3.2.16

Claudiu Farcas (1):

• Adding a basic RADIUS MFA implementation. (2a5c761)

Jamie Snape (204):

• Allow MySQL driver options to be specified in database.ini (193ae72)
• Minor fixes to tracker dashboard (9adeca0)
• Add an API call for creating an item containing a link bitstream (fe41983)
• Add parameters for specifying length and checksum of files to which link points (f8be410)
• Add old style API call for creating link and tweak name of new style call (a4bbd06)
• Remove duplicate keys in ini file (485096b)
• Fix PDO error when accessing installation page (129f55e)
• Remove duplicate case in switch statement (4eddc18)
• Remove duplicate array keys (9cff9fa)
• Remove assignment with left and right sides equal (8ff3d80)
• Remove redundant closing tags (4a6b62c)
• Consistently use lowercase true, false, null (fee0cb9)
• Replace tabs with spaces (277f6ac)
• Consistently indent class and function braces (b28667c)
• Ensure one new line at the end of each file (4965289)
• Remove trailing spaces (c5a3b16)
• Ensure consistent spacing between if, for, etc. and parenthesis (f48f6a6)
• Miscellaneous PHP formatting tweaks (b8570e2)
• Consistently use else if instead of elseif (136754f)
• Consistently order abstract, visibility, access modifiers (df084fa)
• Add or update file headers (63514d0)
• Add Markdown formatted README (cd5475b)
• Update module template (db57943)
• Formatting tweaks in tests folder (bf8fda3)
• Ignore .DS_Store files in UTF-8 test (6273fb1)
• Add missing style tests (6d3a4b1)
• Fix failing style tests (d841910)
• Fix failing tests (983967c)
• Update Zend Framework to 1.11.15 (d8c23ed)
• Add Travis CI testing (e7d5114)
• Update Markdown parser to 1.2.8 (ba81d0b)
• Update Zend RESTful Framework to 7ae983a5ca (8cbd95e)
• Remove unused Selenium libraries (2dfa502)
• Remove unused CMake file (877fb22)
• Add updated license header to KWUtils file (607179e)
• Correct spelling, grammar, and formatting on first installation page (a96afa7)
• Correct misspelling of connection action (6b66205)
• Correct misspelling of error component and fatal error (505852a)
• Consistently format ini files (3d21387)
• Cleanup install controller and use PDO to test database connectivity (e3cc6a7)
• Update UtilityComponent to use PDO (785e63d)
• Add missing license headers (2f5301b)
• MySQL blob or text fields cannot have a default value (108fd90)
• Small tweaks to some SQL scripts (5dee536)
• Tidy index page and do not require log directory to be writable (cfae682)
• Enable use of memcache (5fc1d3c)
• Tweak logging to set correct levels for development and production (6ddeb3d)
• Update more license headers and tweak arrangement of files (ffb2ddc)
• Update PHPUnit to 3.5.15 (1f7117d)
• Remove unused files (a9d1820)
• Add more style tests (584ce1d)
• Tweak trailing whitespace test so that fails if file does not exist (ff58016)
• Fix failing style tests (5743275)
• Tweak creation of config file and layout of some files in tests folder (78a5a6a)
• Consolidate PHPUnit libraries into one folder (24621fc)
• Move customized test files out of library and tweak naming (831c158)
• Add basic composer.json file (ea42a6d)
• Add Vagrant and Ansible configuration (d8c297e)
• Tweak .gitignore (55f6ab7)
• Refactor config files path (4e7bad9)
• Refactor log files path (e58c28d)
• Remove obsoleted utilities (bbc020d)
• Fix file permissions (befe626)
• Update Zend Framework to 1.12.7 (f1a0c26)
• Remove redundant PHPUnit files (5e80d04)
• Add extensions and archive to composer.json (33e2aec)
• Update PHPUnit to 3.7.35 (778723a)
• A debug flag to preserve PHPUnit output behavior across versions (12bb1ad)
