDataRequest description if created in Ajax view (#1862)
  • Refactor IrodsDataRequestModifyMixin timeline helpers (#1913)
  • Rename get_igv_omit_override() to get_igv_omit_list() (#1924)
  • Rename check_igv_file_name() to check_igv_file_path() (#1923)
  • Named process pooling and renaming in sheet editor (#1904)

• Taskflowbackend

  • Optimize landing_zone_move iRODS path retrieval (#1882)
  • Set zone status on uncaught errors in run_flow() (#1458)
  • Change TASKFLOW_IRODS_CONN_TIMEOUT default value to 960 (#1900)

Fixed

• General

  • Invalid env var retrieval for AUTH_LDAP*_START_TLS (#1853)

• Irodsbackend

  • Invalid path returned by get_path() if IRODS_ROOT_PATH is set (#1889)
  • Stats badge stuck in updating with non-200 POST status (#1327, #1886)

• Landingzones

  • Stats badge displayed to superusers for DELETED zones (#1866)
  • Zone status updating not working in project details card (#1902)
  • Modifying finished lock status allowed in SetLandingZoneStatusTask (#1909)

• Samplesheets

  • Invalid WebDAV URLs generated in IrodsDataRequestListView (#1860)
  • Superuser not allowed to edit iRODS request from other users in UI (#1863)
  • IrodsDataRequest user changed on object update (#1864)
  • IrodsDataRequest._validate_action() failing with delete action (#1858)
  • Protocol ref editable for new row if disabled in column config (#1875)
  • Sheet template creation failure with slash characters in title/ID fields (#1896)
  • get_pedigree_file_path() used in cancer study app tests (#1914)
  • IGV omit settings not correctly set on project creation (#1925)
  • Germline study cache build crash with no family column (#1921)
  • Source name editing failing in assay table after row insert (#1928)

• Taskflowbackend

  • Hardcoded iRODS path length in landing_zone_move (#1888)
  • Uncaught exceptions in SetAccessTask (#1906)
  • Crash in landing_zone_create with large amount of collections (#1905)
  • Finished landing zone status modified by lock exception (#1909)

Removed

• General

  • LDAP settings OPT_X_TLS_REQUIRE_CERT workaround (#1853)

• Taskflowbackend

  • get_subcoll_obj_paths() and get_subcoll_paths() helpers (#1882)

v0.14.1 (2023-12-12)

Added

• Irodsbackend

  • get_version() helper (#1592, #1817, #1831)
  • get_access_lookup() helper (#1832)

• Irodsinfo

  • iRODS v4.3 auth scheme support in client environment (#1834)

• Samplesheets

  • Custom validation for sheet_sync_url and sheet_sync_token (#1310, #1384)
  • hpo.jax.org in SHEETS_ONTOLOGY_URL_SKIP (#1821)
  • Missing Django settings in siteinfo (#1830)

• Taskflowbackend

  • iRODS v4.3 support (#1592, #1817, #1832)
  • BatchCalculateChecksumTask exception logging (#1843)

Changed

• General

  • Upgrade to Django v3.2.23 (#1811)
  • Upgrade to django-sodar-core v0.13.3 (#1810)

• Irodsbackend

  • iRODS collection modal copy button icon (#1851)

• Landingzones

  • Disable locked zone controls in template for non-superusers (#1808)
  • Rename and refactor disable_zone_ui() template tag (#1808)

• Samplesheets

  • Upgrade Vue app dependencies (#1811)
  • Change default IGV genome to b37_1kg (#1812)
  • Update existing b37 IGV genome settings with a migration (#1812)

• Taskflowbackend

  • Improve landing_zone_move zone status info messages for validation (#1840)

Fixed

• General

  • Add workaround for AUTH_LDAP_CONNECTION_OPTIONS duplication (#1853)

• Irodsbackend

  • Opening redundant iRODS connection in server version retrieval (#1831)

• Landingzones

  • No wait for async CurrentUserRetrieveAPIView call result (#1732, #1807)
  • BaseLandingZoneStatusTask.set_status() failure with concurrent sheet replacing (#1839)

• Samplesheets

  • ColumnToggleModal study checkbox states rendered under assay (#1848)
  • ColumnToggleModal group toggle not updating checkboxes in UI (#1849)

• Taskflowbackend

  • project_create timeline event user reference (bihealth/sodar_core#1301, #1819)
  • Incorrect write access messages in landing_zone_move when validating only (#1845)

Removed

• Taskflowbackend

  • Duplicate SetAccessTask tests (#1833)

v0.14.0 (2023-09-27)

Added

• General

  • Release cleanup issue template (#1797)
  • LDAP settings for TLS and user filter (#1803)

• Irodsbackend

  • get_trash_path() helper (#1658)
  • iRODS trash statistics for siteinfo (#1658)

• Irodsinfo

  • IrodsEnvRetrieveAPIView for retrieving iRODS environment (#1685)

• Landingzones

  • Landing zone updating (#1267)
  • "Nothing to do" check for landing zone validation and moving (#339)
  • iRODS path clipboard copying button in iRODS collection list modal (#1282)
  • constants module for zone constants (#1398)
  • Assay link from zone assay icon (#1747)
  • Missing permission tests (#1739)

• Samplesheets

  • User setting for study and assay table height (#1283)
  • Study table cache disabling (#1639)
  • SHEETS_ENABLE_STUDY_TABLE_CACHE setting (#1639)
  • cytof assay plugin (#1642)
  • New ISA-Tab templates from cubi-isa-templates (#1697, #1757)
  • General iRODS access ticket management for assay collections (#804, #1717)
  • Disabled row delete button tooltips (#1731)
  • IrodsDataRequest REST API views (#1588, #1706, #1734, #1735, #1736)
  • Davrods links in iRODS delete request list (#1339)
  • Batch accepting and rejecting for iRODS delete requests (#1340, #1751)
  • Cookiecutter prompt support in sheet templates (#1726)
  • "Create" tag for sheet versions (#1296)
  • Template tag tests (#1723)
  • iRODS file count in sheet overview tab (#1295)
  • get_url() helpers for Investigation, Study and Assay models (#1748)
  • normalizesheets management command for sheet cleanup (#1661)
  • Boolean field support in sheet templates (#1757)
  • iRODS access ticket REST API views (#1707, #1800, #1801)

• Taskflowbackend

  • BatchCalculateChecksumTask iRODS task (#1634)
  • Automated generation of missing checksums in landing_zone_move (#1634, #1767)
  • Cleanup of trash collections in testing (#1658)
  • TaskflowPermissionTestBase base test class (#1718)
  • Taskflow session timeout management (#1768)
  • TASKFLOW_IRODS_CONN_TIMEOUT Django setting (#1768)

Changed

• General

  • Upgrade to django-sodar-core v0.13.2 (#1617, #1720, #1775, #1792)
  • Upgrade to cubi-isa-templates v0.1.0 (#1757)
  • Upgrade to python-irodsclient v1.1.8 (#1538)
  • Upgrade Python dependencies (#1620)
  • Upgrade Vue app dependencies (#1620)
  • Upgrade to nodejs v18 (#1765, #1766)
  • Update deprecated Nodejs install method in Docker and dev (#1769)
  • Timeline event names and descriptions if called from syncmodifyapi (#1761)
  • Update tour help (#1583)
  • Enable setting ADMINS via environment variable (#1796)
  • Update ADMINS default value (#1796)

• Irodsadmin

  • Output irodsorphans results during execution (#1319)
  • Order irodsorphans results by project (#1741)

• Landingzones

  • Move iRODS object helpers to TaskflowTestMixin (#1699)
  • Enable superuser landing zone controls for locked zones (#1607)
  • Add DELETING to locked states in UI (#1657)
  • Query for landing zone status in batch (#1684, #1752)
  • Create expected collections if zone sync is called from syncmodifyapi (#1761)
  • Define and use zone status constants (#1398)

• Samplesheets

  • Sample sheet table viewport background color (#1692)
  • Contract sheet table height to fit content (#1693)
  • Hide internal fields from ISA-Tab templates (#1698, #1733)
  • Refactor IrodsDataRequest model and tests (#1706)
  • Update get_sheets_url() helper to only handle Project objects (#1771)
  • Display full path under assay for iRODS data requests in UI (#1749)
  • Return full path under assay from IrodsDataRequest.get_short_path() (#1749)
  • Make request optional in SheetVersionMixin.save_version()

• Taskflowbackend

  • Move iRODS object helpers from LandingZoneTaskflowMixin (#1699)
  • Move iRODS test cleanup to TaskflowTestMixin.clear_irods_test_data() (#1722)
  • Refactor base test classes (#1722)

Fixed

• General

  • Local Chromedriver install failure (#1753, bihealth/sodar-core#1255)

• Ontologyaccess

  • Batch import tests failing from forbidden obolibrary access (#1694)

• Samplesheets

  • perform_project_sync() crash with no iRODS collections created (#1687)
  • iRODS delete request modification UI view permission checks failing for non-creator contributors (#1737)
  • Investigation object ref broken in timeline sheet_replace events (#1774)
  • External links column width estimation crash in table rendering (#1787)
  • Comment field editing with semicolon in data (#1790)
  • Ontology URLs not encoded if passed as query string in wrapper template (#1762)

Removed

• Landingzones

  • Unused data_tables references from templates (#1710)
  • get_zone_samples_url() template tag (#1748)

• Samplesheets

  • SHEETS_TABLE_HEIGHT Django setting (#1283)
  • Duplicate IrodsAccessTicketMixin from test_views_ajax (#1703)
  • IRODS_DATA_REQUEST_STATUS_CHOICES constant (#1706)
  • HIDDEN_SHEET_TEMPLATE_FIELDS constant (#1733)
  • sheet_export* timeline events (#1773)
  • SHEETS_ENABLED_TEMPLATES Django setting (#1756)
  • tumor_normal_triplets ISA-Tab template (#1757)

v0.13.4 (2023-05-15)

Changed

• Samplesheets

  • Update ISA-Tab template dependency to cubi-isa-templates (#1667)
  • Allow assay tables with no materials after sample (#1676)

Fixed

• General

  • django-autocomplete-light Docker build crash with whitenoise (#1666)
  • Chrome install script issues (#1677)

• Samplesheets

  • Multi-file upload not working (#1670)
  • Template create form allowing multiple ISA-Tabs per project (#1672)

v0.13.3 (2023-05-10)

Added

• Samplesheets

  • ProjectIrodsFileListAPIView in REST API (#1619)
  • SIMPLE_LINK_TEMPLATE helper for simple link creation

Changed

• General

  • Upgrade to Django v3.2.19 (#1646, #1652)
  • Upgrade Vue app dependencies (#1646)
  • Update URL patterns to use path (#1631)

• Samplesheets

  • Refactor meta_ms to remove SPECIAL_FILE_LINK_HEADERS use (#1641)
  • Display study and assay plugin icons to contributors and above (#1354)

Fixed

• Samplesheets

  • Crash from ClearableFileInput with Django v3.2.19+ (#1652)

Removed

• General

  • Unused sodar.users views and URLs (#1663)

• Samplesheets

  • SPECIAL_FILE_LINK_HEADERS hack (#817, #1641)

v0.13.2 (2023-04-18)

Changed

• General

  • Upgrade Python dependencies (#1620)
  • Minor manual updates (#1622)

• Irodsbackend

  • Refactor IrodsAPI._sanitize_coll_path() into sanitize_path() (#1632)
  • Handle unwanted parent strings in iRODS paths (#1632)

• Samplesheets

  • Refactor iRODS access ticket tests

Fixed

• Landingzones

  • Zone list content with user access disabled not displayed for superuser (#1623)
  • Incorrect "saving version failed" message in sheet_edit_finish (#1628)

• Samplesheets

  • Cell width estimation for simple links and contact columns (#1621)

Removed

• Landingzones

  • Unused ProjectZoneView context items (#1624)

v0.13.1 (2023-03-31)

