SODAR Changelog

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

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