• Fix failing tests (d944bf7)
• Fix PHP warning on every request (afcd2ce)
• Fix log path and logging priority for tests database setup (3661f98)
• Remove ob_end_clean() sledgehammer (3a6d059)
• Fix spelling on installation page forms (fed27d7)
• Remove duplicate smartoptimizer (108b2c1)
• Minor tweaks to smartoptimizer (ed3490f)
• Allow for custom data and temp directories (ce47c9e)
• Relax some of the checks for writable folder and enabled modules (342a576)
• Tweak memcache initialization (4b72160)
• Check private modules folder actually exists (63e7d9b)
• Tweak logging initialization (b04473c)
• Fix caching (40234c8)
• Remove trailing spaces (d11847a)
• Be consistent with capitalization of PDO driver names (dcb26ac)
• Add support for socket connections to databases (2be8d79)
• Remove trailing spaces and cleanup some ini files (cfdb680)
• Allow writable folder locations to be specified by environment vars (64851b7)
• Add app.yaml and php.ini for Google App Engine support (6b0c3b3)
• Wrap set_time_limit for instances when it is disabled (0dce3c9)
• Remove trailing space (668fc94)
• Fix display of disk space when necessary functions are disabled (844a7c6)
• Fix warning on querying module.ini files for certain filesystem types (0ac0fba)
• Remove redundant config controllers (9fd8462)
• Add back button to some config pages (30554c2)
• Fix dashboard using wrong data directory (a788b0f)
• Add more time zones (45cfa4a)
• Tweak memcached settings (7910a39)
• Apache 2.4 and PHP FPM support (ac535d2)
• Replace short PHP tags (aaf1068)
• Add missing SQL implementations (1087892)
• Add sample configuration for task scheduler module on App Engine (f16b8de)
• Various utility component fixes (538891b)
• Refactor and fix the writing of config files (0d3a335)
• Fix failing tests (2f0df14)
• Replace rand() with mt_rand() (132c42b)
• Add App Engine email support (43214b9)
• Beautify JS (7eac052)
• Beautify Java (51b1429)
• Beautify CSS (d0b01af)
• Add missing generic font (f94ebd0)
• Remove redundant px unit on zero values (651c42e)
• Remove duplicate and simplify some CSS properties (ef911d2)
• Change MIDAS to Midas Platform and fix some URLs (68d041d)
• Update PHP Markdown to 1.4.1 (6778a25)
• Tweak zipstream naming to match Packagist (9565412)
• Remove phantom PHP folder from PHPCheckstyle source (aa9231d)
• Fix failing tests relating to licenses controller (91489b5)
• Fix result of void function used (e1499e2)
• Update outdated file headers (fce7084)
• Add UTC to list of time zones (6534446)
• Allow zero length links (0adfe9e)
• Allow solr module to index and search metadata fields that contain spaces (a980789)
• Replace deprecated functions (7456179)
• Remove redundant local variables (b36ffe8)
• Remove some redundant closing tags (ca87d40)
• Fix calls to preg_split in googleauth module (f8b9ceb)
• Simplify JS if statements and remove unecessary return statements (353c0a1)
• Remove redundant CSS units (75e87fd)
• Simplify CSS properties (ba3f20a)
• Remove unnecessary .gitignore entries and files (a9d9e66)
• Correct some spelling mistakes (2850638)
• Remove unused private functions (83acfcd)
• Remove redundant notification manager classes (e748c6d)
• Remove empty files (38b5f54)
• Correct typo in dashboard model in validation module (69ff9b5)
• Remove redundant or empty index controllers and actions (5a71431)
• Remove empty functions in subclasses that override empty functions (d98cd5b)
• Tweak logging priorities to improve production performance (26be3db)
• Tweak translator loading to improve performance when translation is not required (f7161fe)
• Remove strange example module test from validation module (ba408ff)