Added

• General

  • API examples in manual (#1600)

• Landingzone

  • Save zone creation metadata as timeline event extra data (#1609)
  • Allow disabling landing zone operations from non-superusers (#1616)
  • LANDINGZONES_DISABLE_FOR_USERS setting (#1616)

Changed

• General

  • Upgrade critical Python dependencies (#1604)

• Landingzones

  • Enable zone deletion if zone root collection is not found (#1606)

• Samplesheets

  • Upgrade Vue app dependencies (#1597, #1604)
  • Enable sheet deletion with data for delegates (#1605)

Fixed

• Samplesheets

  • Sheet version export crash with certain old projects (#1596)
  • Cancer app get_shortcut_column() crash if library name not in cache (#1599)
  • Assay plugin override ignored in _update_cache_rows() (#1603, #1610)
  • Inherited owners unable to delete sheets with data (#1605)

v0.13.0 (2023-02-08)

Added

• Irodsbackend

  • Create iRODS user accounts at login for users with LDAP/SODAR auth (#1315, #1587)

• Landingzones

  • Optional zone write access restriction to created collections (#1050, #1540)
  • Project archiving support (#1573)
  • UI warning for user without access for zone updating (#1581)

• Samplesheets

  • Mac keyboard shortcut support for multi-cell copying (#1531)
  • Study render table caching (#1509)
  • syncstudytables management command (#1509)
  • get_last_material_index() helper (#1554)
  • get_latest_file_path() helper (#1554)
  • "Not found" element for iRODS modal filter (#1562)
  • Existing iRODS file check in material name editing (#1494)
  • Omit IGV session files by file name suffix (#1575, #1577)
  • SHEETS_IGV_OMIT_BAM and SHEETS_IGV_OMIT_VCF Django settings (#1575, #1595)
  • get_igv_omit_override() and check_igv_file_name() in study app utils (#1575, #1577)
  • Project archiving support (#1572)
  • igv_omit_bam, igv_omit_vcf and igv_genome project settings (#1478, #1577)
  • Project-wide genome selecting for IGV session generation (#1478)

Changed

• General

  • Upgrade to django-sodar-core v0.12.0 (#1567, #1576)
  • Use default Gunicorn worker class in production (#1536)
  • Upgrade to fastobo v0.12.2 (#1561)
  • Update .coveragerc (#1582)
  • Upgrade checkout and setup-python GitHub actions (#1591)

• Irodsbackend

  • Update backend iRODS connection handling (#909, #1542, #1545)
  • Rename IrodsAPI.get_child_colls()

• Landingzones

  • Refactor permissions (#1573)

• Samplesheets

  • Upgrade critical Vue app dependencies (#1527, #1571)
  • Remove redundant node UUIDs from render tables (#708)
  • Improve IGV session file XML generating (#1585)
  • Do not create sheet_edit_start timeline events (#1570)
  • Use role ranking in EditConfigMixin (#1589)

• Taskflowbackend

  • Remove legacy landing_zone_create build error handling (#1530)

Fixed

• General

  • Missing LDAP_ALT_DOMAINS Django setting (#1594)

• Irodsbackend

  • Unhandled backend init exception in IrodsStatisticsAjaxView (#1539)
  • iRODS session disconnection issues (#909, #1542)
  • Ajax view access for inherited owners (#1566)

• Landingzones

  • Typo in LANDINGZONES_TRIGGER_MOVE_INTERVAL (#1541)

• Samplesheets

  • Crash from incompatibility with packaging==0.22 (#1550)
  • Cancer shortcuts expecting specific naming convention (#1554, #1563)
  • Cancer shortcut caching with identical library names in study (#1560, #1564)
  • iRODS modal filter input not cleared on modal re-open (#1555)
  • Column config editing access for inherited owners (#1568)
  • iRODS delete request accept view crash with collection request (#1584)
  • Germline study shortcuts enabled if sample not found in assay (#1579)

Removed

• Irodsbackend

  • Backend API conn argument (#909)
  • IrodsAPI.collection_exists() helper (#1546)
  • IrodsAPI.get_coll_by_path() helper

• Landingzones

  • Legacy LandingZoneOldListAPIView (#1580)

• Samplesheets

  • Unused config_set and num_col header parameters (#1551)
  • get_sample_libraries() helper (#1554)
  • get_study_libraries() helper (#1554)
  • GenericMaterial.get_samples() (#1557)

v0.12.1 (2022-11-09)

Added

• Landingzones

  • LANDINGZONES_TRIGGER_ENABLE Django setting (#1508)

Changed

• General

  • Upgrade to Django v3.2.16+ (#1515)
  • Move include examples to include_examples (#1493)

• Samplesheets

  • Upgrade Vue app dependencies (#1518)
  • Improve study app logging (#1507)
  • Optimize germline study app get_shortcut_column() (#1519)
  • Add study app tests (#1523)
  • Optimize germline study app cache updating (#1506)
  • Improve default IGV BAM track colour (#1514)

• Taskflowbackend

  • Improve project lock error messages (#1496, #1500, #1511)

Fixed

• General

  • Invalid REDIS_URL default value (#1497)
  • Invalid modify API settings in production config (#1503)

• Landingzones

  • Missing zone status check in ZoneMoveView (#1520)

• Samplesheets

  • Uncaught project lock exceptions in iRODS delete request accepting (#1495)
  • Missing CSS classes for failed iRODS delete requests (#1513)
  • User alerts/emails sent for own iRODS delete requests (#1502)

• Taskflowbackend

  • Unhandled project lock exceptions (#1496, #1500, #1511)
  • Landing zone status not updated on flow lock/build errors (#1498)
  • Role deletion failing for categories (#1521)

Removed

• Samplesheets

  • .gitkeep for config directory (#1493)

v0.12.0 (2022-10-14)

Added

• General

  • Coverage reporting with Coveralls (#1471)
  • _login_extend.html example (#1462)
  • Overview video link in docs and README (#1452)
  • Sentry JS include for production (#1393)

• Irodsbackend

  • get_zone_path() helper (#1399)
  • get_user_group_name() helper (#1397)
  • get_ticket() method

• Landingzones

  • LandingZone.can_display_files() helper (#1401)

• Samplesheets

  • Statistics badge in iRODS dir modal (#1434)
  • External links column hyperlink support (#1475, #1476)
  • SHEETS_EXTERNAL_LINK_PATH Django setting (#1477)
  • get_ext_link_labels() helper (#1477)
  • samplesheets/config directory for config files (#1477)

• Taskflowbackend

  • Add app from SODAR Core (#691)
  • Add Taskflow functionality from SODAR Taskflow (#691, #1464)

Changed

• General

  • Refactor Taskflow functionality for integrated code (#691, #1397, #1466, #1469, #1480)
  • Use general REDIS_URL Django setting (#1396)
  • Replace get_taskflow_sync_data() methods with modify API calls (#1397)
  • Upgrade to django-sodar-core v0.11.0 (#1459)
  • Upgrade general Python dependencies (#1453)
  • Upgrade minimum PostgreSQL version to v11 (bihealth/sodar-core#303)
  • Enable all tests in GitHub Actions CI (#1168)
  • Replace hardcoded include templates with examples (#1462)

• Irodsbackend

  • Disable iRODS environment debug logging (#1455)

• Landingzones

  • Move Celery tasks into tasks_celery (#1400)

• Samplesheets

  • Move Celery tasks into tasks_celery (#1400)
  • Ignore whitespace in simple link regex (#1474)
  • Read external link labels from JSON file (#1477)
  • Do not provide external_link_labels to UI without investigation

Fixed

• General

  • Docker build tagging failing for release tags (#1451)
  • URL config entrypoint for nonexistent about.html (#1481)
  • Postgres role errors in CI (#1465)

• Landingzones

  • iRODS file status displayed for zones with unsuitable status (#1401)

• Samplesheets

  • iRODS delete request error messages not updated in modal (#1463)
  • Ticket created for new iRODS collections with disabled anon access (#1479)

Removed

• General

  • get_taskflow_sync_data() methods (#1397)
  • GitLab CI support (#1168)
  • test_local settings file (#1395)
  • Codacy support (#1471)
  • Legacy docs URL in urls.py (#1489)

• Samplesheets

  • Taskflow API views (#691, #1397)
  • BIH specific hardcoded external link labels (#1477)
  • SHEETS_EXTERNAL_LINK_LABELS Django setting (#1477)

v0.11.3 (2022-07-20)

Added

• General

  • GitHub issue templates (#1441)
  • Contributing and code of conduct docs (#1426)

• Samplesheets

  • Enable bulk_rnaseq ISA-Tab template (#1430)
  • Enable microarray ISA-Tab template (#1430)
  • Enable single_cell_rnaseq ISA-Tab template (#1430)
  • Enable tumor_normal_triplets ISA-Tab template (#1430)

Changed

• General

  • Upgrade to django-sodar-core v0.10.13 (#1391, #1406, #1418)
  • Upgrade to black v22.3.0 (bihealth/sodar-core#972)
  • Default BASICAUTH_REALM message (#1410)
  • Add LocalAuthAPIView URL to SECURE_REDIRECT_EXEMPT (#1411)
  • Rename default iRODS zone into sodarZone (#1417)
  • Manual updates (#1386, #1387, #1408)
  • Combine development documentation into manual (#1345)
  • Update README badges for recreated GitHub repository (#1428)
  • Update .pylintrc (#1429)
  • General code cleanup (#1429)
  • Upgrade cubi-tk (#1430)
  • Upgrade to python-irodsclient v1.1.3 (#1431)
  • Update env.example for sodar-docker-compose dev environment
  • Upgrade to Node v16 (#1432, #1448)
  • Upgrade to lxml v4.9.1 (#1450)

• Samplesheets

  • Update Vue app browserslist (#1424)
  • Upgrade Vue app to ag-grid v28 (#1447)
  • Upgrade general Vue app dependencies (#1330, #1448)
  • Hide sheet template fields not meant to be edited (#1443)

Fixed

• General

  • build-docker.sh failing with special characters in tag name (#1385)

• Irodsinfo

  • Info page title (#1416)
  • Manual link pointing to expired URL (#1442)

• Ontologyaccess

  • Redundant file info in import logging (#1436)

• Samplesheets

  • Unset study protocol export ordering (#1419)
  • Bootstrap tooltip issues in sheet tables (#1415)
  • cubi-tk install failure due to missing libbz2-dev (#1425)
  • OntologyEditModal warning message for missing ontologies (#1444)
  • OntologyEditModal search input not trimmed (#1446)
  • Sheet table horizontal scrolling on Firefox (#1445)

Removed

• General

  • Login page user domain autofill (#1409)
  • Custom login template (#1409)
  • Separate development documentation (#1345)

v0.11.2 (2022-03-04)

Added

• General

  • .readthedocs.yaml file (#1362)

• Samplesheets

  • Investigation.get_assays() helper (#1359)
  • View tests for search (#556)

Changed

• General

  • Upgrade to django-sodar-core v0.10.10 (#1361, #1376)
  • Link manual to readthedocs.io (#1358)
  • Upgrade to python-irodsclient v1.1.2 (#1389)

• Landingzones

  • Make description optional in _make_landing_zone() (#1360)

• Samplesheets

  • Allow replacing sheets if unfinished landing zones exist (#1356)
  • Update project list file column legend (#1366)
  • Upgrade Vue app dependencies (#1369)
  • Upgrade Vue app to ag-grid v27 (#1370)
  • Improve search results layout (#1373)

Fixed

• General

  • Invalid Python version in readthedocs build (#1362)

• Landingzones

  • Zone list title column layout issues (#1380)

• Samplesheets

  • LandingZone objects deleted by API sheet replacing (#1356)
  • Invalid Investigation timeline object reference for sheet replacing (#1357)
  • IrodsStatsBadge query error handling (#1371)
  • Keyword type:file not limiting search (#1374)
  • Redundant iRODS connections in search result rendering (#1375)
  • Tooltip hide not working in ontology column config (#1379)

Removed

• General

  • Local manual build (#1358)

• Landingzones

  • Unused sodar-popup-overlay elements from project_zones.html (#1363)

v0.11.1 (2022-02-04)

Added

• Irodsbackend

  • format_env() helper for iRODS environments (#1351)

• Irodsinfo

  • Use IRODS_HOST_FQDN for client environment and display (#1349)

• Samplesheets

  • Toggle WebDAV IGV proxy with IRODS_WEBDAV_IGV_PROXY (#1324)

Changed

• General

  • Upgrade minimum Python version to v3.8, add v3.10 support (bihealth/sodar-core#885)
  • Upgrade to django-sodar-core v0.10.8 (#1337)
  • Upgrade Python dependencies (#673, #1337, #1348, bihealth/sodar-core#884, bihealth/sodar-core#901, bihealth/sodar-core#902)
  • Upgrade to Chromedriver v97 (bihealth/sodar-core#905)

• Samplesheets

  • Upgrade Vue app dependencies (#1330)

Fixed

• General

  • Manual building in readthedocs (#1343)

• Irodsinfo

  • Invalid value formats in iRODS environment generation (#1351)

• Ontologyaccess

  • Opening OWL data for parsing not working for specific URLs (#1352)

v0.11.0 (2021-12-16)

Added

• General

  • Siteinfo app in default LOGGING_APPS value (#1219)
  • LOGGING_LEVEL setting (bihealth/sodar-core#822)
  • PROJECTROLES_EMAIL_HEADER and PROJECTROLES_EMAIL_FOOTER settings (#1231)
  • Codacy coverage reporting (#1169)

• Irodsbackend

  • colls parameter in list retrieval (#1156)
  • IRODS_ENV_DEFAULT setting (#1260)
  • LocalAuthAPIView REST API view and IRODS_SODAR_AUTH setting (#1263)

• Landingzones

  • busyzones management command (#1212, #1314)
  • App alerts for sheet cache updates (#1000)
  • App alerts for zone owner for zone actions (#1204, #1240)
  • member_notify_move app setting (#1203)
  • Project member notifications from zone moving (#1203, #1232)
  • LandingZone.user_message field (#1203)
  • finished parameter for LandingZoneListAPIView (#1234)
  • LandingZone.is_locked() helper (#321)
  • Zone locked status in UI and LandingZoneRetrieveAPIView (#321)
  • Display collections in iRODS file list (#1156)
  • UI documentation in user manual (#1181)

• Ontologyaccess

  • App documentation in user manual (#1301)

• Samplesheets

  • Simple link support for string cell rendering (#1001)
  • generic_raw assay plugin (#1128)
  • Overriding assay plugin via assay comment (#1128)
  • App alerts for sheet cache updates (#1000, #1265)
  • Tooltip to clarify the Finish Editing button (#1109)
  • Tooltips for buttons disabled due to an unsaved row (#1056)
  • Default ontology column value (#1061)
  • Confirmation for field value overwrite on node rename (#1060)
  • Sheet version description (#754)
  • Batch sheet version deletion (#773)
  • Assay app support for "transcriptome profiling" measurement type (#1255)
  • Saving version with description in editor UI (#1109)
  • Automatic study/assay table filtering from search results (#634)
  • UI documentation in user manual (#1180)

Changed

• General

  • Upgrade to django-sodar-core v0.10.7 (#1217, #1220, #1243, #1272, #1332)
  • Upgrade to python-irodsclient v1.0.0 (#1223)
  • Upgrade to Chromedriver v96 (bihealth/sodar-core#772, #1254, bihealth/sodar-core#847, bihealth/sodar-core#852)
  • Upgrade to Node v12
  • Improve production logging (#1257)
  • Upgrade to django-webpack-loader v1.4.1 (#1198)
  • Upgrade to redis v3.5.3 (#1297)
  • Use ManagementCommandLogger for command output (#1276)
  • Update user manual (#1304, #1318)
  • Replace deprecated MAINTAINER label in Dockerfile (#1316)
  • Enable setting SECURE_REDIRECT_EXEMPT in env vars (#1331)

• Irodsbackend

  • Retrieve iRODS config from IRODS_ENV_BACKEND setting (#1221)
  • Use data attributes in templates (bihealth/sodar-core#530)
  • Rename data_objects to irods_data in return data (#1156)
  • Get default iRODS environment values from default env (#1260)

• Irodsinfo

  • Retrieve iRODS config from IRODS_ENV_CLIENT setting (#1221)
  • Display IRODS_ENV_CLIENT in siteinfo via info_settings
  • Get default iRODS environment values from default env (#1260)

• Landingzones

  • Do not load finished landing zones in zone list view (#1205)
  • Rename STATUS_ALLOW_CLEAR to STATUS_FINISHED (#1205)
  • UI improvements in project zone list (#1235)
  • Hide zones with NOT CREATED status from detail card (#1236)
  • Handle NOT CREATED landing zone status (#1237)
  • Use CurrentUserFormMixin in forms (#660)
  • Enable automated collection generation by default in UI (#1266)
  • Clarify collection creation message in UI (#1275)
  • Default status info for MOVING (#1305)
  • Do not count inactive zones in project list (#1306)

• Samplesheets

  • Move TestSheetSyncBase into test_views_taskflow
  • Update app setting labels (#1230)
  • Use CurrentUserFormMixin in forms (#660)
  • Rename get_name() and get_full_name() in ISATab model (#1247)
  • Update sheet version list layout (#1246)
  • Replace version compare menu with operation dropdown entry (#1251)
  • Update subpage navigation (#1252)
  • General refactoring (#1248, #1250, #1253)
  • Move Ajax view version saving to SheetVersionMixin (#1109)
  • Use AppSettingAPI.delete_setting() for display config deletion (#854)
  • Make UI specific data optional in build_study_tables() (#694)
  • Do not require user for sheet_sync_task (#1273)
  • Hide navigation dropdown if no sheets are available (#1285)
  • Reverse import/create order in Sheet Operations dropdown (#1286)
  • Improve ontology editor layout (#1293)
  • Improve study and assay title layout (#1291)
  • Improve iRODS access ticket list layout (#1302)
  • Remote sheet sync refactoring (#1317, #1325, #1326)
  • Upgrade Vue app dependencies (#1328, #1329)

Fixed

• General

  • API version settings not updated (#1218)
  • Disable cache as workaround for Docker build issues (#1225)
  • Github Actions CI failure by old package version (bihealth/sodar-core#821)
  • Build warning in docs_dev (#1182)

• Irodsadmin

  • Missing cleanup in command test tearDown() (#1244)

• Irodsbackend

  • Redundant slash prefix for root level items in collection list (#1245)
  • IRODS_ENV_BACKEND value conversion issues (#1259)
  • Unavailable iRODS connection not handled in BaseIrodsAjaxView (#1322)

• Landingzones

  • PROJECTROLES_SEND_EMAIL not checked in Taskflow views (#1229)
  • Collection hint alert from zone list UI (#1266)
  • Zone move failure on Celery task crash in TaskflowZoneStatusSetAPIView (#1298)
  • status_info overflow crash in TaskflowZoneStatusSetAPIView (#1307)
  • Uncaught exceptions in inactivezones (#1311)

• Ontologyaccess

  • Minor layout issues (#1312)

• Samplesheets

  • Missing label for public_access_ticket app setting (#1230)
  • Incorrect ISATab timestamp in export and compare dropdown (#1247)
  • Unhandled backend exceptions in update_project_cache_task() (#1265)
  • Vue app study navigation failure with additional URL params (#1269)
  • Assay shortcut card extra link icons (#1271)
  • Source map errors in production (#1198)
  • Numeric column default value invalid if range is unset (#1281)
  • ColumnToggleModal errors on entering/exiting edit mode (#1280)
  • Editability not updated in ColumnToggleModal without grid reload (#1279)
  • First column width breaking in Parser Warnings table (#1287)
  • Template creation link visible in sheet replace form (#1288)
  • Default suffix icon in ColumnConfigModal (#1290)
  • Ontology editor edit/check button icon misalignment (#1292)
  • iRODS file list modal button column alignment (#1299)
  • Random crash in StudyShortcutsRenderer unit tests (#1294)
  • Sheet import and create view access permitted with sheet sync enabled (#1309)
  • Project list sheet import link visible with sheet sync enabled (#1309)
  • No placeholder for missing investigation title in details card (#1313)

Removed

• General

  • ADMIN_URL setting from production.py (#1228)

• Irodsbackend

  • IRODS_ENV_PATH setting (#1221)

• Irodsinfo

  • IRODSINFO_ENV_PATH setting (#1221)
  • IRODSINFO_SSL_VERIFY setting (#1226)

• Landingzones

  • ZoneClearView UI view (#1205)
  • _list_buttons.html template (#1205)

• Samplesheets

  • SampleSheetVersionCompareForm (#1251)
  • Unused config argument from SampleSheetIO.save_isa()
  • Unused basic_val arg from _add_cell() (#1262)

v0.10.1 (2021-07-07)

Added

• General

  • LABEL and MAINTAINER in Dockerfile (#1186)
  • Manual building in Docker setup (#1195)
  • SAML configuration (#990)
  • LOGGING_APPS and LOGGING_FILE_PATH Django settings (#1209)

Changed

• General

  • Upgrade to django-sodar-core v0.10.3 (#1201)
  • Allow modifying all relevant SODAR Django settings from env

• Samplesheets

  • Upgrade vue app dependencies (#1185)
  • Refactor vue app code and tests for new dependencies (#1185)
  • Preserve line breaks in parser warnings (#1188)
  • Move DEFAULT_EXTERNAL_LINK_LABELS to constants

Fixed

• General

  • Docker entry points for Celery and Celerybeat (#1193)
  • Docker image build issues (#1194)
  • Missing migrations for JSONField and site (#1196)
  • irodsadmin debug logging disabled (#1209)
  • Manual layout broken by docutils>=0.17 (#1210)

• Samplesheets

  • Loading icon in vue app iRODS status badge (#1192)
  • Workaround for Webpack source map file crash (#1198)

v0.10.0 (2021-06-11)

Added

• General

  • Release notes and changelog sections in manual (#1098)
  • setup_database.sh from SODAR Core
  • Enable appalerts app (#1124)
  • Display relevant Django settings values in siteinfo app (#1123)
  • taskflowbackend in site logging (#1137)
  • New Docker setup (#1129, #1163, #1165)
  • GitHub Actions CI (#1033)
  • iRODS study and assay data linking documentation in manual (#1127)

• Irodsbackend

  • Support for IRODS_ROOT_PATH setting (#1067)
  • get_root_path() and get_projects_path() helpers (#1067)
  • Optional user_name and user_pass in IrodsAPI init kwargs (#1139)
  • Public guest access support for Ajax queries (#1140, #1144)

• Landingzones

  • Optional automated creation of expected zone collections (#391)
  • _assert_zone_coll() helper in LandingZoneTaskflowMixin

• Samplesheets

  • Warning for unrecognized assay plugin in sample sheet import (#1070)
  • Sheet creation from templates using cubi-tk (#1068)
  • clean_sheet_dir_name() helper
  • iRODS delete requests for data objects and collections (#277, #1087, #1089, #1090, #1093, #1134)
  • Allow per-project restriction of column config updates (#995)
  • Diff comparison for sheet versions (#1007, #1110, #1117)
  • Enable remote sync for sample sheets (#959, #1102, #1103)
  • Icon component in vue app for django-iconify icon access (#1113)
  • App alerts for iRODS data request actions (#1084)
  • Public guest access support for sample data (#1100)
  • get_webdav_url() helper (#1100)
  • view_versions permission (#1138)
  • Management command tests (#1170)