• Fix MIME type computation (ebb0403)
• Delete some redundant files (0accfe5)
• Default environment to production to improve performance/security for forgetful admins (e40274f)
• Remove broken MongoDB support (5a9bae1)
• Fix capitalization in sidebar (6ee4182)
• Make spelling of "email" consistent (b4987dd)
• Fix capitalization of "API" and some form labels (c4fc33f)
• Replace deprecated functions (8e6cc4f)
• Remove duplicate keys in MIME types array (0a5a9ea)
• Remove redundant commas and semicolons in JavaScript (43bbc70)
• Fix syntax errors in SQL (c738989)
• Add missing comma in PHP file in visualize module (52df76c)
• Tweak some empty HTML elements (ee666f1)
• Remove some redundant local variables (5c0c37f)
• Fix some spelling mistakes (ad6f546)
• jQuery performance improvements (877dacc)
• Fix obscure error when an invalid controller is specified while logged in (c59f877)
• Fix Darwin/Windows issue with task scheduler server load function (4d455ec)
• Fix no default value for module logger error and log priority undefined error (0429b26)
• Cleanup up dead code and database tables from task scheduler (a81f794)
• Add an API method for searching by item and folder name (d59fd04)
• Add API method to search for item by name and folder id (3f0ddb0)
• Add method to get all scalar DAOs for a submission in the tracker module (1a4808e)
• Upgrade XML_Parser and XML_Serializer in api module to latest versions (73288f4)
• Add use strict and some missing semicolons to JS (054666c)
• Reformat tree table JS (9c1072e)
• Move Java and Python source files out of web accessible locations (ff126a1)
• Update phMagick to latest version (8b0ce9d)
• Add SCSS files (6d6e43e)
• Add scssphp and remove smart optimizer (d309d81)
• Add some Bourbon and mix (abfaa2c)
• Add normalize.scss (c1403ae)
• Fix style issues with bootstrap (0775dfa)
• Add compiled CSS files (48f27ef)
• Minify third-party CSS files (6593276)
• Cleanup layouts (4518cfa)
• Remove some superfluous echo time() (d1add32)
• Various HTML fixes (bd12e49)
• Remove empty constants files (96eb2f7)
• More JavaScript cleanup (b254427)
• Remove a stray echo shorthand tag (d961d2b)
• Add style tests to googleauth module (893ebf5)
• Remove executables from repository (a07a658)
• Normalize capitalization on admin form (6e58020)
• Refactor Java upload and download applet into a module (41b8b3a)
• Remove Flash uploader for security reasons (0b674a6)
• Refactor demo mode into a module (ed304f3)
• Remove unimplemented Amazon asset store (01d6ddd)
• Replace use of tempnam, which is unavailable on App Engine (25f836f)
• Fix new revision upload to use same mechanism as new item upload (d8be385)
• Audit and reformat code for PSR-2 compliance (4e4a301)
• Fix upload/download controller tests (11e9d50)
• Fix incorrect database extension check in install controller (c604f5c)
• Fix regex for validating administrator email addresses and an issue with AJAX call detecting database connection (742e4e9)
• Refactor LDAP module to use utility component for email (dc76079)
• Encode filenames sent from upload form (92c4f28)
• Refactor Google OAuth module to not require curl (cfed6eb)
• Manage third-party dependencies with Composer and Packagist (f7cd291)
• Disambiguate module test names and add support for using PHPUnit without CTest (09ad2e3)
• Fix style issue in ldap notification (deb16f9)
• More PSR-2 and other style fixes (64557aa)
• Remove old-style coverage tests (30fab4b)
• Collapse the many style tests into a few less (df0313d)
• Add Coveralls configuration (6c978ee)
• Cleanup database files and add SQLite support (f48bec7)