Changed

• General

  • Upgrade to django-sodar-core v0.10.2 (#1096, #1113, #1118, #1121, #1135, #1158, #1166)
  • Upgrade to Python v3.8 and Django v3.2 (#1113)
  • Update project icons (#1113, #1125, #1154)
  • Unify ISA-Tab naming (#1082)
  • Upgrade to Chromedriver v90 (bihealth/sodar-core#731)
  • Upgrade to altamISA v0.2.9 (#1099, #1106)
  • Upgrade versioneer
  • Upgrade general python dependencies (#1112)
  • Update taskflow actions for SODAR Taskflow v0.5 compatibility
  • Cleanup for public GitHub release (#1119)

• Irodsbackend

  • Split long queries in get_objs_recursively() (#1132)
  • Refactor Ajax views (#841)
  • Require project and user args for get_webdav_url() template tag (#1144)

• Irodsinfo

  • Move iRODS connecting guide into the user manual (#262)

• Samplesheets

  • Fail gracefully for ISAtab import with empty tables (#903, #1075)
  • Implement study/assay app retrieval in model get_plugin() helpers (#1076)
  • Change timeline event names for sheet import/create/replace (#1079)
  • Refactor and simplify view pagination settings
  • Provide sodar context alert data as HTML instead of string (#1089)
  • Unify iRODS URL patterns (#1086)
  • Duplicate sodar_uuid views in REST API nested lists (#1074)
  • Unify subpage navigation (#1085)
  • Reorder critical warning check and render test in sheet import (#1107)
  • Upgrade Vue app dependencies (#1114)
  • Rename IrodsCollsCreateView
  • Enable public guest access to project sheets view (#1141)
  • Enable sheet export for project guests (#1138)
  • Enable sheet version viewing and export for project guests (#1138)
  • Allow no user in update_project_cache_task() (#1171)
  • Use logging in syncnames (#1170)

Fixed

• General

  • Production config requirement in docs_manual

• Irodsadmin

  • Irodsorphans project UUID not returned if path ends in project UUID (#1071)

• Irodsbackend

  • Long queries raising CAT_SQL_ERR in iRODS (#1132)
  • Redundant iRODS connection opened by _check_collection_perm() (#1142)
  • Missing permission check in IrodsStatisticsAjaxView POST request (#1143)

• Irodsinfo

  • Server status card layout on low resolutions (#1176)

• Landingzones

  • Root level backend plugin retrieval in template tags
  • CSS in project zone list (#1027)
  • Uncaught irodsbackend exceptions in TriggerZoneMoveTask (#1148)
  • Project list column retrieval failing with anonymous user (#1155)
  • Inactive zones deleted from all projects on zone clear (#1150)

• Samplesheets

  • MaxQuant results not correctly linked in pep_ms assay app (#1072)
  • Incorrect timeline event for sheet_create (#1080)
  • Assay shortcut card layout breaking on Chrome (#1094)
  • Node names not properly sanitized on sheet import (#798)
  • Root level backend plugin retrieval in template tags

Removed

• General

  • Legacy raven dependency (#1147)
  • References to unused django-db-file-storage component (#1153)
  • Legacy Docker setup (#1129)
  • syncgroups user command, updated version found in projectroles (#1172)
  • Unused sodar.users.utils (#1172)
  • Unused .travis.yml
  • backports.lzma dependency (#1197)

• Irodsbackend

  • Support for Ajax queries without project
  • Unused template tags get_webdav_url_anon() and get_webdav_user_anon()
  • is_webdav_enabled() template tag, use get_django_setting() instead

• Samplesheets

  • find_study_plugin() helper, use Study.get_plugin() instead (#1076)
  • find_assay_plugin() helper, use Assay.get_plugin() instead (#1076)

v0.9.0 (2021-02-05)

Added

• General

  • Missing user model migration
  • Makefile for selected management commands (#989)

• Irodsadmin

  • Add app for iRODS data administration (#972)
  • irodsorphans management command (#972, #997, #1035, #1045)

• Irodsbackend

  • get_query() helper for SpecificQuery initialization (#1003)
  • Support for multi-term search (#1065)

• Landingzones

  • Zone UUID clipboard copying link (#970)
  • inactivezones management command (#1010, #1046)

• Ontologyaccess

  • Add site app for ontology storage and access (#937, #947)
  • importobo and importomim management commands (#937, #980)
  • ontologyaccess_backend backend plugin (#958)

• Samplesheets

  • microarray assay app (#941)
  • _update_cache_rows() helper for assay app plugins (#954)
  • NodeMixin for node field/header helpers (#922)
  • Ontology term editing (#688, #699)
  • Extract label editing as string (#964)
  • Simple editing for external links columns (#976)
  • SampleDataFileExistsAPIView for querying file status by checksum (#1003)
  • Track hub and iRODS ticket support for UCSC Genome Browser integration (#238)
  • Django setting SHEETS_ONTOLOGY_URL_SKIP for template skip patterns (#1022)
  • Support for multi-term search (#1065)

Changed

• General

  • Upgrade to altamISA v0.2.7
  • Upgrade to Bootstrap v4.5.3 and jQuery v3.5.1 (#1011)
  • Upgrade to Chromedriver v87
  • Upgrade to python-irodsclient v0.8.6 (#1009, #1058)
  • Upgrade to django-sodar-core v0.9.0 (#1051)
  • Refactor Project.get_full_title() usage (#1062)
  • Update iRODS install instructions in docs_dev (#1028)

• Irodsbackend

  • Standardize Ajax view output (#841)
  • Support name_like as a list in get_objs_recursively() (#1065)

• Irodsinfo

  • Update iCommands instructions (#1028)

• Samplesheets

  • Display assay plugin icon for all users with sheet edit permissions (#940)
  • Refactor assay row cache updating (#954)
  • Refactor ontology value rendering (#693)
  • Move ATTR_HEADER_MAP to models
  • Refactor recognizing ontology/unit columns in rendering (#962)
  • Disable "Finish Editing" link with unsaved rows (#987)
  • General vue app refactoring (#747)
  • Prevent insertion of identical rows (#1023)
  • Move iRODS content setup for ajax views to plugins.get_irods_content()
  • Rename Ajax views and standardize output (#857, #858)
  • Change default value of allow_editing to True (#1069)

Fixed

• General

  • Missing raven dependency in production config (#1048)

• Samplesheets

  • Assay iRODS links enabled if null path is returned by assay app (#951)
  • Empty ontology/unit column type not recognized in rendering (#962)
  • Legacy field header type still in use
  • Row insert failing if the last node is a process (#974, #975)
  • Row insert failing with single column source node (#965, #986)
  • Sample deleted from study not removed from assay sample selection (#988)
  • Default value in column config not validated against range (#1031)
  • Editor input not correctly trimmed (#1032)
  • Icon updating on row deletion cancel (#1012)
  • Ontology URL template forced on incompatible accession URLs (#1022)
  • Redundant iRODS queries for empty paths in _update_cache_rows() (#957)
  • Saving multi-column node for a new row using default suffix (#1040)
  • UNIT column type override if empty unit given in config (#1052)
  • Column config copy/paste enabled for contact, date and external links (#1053)
  • Incompatible format not handle in column config paste (#1029)

Removed

• General

  • Management commands replaced by Makefile (#989)

• Irodsbackend

  • _get_obj_list() and _get_obj_stats() helpers (#1066)

• Samplesheets

  • Workarounds for legacy sample sheet imports (#946)

v0.8.0 (2020-09-15)

Added

• General

  • Celery beat setup (#702)
  • Configuration of support contact info in footer via site settings (#863)

• Landingzones

  • Automated triggering of landing zone validation/moving by iRODS file (#702)

• Samplesheets

  • ISAtab export through the REST API via SampleSheetISAExportAPIView (#849, #851)
  • Sample sheet column display configuration saving (#539)
  • Material and process renaming (#852)
  • Study and assay iRODS paths in InvestigationRetrieveAPIView (#895)
  • Protocol selection (#871)
  • Editing of performer, perform date and contacts (#881)
  • Editing of non-ontology list values (#886)
  • Display name_type for processes
  • Set default protocol automatically in edit config (#879)
  • Row insertion (#834)
  • Row deletion (#868)
  • Sheet config versioning (#904)
  • Automated rebuilding of expired sheet configs (#904)
  • Node name suffix config and automated filling (#912, #925)
  • get_node_obj() helper (#922)
  • Update sheet config default protocols on sheet restore (#901)
  • Export unarchiving notification for Windows users (#894)

Changed

• General

  • Upgrade to django-sodar-core v0.8.3-WIP
  • Move ISAtab export functionality to SampleSheetISAExportMixin (#849)
  • Upgrade to Chromedriver v85 (bihealth/sodar-core#569)

• Irodsbackend

  • Improve connection error logging

• Irodsinfo

  • Improve iRODS server/backend status (#908, #909)

• Landingzones

  • Refactor zone modification mixins in landingzones.views

• Samplesheets

  • Re-initialize Vue app with Vue-CLI v4 (#837)
  • Partial refactoring and cleanup of Vue app code (#537, #837)
  • Always store original header name in table rendering
  • Allow column config editing with edit_sheet permission (#880)
  • Allow empty DATA material names in editing (#898)
  • Refactor helpers in SampleSheetTableBuilder
  • Refactor sheet config helpers into SheetConfigAPI (#905)
  • Include top header in column width estimation for rendering (#649)
  • Use node header for recognizing unit enabled columns without data (#914)
  • Prevent simultaneous editing of cells in multiple tables (#765)
  • Preserve display configs on sheet replace if headers match (#906, #933)

Fixed

• General

  • Hardcoded plugin settings in production config (#910)

• Samplesheets

  • Row sorting not working with updated column type definitions (#847)
  • Lists of strings assigned ONTOLOGY column type in rendering (#885)
  • Last single column node not visible in ColumnToggleModal (#877)
  • Column config update randomly breaking table rendering (#850)
  • Whole cell copying active when in cell edit mode (#882)
  • File link CSS in edit mode (#896)
  • Data material name regex not accepting common file name characters (#875)
  • Incorrect padding for edit button in field header CSS (#862)
  • Prevent user for enabling unit for columns where it isn't supported (#889)
  • Keyboard event handling issues in DataCellEditor (#690, #917, #919)
  • Do not look for iRODS link columns in vue app if in edit mode (#866)
  • Contact column width estimation (#887)

Removed

• General

  • Unused Pillow dependency (bihealth/sodar-core#575)

v0.7.1 (2020-04-27)

Added

• Samplesheets

  • IrodsCollsCreateAPIView for iRODS collections creation via API (#826)
  • Host name input confirmation for sample sheet and data deletion (#833)
  • SampleSheetImportAPIView for ISAtab import via REST API (#802)
  • Study identifier display in Overview (#791)
  • Pagination in sheet version list (#743)

• Tokens

  • Enable app from django-sodar-core v0.8.0+ (#822)

Changed

• General

  • Upgrade to Django v1.11.29
  • Upgrade to django-sodar-core v0.8.1 (#835, #845)
  • Upgrade Python requirements to match djagno-sodar-core v0.8.0 (#835)
  • Upgrade to Chromedriver v80
  • Rename references to iRODS collections (#785)
  • Rename IRODS_SAMPLE_COLL and IRODS_LANDING_ZONE_COLL settings (#785)
  • Rename the samplesheets.create_colls permission (#785)
  • Use base Ajax API view classes from SODAR Core (#805)

• Landingzones

  • Disallow replacing sample sheets if active landing zones exist (#713)
  • Display moved and deleted zones of other users with view_zones_all perm (#806)
  • Return landing zone iRODS path on creation (#843)
  • Use SODARUserSerializer in LandingZoneSerializer (#842)

• Samplesheets

  • Upgrade non-breaking Vue app dependencies (#836)
  • Reorganize views and URL patterns (#801)
  • Refactor Ajax views and URL patterns (#736, #824)
  • Improve sheet import logging (#832)
  • Move ISAtab Zip archive validation to SampleSheetIO.get_zip_file()
  • Move ISAtab multi-file reading to SampleSheetIO.get_isa_from_files()
  • Refactor SampleSheetImportMixin to work with API views
  • Hide path from sheet configuration information (#779)
  • Improve notation for missing study shortcut file types (#799)
  • Temporarily disable Bootstrap tooltips in custom project list cells (#787)