Jean-Christophe Fillion-Robin (3):

• Use explicit error message in Midas loader. (054f3bf)
• Fix midas.empty css and js (5c43a65)
• Fix scrolling when no layout is used. See #5 (2da032d)

Julien Jomier (1):

• one 's' too many (001d98b)

Michael Grauer (5):

• Deprecated old API, corrected item.getmetadata rest comments. (1b9cac1)
• Added rest user methods tests. (b4da867)
• Fix style errors. (c5d197e)
• Fix missing load. (b71b140)
• Fix for mysql midas clean install on folder table. (08092f9)

Patrick Reynolds (43):

• Starting to clean up return types. (5116b08)
• Fixing the output on several types. (0b875f2)
• Fixing style tests from anonymous functions. (f71faf3)
• Adding a get for itemrevisions and fixing group output. (96f89cf)
• Fixing the item rename (for counting). (b008243)
• Fixing the upload tokens and output encoding. (ae02e71)
• Only check for duplicate siblings on folder add. (6038728)
• Removed unnecessary component loading. (db5cd7e)
• The addItem call was not saving the revised item name. (7343128)
• Fixing the upload link controller. (58c01ed)
• Fixing date formating and whatnot make MySQL happy. (94ce00b)
• refs #1027 Adding radius server configuration to mfa admin config tab. (ab6a7de)
• Adding some documentation and headings to the config page. (9c2e607)
• Fixes a failing test due to bad notifier in registry. (05a38e0)
• Adding fixes to harden and generalize the mfa module. (f36be0a)
• Adding a first cut at folder readme support. (ccd3dc3)
• Adding the readmes to the community view. (33fd506)
• Fixing style issues in the readmes components. (5ccb45e)
• Adding tests for the readmes api calls. (973d592)
• Adding better dashboard and config for DICOM Extractor. (43a27ba)
• Adding markdown interpretation. (dcc886e)
• Fixing a bug resulting from an extra api config parameter. (2e25bb6)
• Fixing bug in solr notification. (8ae7ffe)
• Updating the dicomanonymize plugin to use the latest version of CTP. (c465928)
• Better styling on the DICOM upload tab. (3118743)
• Defaulting to 'upload here' if the user is on a folder view. (b3dba17)
• Adding a downloadObject class for plugin customization. (9d09ab7)
• Sign with a newer self-signed cert. (f7013df)
• Fix linked item support to handle https and bitstream download clicks. (8fe66c4)
• Zach suggest the better regex. (9ea1151)
• Missed a regex. (4822bd8)
• Fixing scalar detail back-button bug. (512060b)
• Moving the license controllers and views to licenses to fix admin console. (b34ec76)
• Alphabetically sort scalars. (806cbc9)
• Sort in producer view. (f0fbdd2)
• Making producer selection consistent. (ad1d062)
• Sort scalar items by label (4a2b4bf)
• Properly supporting branch trend removal. (845947d)
• Adding a callback for adding to the scalar detail view. (5b2b3fe)
• Fixing upgrade script on tracker with MySQL 5.6.20 (5186a3b)
• Adding SMTP configuration options. (22b81c9)
• Fix style issue in UtilityComponent. (6d6a530)
• Updating CTP to latest version for DICOM Anonymizer. (3b7f652)

Yuzheng Zhou (23):

• Added RESTful Web APIs. Added RESTful api documents sample using Swagger (19afa97)
• Moved userapi and token models to core; moved authentication component to core. (d65efd4)
• Fixed the response in html format. (a7cb325)
• Create API docs using Swagger UI (1a37873)
• Minor changes on Swagger UI. (0796d95)
• More UI changes. (ed429f2)
• Fixed the expand/collapse operations for non-core module APIs. (89cac1b)
• Moved more existing apis to new REST apis (e7aa956)
• Moved all the remaining apis (in api module) to core. (cccee69)
• Make some module APIs accessible for REST API. They are also the samples for other module apis. (613a56f)
• Extended test framework for testing rest apis; move api related callbacks from api module to core. (156f33f)
• Move the apikey controller out of restapi module. (4dd7199)
• Split Apicomponent to multiple components. (944a529)
• Provide back compatibility for existing apis after Apicomponent is splited. (c6e13bd)
• Added solr advancedSearch to Restapi. (66b9a21)
• Fixed #0996 (community search doesn't work for name), plus minor style fixes (227de6e)
• Updated return type for solrsearch API to be consistent with itemGet API. (0c4b7f0)
• Remove the only left update clause of mysql date_update columns (c561e50)
• Save folder description when folder is created. (2eab3ce)
• Support folder search in Solr module. (2aee765)
• Fixed the "module not supported in windows" message shown in a Linux server. (641f42e)
• Fixed the DICOM Server status in dashboard. (98ed065)
• Fixed the DICOM Rest API. (bad2ddc)