Fixed

• Irodsbackend

  • Ajax view permission checking and status codes
  • Hardcoded time zone reference in api._get_datetime() (#807)

• Landingzones

  • REST API view permission checks not working with Knox token auth (#823)
  • Title suffix not optional in LandingZone serializer (#825)
  • Initial workaround for active landing zone deletion on sheet replace (#713)

• Samplesheets

  • REST API view permission checks not working with Knox token auth (#823)
  • Crashes caused by sheet config not correctly updated on sheet replace (#829)
  • Sample sheet version saved for unsuccessful replace (#838)
  • Editor select box padding for Firefox and Chrome (#726)
  • CSS issue with sodar-list-btn and Chrome (#844, bihealth/sodar-core#529)

Removed

• General

  • Unused django-db-file-storage requirement

• Samplesheets

  • Unused models.get_zone_dir() and io.get_assay_dirs() helpers
  • Base API view classes moved to SODAR Core (#800)
  • Unneeded SheetSubmitBaseAPIView base class

v0.7.0 (2020-02-12)

Added

• General

  • Support for local third party JS/CSS includes (#770)
  • Sentry support (#476)
  • ENABLE_IRODS Django setting (#796)

• Irodsbackend

  • Enforce MD5 hash scheme in client configuration (#740)
  • Enable conn keyword argument in API initialization (#793)

• Landingzones

  • Extra columns for project list (#579)
  • Missing permission and view tests
  • Initial REST API (#780)

• Samplesheets

  • Editing of selected sample sheet column values (#550)
  • Project settings for sample sheet configuration (#687)
  • manage_sheet permission (#696)
  • Column management UI for sample sheet configuring (#698)
  • get_name() helper in ISATab
  • Saved sample sheet version browsing and deletion (#662)
  • Sample sheet version export (#739)
  • Sample sheet version restoring (#701)
  • Save and restore sheet configuration with ISATab version
  • Deletion of ISATab versions on sheet delete (#746)
  • Extra columns for project list (#579)
  • MiscFiles assay shortcut for all assays (#766)
  • ResultsReports assay shortcut for all assays (#767)
  • Investigation info retrieval API view (#780)
  • utils.get_top_header() helper (#817)
  • Linking for metabolite assignment files in meta_ms assay app (#817)
  • Hack for "Report File" column file linking (#817)

Changed

• General

  • Upgrade to django-sodar-core v0.7.2
  • Upgrade to python-irodsclient v0.8.2 (#731)
  • Upgrade to altamISA v0.2.6
  • Upgrade to Chromedriver v79
  • Upgrade to Django v1.11.27
  • Enable logging propagation (#792)
  • Only log ERROR level messages if not in debug mode (#526)

• Irodsbackend

  • Refactor api.get_info()
  • Refactor iRODS connection handling in API (#793)

• Irodsinfo

  • Display iRODS server information when connection fails (#761)

• Landingzones

  • Prevent opening unnecessary iRODS connections with irodsbackend API (#796)
  • Reorganize views and URL patterns (#801)

• Samplesheets

  • Rename table_data member to tables in rendered table data (#219)
  • Move _get_isatab_files() and _fail_isa() into SampleSheetIOMixin
  • Refactor utils.get_index_by_header()
  • Replace v-clipboard package with vue-clipboard2 (#719)
  • Move UI notifications to NotifyBadge.vue (#718)
  • Refactor column data retrieval in ColumnToggleModal (#710)
  • Rename getGridOptions() to initGridOptions() (#721)
  • Dynamically add/omit cell unit, link and tooltip in rendering (#708)
  • Improve column type detection (#730)
  • Refactor sample sheet import/replace handling in views (#701)
  • Replace extra content table with standard assay shortcut table (#782)
  • Change assay sub-app get_extra_table() into get_shortcuts() (#782)
  • Change ExtraContentTable.vue into AssayShortcutCard.vue (#782)
  • Prevent opening unnecessary iRODS connections with irodsbackend API (#796)
  • Remove file suffix restriction from assay app data file linking (#817)

Fixed

• Irodsbackend

  • Cleanup skipped by uncaught exceptions in init_irods() (#723)
  • Data object replicates included in file and stats queries (#722)

• Landingzones

  • Cache update initiated synchronously in TaskflowZoneStatusSetAPIView (#783)
  • Missing zone status checks in zone deletion/moving views (#813)

• Samplesheets

  • getGridOptionsByUuid() returned column API instead of grid options (#706)
  • getGridOptionsByUuid() returned initial options without applied updates (#721)
  • Incorrect Investigation UUID passed to ISATab on replace (#742)
  • Restrictive tooltip boundary value in IrodsButtons.vue
  • Study UUID changed if modifying study identifier when replacing sheets (#789)

Removed

• General

  • Unused raven requirement (#476)

• Filesfolders

  • Remove app as files will be placed under MiscFiles in iRODS (#766)

• Irodsbackend

  • test_connection() helper (#795)

• Samplesheets

  • Unused study_row_limit setting (#641)
  • Support for SODAR v0.5.1 parsing of characteristics lists (#619)
  • Support for old style comments parsing (#631)
  • Redundant columnValues structure (#711)
  • link_file, num_col and align parameters from rendering (#708)
  • get_assay_list_url() template tag (#737)
  • Unused SourceIDQueryAPIView and related classes (#820)

v0.6.1 (2019-11-15)

Added

• Irodsbackend

  • Supply optional iRODS options in environment file (#714)
  • IRODS_ENV_PATH settings variable (#714)

• Irodsinfo

  • Supply optional iRODS options in environment file (#717)
  • IRODSINFO_ENV_PATH settings variable (#717)
  • Logging for environment generating and certificate loading

Changed

• Irodsbackend

  • Enable reading IRODS_CERT_PATH from environment variables
  • Improve connection logging
  • Refactor api.test_connection() (#715)

Fixed

• Landingzones

  • Misleading alert text in landingzone_confirm_move.html (#689)

• Samplesheets

  • Initial study context sorted by title instead of parsing order (#692)
  • Rendering crash from missing value type check for units (#697)

v0.6.0 (2019-10-21)

Added

• General

  • Missing Celery broker URL in env.example (#607)

• Samplesheets

  • ISAtab export (#95)
  • Model support and parsing for multiple missing ISAtab fields (#95, #581, #626)
  • extra_material_type field in GenericMaterial
  • archive_name field in Investigation
  • Temporary get_comment() and get_comments() helpers (#629, #631)
  • Timeline logging for import and export warnings (#639)
  • Timeline logging for failed ISAtab import (#642)
  • SHEETS_ALLOW_CRITICAL setting for handling critical import warnings (#573)
  • PacBio support in dna_sequencing assay app (#628)
  • Rendering for Assay Design REF columns (#652)
  • Rendering for First Dimension and Second Dimension columns (#652, #653)
  • Saving of original ISAtab data into the SODAR database (#651)
  • get_igv_irods_url() helper (#402)
  • IGV merge shortcuts in study links modal (#402)
  • ISAtab import from multiple uncompressed files (#593)
  • ISAtab export option for RemoteSheetGetAPIView (#670)
  • Support for Study and Assay in get_object_link()
  • Timeline logging for ISAtab and Excel export
  • Assay app meta_ms for metabolite profiling / mass spectrometry (#675)
  • Ability to define alerts in context API view (#681)
  • Alert for sheets parsed with an old altamISA version (#681)

Changed

• General

  • Upgrade site to django-sodar-core v0.7.0
  • Upgrade Python requirements to match django-sodar-core v0.7.0
  • Move graph creation dependencies to local_extra.txt (#609)
  • Move redis requirement to base.txt (#610)
  • Include backend Javascript and CSS as implemented in django-sodar-core v0.7.0 (#533)
  • Upgrade to Chromedriver v77

• Samplesheets

  • Color potentially dangerous links (bihealth/sodar-core#64)
  • Refactor sheet cell data access and sorting (#597)
  • Upgrade Vue.js app dependencies (#580)
  • Update ISAtab importing to support altamISA v0.2+ (#617)
  • Improve characteristics list parsing (#616, #618)
  • Always import material_type field for GenericMaterial
  • Do not replace title or description in Investigation if not provided
  • Display configuration in Overview as badge
  • Improve comments display in Overview (#632)
  • Refactor io module into a class (#562)
  • Suppress altamISA warnings during testing (#637)
  • Fail when encountering critical altamISA warnings in ISAtab import (#573)
  • Use file name as study/assay key in parser warning data (#644)
  • Upgrade to altamISA v0.2.5 (#676)
  • Rename and refactor get_igv_session_url() (#402)
  • Use reference table building classes from altamISA
  • Enforce ordering in Study.get_nodes() to maintain row order (#510)
  • Ignore file name when searching for germline study pedigree files (#602)
  • Replace TSV table export with Excel file export (#613)
  • Allow ACTIVE landing zones when replacing sample sheets
  • Sort displayed studies and assays by parsing order instead of file name (#683)

Fixed

• General

  • Missing .venv ignore in Flake8 config (bihealth/sodar-core#300)
  • Installation document omissions (#606)
  • Columns with integer and float values sorted lexicographically (#596)

• Samplesheets

  • "Sequence item 1" render error manifesting with BII-I-1 example (#620)
  • Redundant unit/value parsing for comments during import (#629)
  • Missing label for unknown configuration in Overview (#638)
  • Overview statistics table margin change (#630)
  • Leftover database objects from ISAtab import crash (#643)
  • Extract label rendering as an ontology term (#563)
  • Cache updated on sheet replace with iRODS collections not created (#622)
  • Name column rendering for Labeled Extract Name materials (#652)
  • Data File name column rendering (#652)
  • Crash in importing First Dimension and Second Dimension fields (#653)
  • Display value copied to clipboard instead of full value in multi-cell select (#521)
  • Multi-cell clipboard copying wrong cells with custom row ordering (#664)
  • Crash in search if iRODS connection fails (#680)
  • Parser warnings layout breaking with long strings (#685)

Removed

• General

  • Unused storage requirements from production config (#610)

• Samplesheets

  • Reference table building classes from rendering.py
  • write_csv_table() helper from samplesheets.utils (#613)

v0.5.1 (2019-07-09)

Added

• Samplesheets

  • iRODS data corruption warning in sheet replacing (#557)
  • Temporary setting SHEETS_ENABLE_CACHE to fix CI (#556)
  • Investigation model fields parser_version and parser_warning (#527)
  • Multiple new model fields to support AltamISA v0.1 API (#527)
  • _get_value() helper in rendering
  • altamISA version storing and logging in rendering (#527)
  • altamISA v0.1 validation (#527)
  • Handling of altamISA warnings (#527)
  • Helper script run_demo.sh to run in local demo mode
  • Vue.js app view for displaying parser warnings
  • Support for altamISA v0.1 column sorting (#86, #566)
  • Display comments, performer and perform date in tables
  • _get_ontology_url() helper in SampleSheetTableBuilder

Changed

• General

  • Upgrade site to django-sodar-core v0.6.2 (#569)
  • Update setup.py (#551)

• Samplesheets

  • Update project iRODS cache when replacing sheets (#554)
  • Use delete_cache() in TaskflowSheetDeleteAPIView (bihealth/sodar-core#257)
  • Upgrade to CUBI altamISA parser v0.1 (#527)
  • Update ISAtab importing for altamISA v0.1 (#527)
  • Update models for altamISA v0.1 (#527)
  • Raise exception from parser errors when in debug mode
  • Update test ISAtab files for altamISA v0.1 (#527)
  • Refactor io module
  • Improve io module logging
  • Change GenericMaterial.extract_label into a JSON field (#527)
  • Update project iRODS cache when creating or updating iRODS collections (#565)
  • Disable operations dropdown for guest users (#497)
  • Refactor Vue.js subpage navigation
  • Refactor legacy table rendering (#111, #566)
  • Store ontology URL template in settings.SHEETS_ONTOLOGY_URL_TEMPLATE
  • Align columns uniformly with cells containing integer or float values (#598)
  • Clarify "sample repository available" message on details page card (#587)