Zach Mullen (133):

• Add callback hook into api authentication component (f28a4bd)
• Db, models, and api auth callback handlers for oauth module (cebe822)
• Add grant authorization endpoint (aad45b0)
• Give proper names to tab anchors in user settings page (9d73e29)
• User settings page for managing oauth clients and auths (2ef9a20)
• Allow all valid HTTP 400 series codes to be passed through (9c94e7f)
• Redirect in access denied or malformed request condition (261d7d4)
• Implement oauth2.0 token endpoint (f1c7629)
• Map api endpoints to semantic permissions scopes (3d173e1)
• Ability for users to de-authorize tokens via the UI (6f1f1cc)
• Delete client implementation (de73e66)
• Add authorize endpoint testing for oauth module (6b84fc5)
• Add token endpoint testing (d891447)
• Test token deauthorization (f195e4b)
• Minimal skeleton and config controller for pvw module (e807dea)
• Added instance model and db table (2aa414c)
• Upgrade jquery and its plugins to 1.8 compatibility (8bab69c)
• Fix qtip to use stable version (248297f)
• Update our catcomplete custom code (4add217)
• Can now interact with a session (no data yet) (392e499)
• Added port resource pool allocator (cae1f1f)
• Fix failing style test (b7d9673)
• Swagger docs should be centrally registered (70b7ba0)
• Symlink the item and expose it to pvpython instance (8ab9d55)
• Enable basic volume rendering in midas.py app (cfc6dd5)
• Properly setup camera position for VR (bf3c87f)
• Enable camera preset button functionality (34b5ce7)
• Upload applet fixes (505defe)
• Fix session management for java uploader (9ba7639)
• Fix failing tests (b36975a)
• Java upload/download applet improvements (02c1f8d)
• Upgrade dotdotdot plugin for jquery compatibility (eef092c)
• Upgrade qtip (again) to fix text input bug (0dc241b)
• Fix keyfiles out of memory bug (5c1944f)
• Pass callable by reference to further reduce memory use (ba62fe7)
• Remove memory limit on hierarchy-traversal actions (83a64db)
• refs #997 #1000. Upload the selected directory as the top level (7d420b7)
• Load session when page loads (5947fe8)
• Add option for secure visualization (447edda)
• Make extract subgrid work (bde61ce)
• Enable scalar opacity controls (e65c69c)
• Enable scalar color mapping (same as the old way) (cf2814b)
• Accomodate port range settings (2072d18)
• Basic slice view functionality (aee5db6)
• Window/level and slice controls for slice viewer (8dc741e)
• Admin pvw instance management page (3bb3ced)
• Surface viewer (81f1f1a)
• Re-enable optional WebGL viewer for surface models (2c9e5a8)
• Add instructions link for interaction help (74ca34d)
• Fix admin dashboard static content dir entry (b032242)
• Add DISPLAY env var config parameter (8184b48)
• Add rudimentary security to pvw sessions (04834b8)
• Fix a couple of broken deprecated api calls (f675038)
• Add instance info to the info API method (cc96f12)
• Enable background color selection (a1a430a)
• Fix add metadata javascript crash (963c42f)
• Ability to include secondary meshes in scene (528b7df)
• Add surface slicing capabilities to slice viewer (52dffb8)
• Add simple locking mechanism to slice/window updating (088743c)
• Add color transfer function preset capability to volume view (fad70bb)
• Extract subgrid: init to current subgrid state (fe32c57)
• Properly use extent instead of bounds for slicing (fe8b45f)
• Fix jerky sidebar scrolling (262a54d)
• Remove json_encode from error output method (0896c2b)
• Add community callbacks for actions and deletion (ba0a225)
• Use new modular app, and use WAMP authentication features (21245a6)
• Enable point selection in slice view (851a733)
• Remove view init code from initialize method (9fad44d)
• Fix encoding bug when no scopes passed to authorize ctrlr (ded8f1e)
• Rudimentary session sharing feature (64d7d48)
• Fix point selection after changing slice (81d08e0)
• Remoteprocessing should not depend on visualize (10c02d1)
• Don't use base64 for random string (a2e409c)
• More granular repository browser URL settings (7d562c1)
• Don't use core authentication if module auth enabled (b9b1dc4)
• More fixes for upgrade process (2a77257)
• Fix API resource download redirects (d453227)
• Fix folder download containing empty items (9998fce)
• Move inactivity timeout code to common js (ae182df)
• Don't fetch folder sizes (a42e676)
• Human readable sizes in info panel (480150b)
• Refactor to support vtkWeb API changes (754baed)
• Set initial pid value, broke on mysql5.6 (3636ba2)
• Fix date format for mysql 5.6 (cf57855)
• Put some -- where size used to be. (3b772f6)
• Support latest PVW python API (419a96a)
• Replace simple uploader with a new HTML5 uploader (9ab882c)
• Fix small progress reporting bug (541c8b7)
• Fix UI behavior when validating files to upload (3451889)
• Enable resume of a partially completed upload (0cccff3)
• Uploaded items should inherit parent permissions (50c6f93)
• Add optional build result link to the scalar data model, and expose it via the API (63e1bfc)
• Add support in batch scalar upload endpoint for build result URL (e6a3682)
• Show build result link on scalar details view if it is set (03da3c4)
• Show unofficial submissions to all users, not just the user who submitted it (819b6ae)
• Frontend controls for toggling visibility of unofficial scalars (54d1623)
• Change to "applet" tag, otherwise applet wouldn't load for me (1f0f2b6)
• Add "branch" field support in data model and web API (2518e4c)
• Show branch name in scalar details view (da095d9)
• Add ability to filter trend view by a branch name (ee0c33a)
• Make trend chart take up full width of container (883426d)
• Allow filtering scalar results by branch in the pdo layer (2355833)
• Initial google oauth module with basic config in place (eb0579a)
• Google OAuth workflow, part 1: link to authorization consent (a46b05b)
• We now successfully get the user info from the g+ api (8679bf7)
• Working end-to-end google oauth login (014e708)
• Remove tests dir (oops) (669c15d)
• Add missing license header (dda4b79)
• Add docstring, remove unnecessary gitignore (84d011d)
• Add missing docstrings (869912c)
• Add missing license header (5430304)
• Add missing license header (a448016)
• Remove useless translation file (1bc16c4)
• Respect closed registration setting in googleauth module (eb0e75c)
• Allow users to be created without a password, to support inviting users via OAuth (af601f1)
• Fix failing style test (12f984f)
• Use the long-duration cookie for users logging in with google oauth (3db97dc)
• Fixes #30 Typo caused undefined var bug when googleauth module is off (04c4119)
• On googleauth login, redirect user to the page they were previously on (bc733f6)
• Combo box selection for branches in trend view (31c7913)
• Fix thumbnailcreator breakage resulting from refactor (83bae7e)
• Allow multiple branch selection on trend view page (32b0482)
• Modernize style of trend jqplot rendering (ed32e40)
• Remove shadows from markers in trend view plot (b12236d)
• Some more style tweaks to trend plot (12cdaa2)
• Fix failing white space style test (ebfb370)
• Address QA feedback (f2efd5d)
• Add blob fields for extra params and URLs (543c4f0)
• Support new scalar fields in controller layer (d9a7b3d)
• Display extra links and params on the scalar details page (e9d5896)
• Fix bug when no extra urls exist on scalar (41fb920)
• Support data click event in multiple branch trend case (f076c69)
• Fixes #33. Use session token for googleauth login to protect from CSRF (b48e17c)