Fixed

• Samplesheets

  • Assay UUIDs modified when replacing sheets (#554)
  • Default fetch() credentials failing with certain old browsers (#559)
  • Crash in germline study app get_shortcut_column() with empty family column (#560)
  • Germline study app update_cache() failing with empty family column
  • Sheet deletion error not displayed to user (#568)
  • Crash in SampleSheetStudyTablesGetAPIView if Study object not found (#578)
  • Leading or trailing spaces in parsed field values (#584)
  • Crash in germline study app get_shortcut_column() if IGV URL was not generated (#589)
  • Errors in DataCellRenderer trying to access unset renderData (#595)
  • Contact fields not rendered if using non-standard notation (#595)

Removed

• Samplesheets

  • Model fields characteristic_cat and unit_cat from Study
  • Model field header from Study and Assay
  • Model field scan_name from Process
  • Redundant warning for missing protocol reference in ISAtab import
  • Duplicate database indexes (#582)

v0.5.0 (2019-06-05)

Added

• General

  • Unsupported browser warning (#535)

• Irodsbackend

  • API function get_url() (#438)
  • iRODS collection path sanitizing (#488)
  • Statistics for the siteinfo app (#503)
  • API function test_connection() (#514)

• Irodsinfo

  • IRODSINFO_SSL_VERIFY setting for toggling SSL verification in iRODS configuration JSON (#516)

• Landingzones

  • Call samplesheets project cache updating after moving zone files (#508)

• Samplesheets

  • New Vue.js based sample sheets viewer (#426)
  • Get shortcut table data from study apps using get_shortcut_table()
  • get_sheets_url() helper
  • Sodarcache iRODS file info caching for study apps (#241)
  • set_configuration() helper for unit tests
  • get_igv_url() helper in study app utils
  • get_study_libraries() helper in samplesheets.utils
  • get_extra_table() function in SampleSheetAssayPluginPoint
  • app_name member in SampleSheetAssayPluginPoint
  • Multi-cell selection and clipboard copying
  • Temporary manual sample sheet cache updating (#474)
  • Deletion of project samplesheets cache on sheet/data deletion (#509)
  • Temporary view RemoteSheetGetAPIView for remote sample sheet access (#388, #523)
  • UI for toggling column visibility (#466)
  • Filtering for iRODS collection list modal (#18, #467)

Changed

• General

  • Upgrade site to django-sodar-core v0.6.0
  • Update login template to match django-sodar-core v0.6.0

• Irodsbackend

  • Modify stats badge appearance
  • Refactor URL arguments and URL patterns regarding query strings (#455)
  • Properly URL encode query strings (#456)
  • Always return JSON from API views (#457)
  • Update title and description in plugin
  • Rename get_subdir() into get_sub_path() (#495)
  • Disable loading backend javascript for each page (#532, bihealth/sodar-core#261)

• Landingzones

  • Use get_info_link() for zone descriptions (#501)
  • Temporarily load irodsbackend.js by a manual include (#532, bihealth/sodar-core#261)

• Samplesheets

  • Update and refactor server side rendering for client-side sheet UI (#426)
  • URL patterns for samplesheets:project_sheet updated for Vue.js routes (#426)
  • Refactor and update sample sheet rendering for new renderer (#111, #426)
  • Expect full table data with headers for assay app get_row_path()
  • Add table data to get_last_material_name() args
  • Return iRODS path instead of Davrods URL from study app file locating helpers
  • Redesign study apps to work with Vue.js viewer (#436)
  • Display study shortcuts as link column instead of separate table (#464)
  • Do not display shortcuts in cancer study app for mass spectrometry assays (workaround for #482)
  • Move get_material_count() from views into Investigation model
  • Disable sheet replacing if active landing zones exist in the project (#525)
  • Temporarily load irodsbackend.js by a manual include in details card (#532, bihealth/sodar-core#261)
  • Move TSV table generation into utils.write_csv_table() (#523)

Fixed

• Irodsbackend

  • Exceptions raised by API for collection paths with trailing slash (#488)
  • Crash from invalid iRODS authentication in multiple locations (#514)

• Irodsinfo

  • Crash from invalid iRODS authentication in IrodsInfoView (#514)

• Samplesheets

  • Crash from certain queries if inactive Investigation objects are present for project (#544)

Removed

• Irodsinfo

  • iRODS certificate issue workaround (#516)

• Landingzones

  • Unused get_info() definition in project app plugin (#541)

• Samplesheets

  • DataTables sample sheet rendering (#100, #223)
  • Unused views, templates and templatetags from main and sub apps (#462)
  • Member variable study_template in SampleSheetStudyPluginPoint (#462)
  • JQuery updating in samplesheets.js (#462, #473)
  • Local DataTables includes (#462)
  • JQuery Dragscroll (#462)
  • Old "hide study columns" functionality from assay tables (#466)
  • Unused get_info() definition in project app plugin (#541)

v0.4.6 (2019-04-25)

Added

• Samplesheets

  • Validate existence and uniqueness of study identifiers during import (#483)

Changed

• General

  • Upgrade site to django-sodar-core v0.5.1 (#480)
  • Upgrade to ChromeDriver v74 (bihealth/sodar-core#221)

• Samplesheets

  • Identify studies in investigation replacing by identifier instead of title (#483)

Fixed

• Samplesheets

  • Crash in investigation replacing if study titles are not unique (#483)

v0.4.5 (2019-04-11)

Fixed

• Samplesheets

  • Hard coded WebDAV URL in IGV links (#468)
  • Add missing SODAR Core v0.5.0 settings variables (#469)

v0.4.4 (2019-04-03)

Added

• Samplesheets

  • Copying HPO term IDs into clipboard (#454)

Changed

• General

  • Upgrade to django-sodar-core v0.5.0

Fixed

• Irodsbackend

  • Repeated CSS overrides moved to irodsbackend.css (#452)

• Samplesheets

  • Tooltips broke study app table layout in small tables (#458)

v0.4.3 (2019-03-07)

Added

• Irodsbackend

  • IRODS_QUERY_BATCH_SIZE setting for batch queries (#432)

• Samplesheets

  • Support for multiple ontology links in _get_ontology_link() (#431)
  • Hack for providing correct HPO ontology into links (#431)
  • Rendering for HPO term links (#431)
  • Rendering for performer and perform date (#187)
  • Transcription profiling support in dna_sequencing assay app (#443)
  • Use IRODS_QUERY_BATCH_SIZE for iRODS updating (#432)
  • External link label x-generic-remote (#448)

Changed

• General

  • Upgrade to django-sodar-core v0.4.5

• Landingzones

  • Secure Taskflow API views with BaseTaskflowAPIView (#435)
  • Adjust form textarea height (#437)

• Samplesheets

  • Improve exception reporting in SampleSheetTableBuilder (#433)
  • Secure Taskflow API views with BaseTaskflowAPIView (#435)
  • Support email link rendering for "contact" fields (#439)
  • Refactor contact field rendering (#439)
  • Query iRODS stats in batches (#432)
  • Enable iRODS buttons by default (#432)
  • Display external ID if label is not found (#449)

Fixed

• General

  • Add missing .coveragerc excludes (#427)

• Samplesheets

  • iRODS button status updating for Proteomics projects (#428)
  • General iRODS button status only updated once per page load (#429)
  • Performance issues in iRODS stats querying with large data (#432)
  • iRDOS buttons not disabled if iRODS collections not created (#445)
  • ISAtab upload wiget error not displayed without Bootstrap 4 workarounds (bihealth/sodar-core#164)

Removed

• General

  • Old Bootstrap 4 workarounds for django-crispy-forms (bihealth/sodar-core#157)

• Samplesheets

  • iRODS wait icon from study apps and assay tables (#430)

v0.4.2 (2019-02-04)

Added

• General

  • Formatting with Black
  • Flake8 and Black checks in CI (#422)
  • General code cleanup and refactoring (#422)
  • IRODSBACKEND_STATUS_INTERVAL setting passed to JQuery (#423)

• Irodsbackend

  • Support for POST in Ajax views (#416)
  • App specific rules (#418)
  • Client side enabling/disabling of iRODS links buttons (#260)
  • Get status updating interval from setting variable (#423)
  • API view permission tests (#386, #417)

• Samplesheets

  • Support alternative notation in contact fields (#382)

Changed

• General

  • Upgrade minimum Python version requirement to 3.6 (bihealth/sodar-core#102)
  • Update and cleanup Gitlab-CI setup (bihealth/sodar-core#85)
  • Update Chrome Driver for UI tests
  • Cleanup Chrome setup
  • Update login.html override to add site messages (bihealth/sodar-core#105)
  • Update site dependency utilities to match django-sodar-core v0.4.1+ (bihealth/sodar-core#90)
  • Upgrade to django-sodar-core v0.4.3
  • Upgrade dependencies to match django-sodar-core v0.4.2+ (#420)
  • Disable USE_I18N (bihealth/sodar-core#117)
  • Changed CONTRIBUTORS.txt into AUTHORS.rst

• Irodsbackend

  • Refactor Ajax API views (#416)
  • Limit the amount of iRODS queries (#414)

• Landingzones

  • Rename Taskflow specific API views (bihealth/sodar-core#104)

• Samplesheets

  • Rename Taskflow specific API views (bihealth/sodar-core#104)
  • Only allow superuser or project owner to delete sheet with iRODS data (#424)

Fixed

• General

  • Login URL was not set to sodar/users/login.html
  • Django docs references (bihealth/sodar-core#131)
  • ProjectAccessMixin.get_project() calls

• Samplesheets

  • DataTables scrolling issue with Bootstrap 4.2.1 (#421)
  • Workaround for DataTables vertical overflow bug (#369)

Removed

• General

  • Unused templates in sodar/pages
  • Unused URL mapping to about.html
  • Local JS/CSS includes for JQuery, Bootstrap and other JS helpers (#379, #420)
  • Legacy Python2 super() calls (bihealth/sodar-core#118)
  • Redundant is_superuser predicates from rules (bihealth/sodar-core#138)

• Irodsbackend

  • Unused module admin.py

• Samplesheets

  • Unused dropup app buttons mode in templates (bihealth/sodar-core#108)

v0.4.1 (2018-12-19)

Added

• General

  • TASKFLOW_TEST_MODE setting for test iRODS server support (bihealth/sodar-core#67)
  • Missing LDAP dev setup script (#385)

• Irodsbackend

  • Project UUID parsing support for get_uuid_from_path()

Changed

• General

  • Update list button and dropdown classes (#381)
  • Upgrade to django-sodar-core v0.4.0
  • Use TASKFLOW_SODAR_SECRET for securing Taskflow API views (bihealth/sodar-core#46)

• Filesfolders

  • Import app from django-sodar-core v0.4.0 (#403)

• Landingzones

  • Use SODAR_API_DEFAULT_HOST in email generation (#396)
  • Hide deleted zones in project overview (#394)

• Samplesheets

  • Normalize alternative material names as lowercase to optimize search (#390)
  • Add real material name in alt_names as lowercase (#390)
  • Reduce Django queries to optimize iRODS file search (#393)
  • Replace IRODS query limit settings with SHEETS_IRODS_LIMIT (#393)
  • Cancer study app: only show shortcuts for genome/exome seq assays (#398)
  • Move germline specific template tags in germline study app (#399)
  • Refactor study app views (#406)

Fixed

• General

  • Potential inheritance issues in test classes (bihealth/sodar-core#74)

• Irodsbackend

  • TypeError in get_path() not correctly raised with invalid object class name (#404)
  • iRODS connections not properly cleaned up in Ajax API views (#413)
  • Ensure iRODS connection cleanup after exiting a decorated function

• Irodsinfo

  • NetworkException not caught if iRODS server is unavailable (#395)

• Landingzones

  • Invalid URLs in zone status update emails (#396)

• Samplesheets

  • Cancer study app source query not filtered by study (#389)
  • Handle cancer app library assay linking errors (#404)
  • Assay links in study overview card (#405)
  • Study app shortcut exceptions always redirected to default study (#406)
  • Cancer study IGV shortcut crash if samples not found (#407)

Removed

• General

  • Unneeded gunicorn dependency in settings/local.py (#383)

• Filesfolders

  • Local app removed (#403)

• Landingzones

  • Unused get_irods_cmd() template tag

v0.4.0 (2018-10-26)

Added

• Adminalerts

  • Import app from djagno-sodar-core

• Projectroles

  • Import app from django-sodar-core

• Taskflowbackend

  • Import app from django-sodar-core

• Timeline

  • Import app from django-sodar-core

• Userprofile

  • Import app from django-sodar-core

Changed

• General

  • Update Django to v1.11.16 (#370)
  • Update requirements to match django-sodar-core v0.3.0 (#370)
  • Update SODAR app requirements to current versions
  • Rebrand project and site as sodar (#166)
  • Update SODAR_CONSTANTS dependencies in local apps (#370)
  • Update sodar_uuid model fields and references in local apps (#370)
  • Update sodar_url references in local apps (#370)
  • Update default templates (#370)
  • Move login Javascript to login.js
  • Update development documentation

• Samplesheets

  • Improve data table CSS during DataTables init (#359)

Fixed

• Irodsbackend

  • Viewing iRODS file list on an empty collection failed (#375)
  • WebDAV URL copying tooltip not rendered correctly inside DataTables (#377)

• Samplesheets

  • IGV session file generating crash if VCF file was not found (#372)

Removed

• General

  • Local Django apps included in SODAR Core v0.3.0 (#370)
  • Unused django-extra-views requirement
  • Unused user templates (#370)

• Samplesheets

  • Duplicate DataTables CSS includes

v0.3.3 (2018-09-25)

Added

• Samplesheets

  • Cancer study app (#371)
  • Generic IGV session file generating function get_igv_xml() in studyapps.utils
  • get_sources() helper in Study model
  • get_samples() helper in GenericMaterial model
  • get_sample_libraries() helper in samplesheets.utils

Changed

• Samplesheets

  • Use get_igv_xml() in germline study app
  • Use get_sample_libraries() in DNA sequencing assay app

v0.3.2 (2018-09-11)

Added

• General

  • BIH Proteomics data transfer docs (Mathias Kuhring)

Changed

• Projectroles

  • Use omics-search-card-body instead of omics-card-body-table (#364)

Fixed

• General

  • Dropdown menu overflow hiding in omics-card-body-table classes (#364)

• Samplesheets

  • Investigation parsing failure when replacing isatab deleted previous version (#365)

Removed

• Landingzones

  • Usage of popupNoFilesHtml (will be removed from omics_core)

v0.3.1 (2018-08-24)

Added

• General

  • SITE_SUBTITLE setting to show beta status or something similar (#311)
  • API settings SODAR_API_DEFAULT_VERSION and SODAR_API_MEDIA_TYPE
  • Domain/system user groups set on login or by management command syncgroups (#313)
  • CSS classes for badge-group (#349)

• Adminalerts

  • Enable Markdown in alert description (#196)
  • Display user in alert details (#330)

• Filesfolders

  • Text style depending on item flag (#303)
  • Optional automated unpacking for uploaded zip files (#327)
  • Setting FILESFOLDERS_MAX_ARCHIVE_SIZE (#327)
  • search() function in plugin (#335)

• Irodsbackend

  • Generic iRODS file statistics view, template tags and Javascript (#181, #188)
  • Missing support for Investigation objects in get_path() (#292)
  • iRODS collection query Javascript (#295)
  • Display collection name in iRODS collection list
  • IrodsObjectListAPIView for iRODS collection list queries (#308)
  • BaseIrodsAPIView for implementing views
  • Logging for error cases (#310)
  • get_sample_path() and get_uuid_from_path() helpers (#289)
  • Param like_name into data object querying (#289)

• Landingzones

  • Send email when zone status is set as MOVED or FAILED (#280)
  • Unit tests for ZoneStatusSetAPIView
  • Display iRODS stats in details card (#188)
  • Ability to add extra flow parameters with get_extra_flow_data() (#297)
  • Script user workaround for non-working tickets in the proteomics use case (#297)
  • Option for validating files without moving (#333)
  • Missing unit tests for LandingZoneMoveView (#248)

• Projectroles

  • Helper email.send_generic_mail() (#280)
  • Common template tag check_backend()
  • Define backend app javascript include in plugin (#300)
  • Common template tag get_setting()
  • CurrentUserFormMixin for providing current using to forms as current_user
  • Helper mixin KnoxAuthMixin for views testing
  • Sanitize search input (#332)
  • Handle project list title cell overflow (#306)
  • No results alert for search (#288)
  • DataTables rendering for search results (#328)
  • Result count in search results (#338)
  • Settings variable PROJECTROLES_SEARCH_PAGINATION (#328)
  • Pagination for search results (#328)
  • Filtering for search results (#328)

• Samplesheets

  • Display original study/assay filenames as tooltips (#283)
  • Display assays for samples in search results (#157)
  • Helper function GenericMaterial.get_sample_assays() (#157)
  • Auto-populate field alt_names in the GenericMaterial model (#285)
  • Management command syncnames to update alt_names (#285)
  • Display project/study file statistics using irodsbackend (#188)
  • Display stats on the project details page card (#188)
  • Proof-of-concept ID Querying API with token authentication
  • iRODS files searchable in site search (#289)
  • Highlighting of search strings (#341)
  • Custom display for "external links" fields (#349)
  • Settings variable SHEETS_EXTERNAL_LINK_LABELS (#349)
  • Custom display for different "contact" fields
  • Handle sheet table cell overflow
  • Settings variable SHEETS_MAX_COLUMN_WIDTH
  • search() function in plugin (#335)
  • Settings variables SHEETS_IRODS_LIMIT_PROJECT and SHEETS_IRODS_LIMIT_TOTAL (#289)

Changed

• General

  • Search button CSS (#351)
  • Refactor search views to allow multiple result sets from apps (#335)
  • Implement search in ProjectAppPlugin.search() instead of template tags (#335)

• Adminalerts

  • Update user when updating alert (#179)

• Filesfolders

  • Refactor timeline event creation for object modification
  • Unify project title printing in search with other apps (#335)

• Irodsbackend

  • Optimize iRODS queries for increased performance (#242)
  • Improve collection listing popup layout
  • Check user perms for iRODS collection when performing queries
  • Omit icp from iRODS path when copying to clipboard (#319)

• Landingzones

  • Use irodsbackend code for statistics queries (#188)
  • Refactor irods_backend references in templates
  • Move javascript to separate file (#181)
  • Hide deleted zones from "other zones" (#302)
  • Use irodsbackend code for collection listing (#295)
  • Sort zones in list by zone tiele (#312)

• Projectroles

  • Minor email refactoring (#280)
  • Hide system users from normal users' UI in member selection (#347)
  • Hide search elements if no results are found (#288)

• Samplesheets

  • Search for VCF files under all family members in germline app (#275)
  • Include alt_name in GenericMaterial search (#285)
  • Improve search results layout
  • Display investigation title on project card (#293)
  • Refactor irods_backend references in templates
  • Use irodsbackend code for collection listing (#295)
  • Move irods buttons to irodsbackend (#301)
  • Move irods clipboard javascript to irodsbackend (#301)
  • Move javascript to separate file (#181)
  • Allow multiple assay field combinations for selecting assay plugin (#315)
  • Enable genome_seq_nucleotide_seq app also for exomes (#315)
  • Rename genome_seq_nucleotide_seq into dna_sequencing (#315)
  • Refactor site search (#289)
  • Exclude "name" column from automated aligning (#350)

Fixed

• General

  • Popover width in CSS (#291)

• Irodsbackend

  • Handle missing user auth in API views without raising an exception (#337)

• Landingzones

  • Incorrectly calculated LANDINGZONES_STATUS_INTERVAL (#305)

• Projectroles

  • Extra spaces and tabs broke search (#290)
  • Search not enabled if selecting previous input with mouse (#307)
  • Case conversion issue caused highlight_search_term() to fail (#341)

• Samplesheets

  • Show correct target in germline app FileRedirectView message (#275)
  • Source/sample name search resulted in a template crash (#287)
  • CSS highlight bug in nav dropdown
  • Content app DataTable header broke layout if following assay anchor (#224)
  • Wrong CSS class in pep_ms (#318)
  • Assays not filtered by project in sample search (#358)

• Timeline

  • Not found label did not reflect timeline_mode (#346)

Removed

• General

  • Unused ProjectAppPluginPoint.search_title attribute (#335)

• Filesfolders

  • find_filesfolders_items() template tag (#335)

• Landingzones

  • LandingZoneIrodsStatisticsGetAPIView and related redundant JQuery scripts
  • LANDINGZONES_STATISTICS_INTERVAL settings variable
  • LandingZoneIrodsObjectListAPIView, use view in irodsbackend instead (#308)

• Projectroles

  • find_projects() template tag (#335)

• Samplesheets

  • MD5 display from file list view
  • Deprecated irods_base_dir from views
  • IrodsObjectListAPIView, use view in irodsbackend instead (#308)
  • samplesheets_common.js, functionality now in irodsbackend (#301)
  • utils.get_last_material_index(), no longer used (#317)
  • find_samplesheets_items() template tag (#335)

v0.3.0 (2018-07-03)

Added

• General

  • Sphinx-based online user manual (#50)
  • Site favicon (#166)

• Irodsbackend

  • Proper cleanup of iRODS session on API deletion
  • Temporary iRODS ticket operations (#240)

• Landingzones

  • Status types DELETING and DELETED (#228)
  • Landing zone special configurations (#240)
  • Configapp sub-app plugin point (#240)
  • Configapp plugin for bih_proteomics_smb (#240)
  • More unit tests for views (#248)

• Projectroles

  • Tag force_wrap() in common template tags

• Samplesheets

  • Add genome_seq_nucleotide_seq assay app (#249)
  • Add pep_ms assay app (#245)
  • Object metadata in sample sheet table rendering (#254)
  • Show investigation configuration in study details table
  • WebDAV clipboard copying links (#257)
  • IGV integration and auth-basic support for germline study app

Changed

• General

  • Update installation and development documentation (#237)
  • Rebrand site as SODAR (#166)
  • Separate manual from development docs (#50, #237)
  • Use Bootstrap4 modal instead of jquery.popupoverlay (#180)
  • Improve login user experience (#229)

• Landingzones

  • Make landing zone deletion async (#228)
  • Refactor zone list item rendering
  • Include iRODS buttons from _irods_buttons.html
  • Display full zone title in project overview
  • Call cleanup_zone() in configapps when setting status to MOVED or DELETED (#240)

• Projectroles

  • Use modal for email preview popups (#180)

• Samplesheets

  • Clarify ISA parsing error message (#236)
  • Separate configapps into study and assay apps (#249)
  • Move get_row_path() to assay app (#249)
  • Make links column hideable by assay app (#249)
  • Move iRODS buttons in separate template for including
  • Change get_assay_path() into a more general get_irods_path() in template tags (#257)
  • Display study and assay links on the project details page (#257)
  • Move commonly used javascript to samplesheets_common.js (#181)
  • iCommands button copies link to clipboard without popup (#257)
  • Improve germline study app layout
  • General table layout updates

Fixed

• Landingzones

  • Buttons not correctly activated during status update (#215)
  • Long landing zone names broke zone list table
  • iRODS client NetworkException not caught by LandingZoneStatisticsGetAPIView (#255)

• Samplesheets

  • Escape cell values (#233)
  • Study and Assay UUIDs changed during replace (#234)
  • Missing iCommands path in popup (#250)
  • Improve study and assay layout
  • Linking of BAM and VCF files if no assay plugin was found (#264)
  • Incorrectly filled Family field broke germline study rendering (#270)

• Timeline

  • Long labels broke timeline table (#225)

Removed

• General

  • jquery.popupoverlay dependencies (#180)

• Landingzones

  • ZoneDeleteAPIView as it's not needed anymore due to async deletion (#228)

v0.3.0b (2018-06-05)

Added

• General

  • Admin link for superuser (#134)
  • Common popupWaitHtml and popupNoFilesHtml Javascript variables
  • Clipboard.js for helping clipboard operations
  • CSS styling for .omics-code-input
  • Height check for project sidebar and dropdown menu switching (#156)

• Irodsbackend

  • Add irodsbackend app (#139)
  • Add get_path() for retrieving iRODS paths for Django objects
  • Template tag get_irods_path() to get object iRODS path in template
  • Add get_session() for direct iRODS API access
  • Add collection_exists() to check collection availability

• Irodsinfo

  • Add irodsinfo site app (#183)

• Landingzones

  • Add landingzones app (#139)

• Projectroles

  • Settings updating to Taskflow for project creation and modification (#139)
  • Add get_all_settings() and get_default_setting() in project_settings
  • Add get_class() in projectroles_common_tags

• Samplesheets

  • iRODS directory creation (#139)
  • iRODS link and iCommands display (#139)
  • Render optional hidden HTML attributes for cell meta data (#139)
  • Add get_dir() and get_display_name() helpers to Study and Assay
  • Add SampleSheetTaskflowMixin for Taskflow test helpers
  • Row numbers for sample sheet tables (#155)
  • Tour help (#145)
  • Row limit to prevent import and rendering of huge data (#192)
  • Render extract label column
  • Project setting study_row_limit (#192)
  • Replacing sample sheets for limited modifications (#195)
  • SampleSheetConfigPlugin for sheet configuration specific sub-apps (#201)
  • Config app bih_germline as an example (#201)
  • Add get_configuration() in the Investigation model (#201)
  • Add get_irods_row_path() to iRODS path to sample sheet row (#172)

• Taskflowbackend

  • Add taskflowbackend app (#139)
  • Add optional omics_url kwarg to submit()

Changed

• General

  • Upgrade to Django 1.11.13
  • Upgrade to django-crispy-forms 1.7.1 (#153)
  • Upgrade to Boostrap 4.1.1 (#144)
  • Improve tour help layout
  • Upgrade to Gunicorn 19.8.1
  • Switch ordering of Filesfolders and Landingzones in project menu (#217)

• Filesfolders

  • Don't show empty folder label if subfolders exist (#135)

• Irodsbackend

  • Implement functionality of omics_irods_rest directly in the app
  • Rename get_object_list() into get_objects()
  • Improve error handling in get_objects()

• Projectroles

  • Use Taskflowbackend only for creating and modifying PROJECT type projects
  • Modify Taskflow API URLs
  • Refactor get_active_plugins()
  • Refactor email sending
  • Properly log and report errors in email sending (#151)
  • Require email sending to succeed for creating invites (#149)
  • Modify ProjectStarringAPIView to use common permission mixins
  • Rename TestTaskflowViewBase to TestTaskflowBase
  • Integrate TaskflowMixin into TestTaskflowBase
  • Improve project list layout (#171)
  • Move iRODS info page into the irodsinfo app (#183)
  • Modify signature of _get_project() in ProjectAccessMixin
  • Allow get_all_settings() and get_project_setting() with no project in project_settings

• Samplesheets

  • Rename top header "legend" to "value" (#129)
  • Allow sample sheet upload for project contributor (#137)
  • Allow sample sheet deletion for project contributor (#168)
  • In taskflow operations, use omics_uuid instead of pk (#99)
  • Refactor table HTML rendering
  • Improve URLs for ontology linking (#170)
  • Hide columns with no data (#184)
  • Do not allow importing sheet or creating iRODS dirs if rendering fails (#192)
  • Upgrade altamISA to commit ddf54e9ab9b47d2b5a7d54ce65ea8aa673375f87 (#191)
  • Display material subtype in top column (#200)
  • Display Process name if set (#207)

• Taskflowbackend

  • Use omics_uuid instead of pk (#139)
  • Only set up PROJECT type projects in synctaskflow

Fixed

• General

  • Add missing email settings in production config (#149)
  • Add python3-distutils to Xenial requirements to fix failing tests caused by recent updates
  • User links visible when logged out on low resolutions (#197)
  • Fix omics-card-table-bordered CSS

• Filesfolders

  • Broken link for subfolders with depth >1 (#136)

• Projectroles

  • Invalid URL in build_invite_url() caused a crash (#149)
  • Project creation failure using taskflow caused database corruption (#162)
  • Proper redirect from failed project creation to home or parent category
  • Project partially modified instead of rollback if update with taskflow failed (#163)
  • Project settings not correctly populated in TestTaskflowBase
  • Allow _get_project() with top level app models from nested apps (#201)
  • README not modified when updating project with Taskflow enabled (#209)

• Samplesheets

  • Delete investigation if import fails (#138)
  • Assay sorting was not defined
  • Assay data could end up in the wrong table with multiple assays under a study (#169)
  • Correctly use request.session.real_referer for back/cancel links (#175)
  • Error rendering sheet tables caused app to crash (#182)
  • Building a redirect URL in export view caused a crash
  • Prevent double importing of Investigation (#189)
  • Zip file upload failed on Windows browsers (#198)
  • Remove possible duplicate sample rows from study tables (#199)
  • Extract label not correctly parsed
  • Back link not working in IrodsDirView (#206)
  • Invalid HTML from rendering extra cell classes together with text-right
  • Correctly parse study description (#208)
  • Numerical value check for right-aligning (#218)

• Timeline

  • Fix event id parameter in Taskflow view

Removed

• General

  • Removed Flynn workarounds, deploying on Flynn no longer supported (#133)

• Projectroles

  • "View Details" link in details page, not needed thanks to project sidebar
  • get_description() templatetag

v0.2.0 (2018-04-13)

Added

• General

  • Automated version numbering in footer (#130)
  • ProjectPermissionMixin for project apps
  • ProjectAccessMixin for retrieving project from UUID URL kwargs
  • The omics_uuid field in models where it was missing (#97)
  • Graph output with pygraphviz for local development

• Projectroles

  • Add get_project_link() in templatetags

• Samplesheets

  • Add samplesheets app
  • ISA specification compatible data model (#76)
  • Importing ISA investigations as sample sheets (#77)
  • Rendering and navigation of sample sheets (#79)
  • Simple sample sheet search (#87)
  • DataTables rendering of sheets (#81)

Changed

• General

  • Upgrade site to Django 1.11.11
  • Upgrade site to Boostrap 4.0.0 Stable (#78)
  • Use omics_uuid instead of pk in URLs and templates (#97)
  • Rework URL scheme for consistency and compactness (#105)
  • Modify subtitle and page content containers for all apps
  • Sticky subtitle nav menu for pages with operations menus or navigation
  • Site-wide CSS tweaks
  • Rename details_position to plugin_ordering in plugins (#90)
  • Refactor app views with redundant SingleObjectMixin includes (#106)
  • Squashed/recreated database migrations (#120) (Note: site must be deployed on a fresh database in this version)

• Projectroles

  • Search view improvements
  • Refactor roles and invites views
  • Split get_link_state tag into get_app_link_state and get_pr_link_state to support new URLs (#105)

• Timeline

  • Use omics_uuid for object lookup in plugins.get_object_link() (#97)

Fixed

• General

  • Update ChromeDriver to eliminate UI test crashes (#85)
  • User dropdown rendering depth (#82)
  • Error template layout breaking (#108)

• Filesfolders

  • Public link form widget always disabled when updating a file (#102)
  • Content type correctly returned for uploaded files and folder READMEs (#131)

Removed

• General

  • Role "project staff" (#121)

v0.1 (2018-01-26)

Added

• General

  • Create new base project using the current version of cookiecutter-django
  • Additional unit tests for site apps
  • Changelog in CHANGELOG.rst
  • User profile page (#29)
  • Highlight help link for new users (#30)
  • Support for multiple LDAP backends (#69)

• Adminalerts

  • Add adminalerts app (#17)

• Filesfolders

  • Import app from prototype
  • Page title to main files list
  • File, folder and link search (#21)
  • Item flagging (#38)
  • History links for items (#35)
  • Folder readme file rendering (#36)

• Projectroles

  • Import app from prototype
  • Sub-navbar with project breadcrumb (#20)
  • Move app and project editing links to project sidebar (#20)
  • Helper functions for project settings
  • Initial project and app object search (#16, #21)
  • More helper functions in Project model: get_parents(), get_full_title()
  • Project list filtering (#32)
  • Project tagging/starring functionality (#37)
  • History links for project members (#35)
  • Import roles from another owned project (#9)
  • User HTML tag in common templatetags (#71)

• Timeline

  • Import app and backend plugin from prototype
  • Object event view history and API (#35)
  • Project model support in event references

Changed

• General

  • Update site for Django 1.11.9 (#1) and Python 3.6.3 (#2)
  • Update site to Bootstrap 4 Beta 3 (#70)
  • Update third-party libraries to their latest versions
  • Layout redesign (#20)
  • Switch from PhantomJS to Headless Chrome for UI tests (improved performance and stability, Bootstrap 4 Beta compatibility)
  • Include CSS and JS imports in testing configs and CI
  • General code refactoring and cleanup
  • Update installation instructions in INSTALL.rst
  • Rename "actions" into "operations" (#41)
  • Message alert boxes made dismissable (#25)
  • Make tables and navs responsive to browser width

• Filesfolders

  • Redesign data model with inheritance to avoid field repetition
  • Internal app name is now filesfolders
  • Project setting allow_public_links is now False by default (#43)
  • Include extra data in item creation and updating
  • Only allow one readme.* file in each folder (#36)

• Projectroles

  • Remove two-level restriction for project and category nesting in models
  • Only allow creation of categories on top level
  • Improved project list layout
  • Move OMICS_CONSTANTS from configuration into models.py
  • Populate Role objects in a migration script instead of a fixture
  • Import patched django-plugins from GitHub instead of including in project directly
  • Include extra data in project creation and updating
  • Move Project settings helper functions to project_settings.py
  • Disable help link instead of hiding if no tour help is available
  • Show notice card if no ReadMe is available for project (#42)
  • Refactor URL kwargs
  • Allow users with roles under category children to view category (#47)
  • Update text labels for role management to refer to "members" (#40)
  • Separate common template tags into projectroles_common_tags
  • Move project settings forms to project creation/update view (#44)
  • Provide reload-safe referer URL in request.session.real_referer (#67)

• Timeline

  • Enable event details popover on the project details page
  • Limit details page list to successful events
  • Allow guest user to see non-classified events
  • Function add_event() raises proper ValueError exceptions

Fixed

• Filesfolders

  • Redirects in exception cases in FilePublicLinkView
  • Unexpected characters in file name broke the file_serve view (ODA #109)
  • Check for existing file if moving file during update (#56)

• Projectroles

  • Check for project title uniqueness
  • Don't allow matching titles for subproject and parent
  • App plugin element IDs in templates
  • Project context for role invite revocation page
  • Project type correctly displayed for user (#27)

• Timeline

  • Tour help anchoring for list navigation buttons
  • User column link was missing the mailto: protocol syntax

Removed

• General

  • The unused get_info() function and its implementations from plugins (provide details_template instead)
  • Unused user app features

• Filesfolders

  • Redundant and deprecated fields/functions from the data model
  • Example project settings

• Projectroles

  • Temporary settings variables for demo and UI testing hacks