- GUIDE-748: added pid similarity warning and error (Timo Wiese)
- GUIDE-752: refactored submission summary page (Timo Wiese)
- GUIDE-702: implemented a cron job to add OTP projects to ILSe (Oydin Iqbal)
- GUIDE-751: refactored feedback form for better user interaction (Timo Wiese)
- GUIDE-749: fixed file is readable icons and test on read only page (Timo Wiese)
- GUIDE-740: changed mail sending recipients in submission process (Timo Wiese)
- GUIDE-746: added pid suggestion to edit page (Timo Wiese)
- GUIDE-706: show adapter sequences for library preparation kit (Oydin Iqbal)
- GUIDE-727: Adapted library preperation kit column for nanopore submissions (Tim Lorbacher)
- GUIDE-728: made tests faster by using the ExtendWith annotation (Oydin Iqbal)
- GUIDE-741: Adapted the Feedback Overview Page (Tim Lorbacher)
- GUIDE-744: Restructured the SeqType overview page to show all options (Oydin Iqbal @iqbalo)
- GUIDE-747: refactored and improved table import (Timo Wiese)
- GUIDE-734: run all validation on page load (Tim Lorbacher)
- GUIDE-745: added send mail check to ticket creation method (Timo Wiese)
- GUIDE-742: make user token visible for users in the GUI (Tim Lorbacher)
- GUIDE-710: implemented functionality that groups together fastq file pairs within submissions with each save (Oydin Iqbal)
- GUIDE-738: implemented a new project overview API (Timo Wiese)
- GUIDE-723: improved sample type category code and remove default value (Timo Wiese)
- GUIDE-726: fixed mails for job states to ignore stopped samples (Timo Wiese)
- GUIDE-737: fixed bug related to 'logged-in status' appearing after server restart (Gregor Warsow)
- GUIDE-732: added timestamp to the name of external metadata tables when written to the file system (Oydin Iqbal)
- GUIDE-736: Fixed false throwing of error "Submission isn't empty" when uploading a submission (Oydin Iqbal)
- GUIDE-714: enable additional table headers for allowed organizational units (Timo Wiese)
- GUIDE-724: deleted bidirectional links from entities (Timo Wiese)
- GUIDE-730: preparation for open source (Timo Wiese)
- GUIDE-729: added ability to make parser components optional (Timo Wiese)
- GUIDE-719: removed merging instructions from 'Submission has been validated' mail (Gregor Warsow)
- GUIDE-722: create a new ticket with REST API to receive a ticket number (Timo Wiese)
- GUIDE-725: added open to all scheduled tasks (Timo Wiese)
- GUIDE-363: added selection for sample type category (Oydin Iqbal)
- GUIDE-449: Implemented that unfinished external submissions will be removed after 90 days (Oydin Iqbal)
- GUIDE-718: added projects to transferred mail (Timo Wiese)
- GUIDE-713: implemented a new API to be able to import submissions (Timo Wiese)
- GUIDE-709: changed species column's explanation text (Oydin Iqbal)
- GUIDE-712: forwarding to the overview with save and exit (Timo Wiese)
- GUIDE-711: added missing catch to handle not mappable column headers (Timo Wiese)
- GUIDE-717: fixed that users can complete submissions with requested values (Timo Wiese)
- GUIDE-715: added the ability to build the guide into a docker container (Timo Wiese)
- GUIDE-700: added trigger endpoint to termination mail subject (Timo Wiese)
- GUIDE-411: created admin GUI for regex manipulation for the validation (Oydin Iqbal)
- GUIDE-705: changed cost center to organizational unit for queries to external metadata source (Timo Wiese)
- GUIDE-708: changed sample type input to convert all letters to lowercase (Timo Wiese)
- GUIDE-668: implemented functionality that users can request SeqTypes (Oydin Iqbal)
- GUIDE-397: converted library preparation kit text field to dropdown field (Oydin Iqbal)
- GUIDE-694: set GUID bit for folders to which tsv files are written out (Gregor Warsow)
- GUIDE-703: fix xlsx empty rows bug (Gregor Warsow)
- GUIDE-354: users can upload external submissions themselves (Timo Wiese)
- GUIDE-586: added new low_coverage_requested column in metadata (Oydin Iqbal)
- GUIDE-695: fixed wrong sample grouping on read only page (Timo Wiese)
- GUIDE-696: fixed wrong ONT paths in mails (Timo Wiese)
- GUIDE-697: Prevented loss of mails that encounter exceptions (Oydin Iqbal)
- GUIDE-699: fetch OE information while initializing Person object; respect accountDisabled status from LDAP (Gregor Warsow)
- GUIDE-680: added server side speed improvements and some refactoring (Timo Wiese)
- GUIDE-691: rows containing data but no fastq filename are no longer skipped, instead an exception is thrown (Timo Wiese)
- GUIDE-692: fixed error message if uploaded files have the wrong format or are not valid (Timo Wiese)
- GUIDE-623: made all mandatory metadata required in external data submission (Oydin Iqbal)
- GUIDE-677: receive organizational unit and organizational unit leader from external api (Timo Wiese)
- GUIDE-687: Send mail when submission was deleted (Oydin Iqbal)
- GUIDE-686: Fixed the deletion of extended submissions (Oydin Iqbal)
- GUIDE-690: fixed api responses against otp can be empty (Timo Wiese)
- GUIDE-548: combined instrument with sequencing kit (Timo Wiese)
- GUIDE-666: Added link to Project Config page in OTP (Timo Wiese, Oydin Iqbal)
- GUIDE-679: Added indicator whether files are readable on transfer (Timo Wiese)
- GUIDE-355: Added working name and comment for extended submissions (Oydin Iqbal)
- GUIDE-682: Changed comment field to only accept certain characters (Oydin Iqbal)
- GUIDE-685: Added field status to ilse import object (Timo Wiese)
- GUIDE-683: Do not write out the UUID column in the exported TSV (Timo Wiese)
- GUIDE-684: Do not export stopped samples (Timo Wiese)
- GUIDE-648: implemented functionality that customers can request values (Oydin Iqbal)
- GUIDE-661: Created reset termination timer button (Oydin Iqbal)
- GUIDE-675: limited finished submission to the latest 100 (Timo Wiese)
- GUIDE-676: fixed UnsupportedOperationException while saving submission (Timo Wiese)
- GUIDE-678: Fixed bug OTP expects a space between species scientific name and strain (Oydin Iqbal)
- GUIDE-681: Fixed bug when requesting new species with mixed-in species (Oydin Iqbal)
- GUIDE-674: improvements for cluster job feature (Timo Wiese)
- GUIDE-370: added reminder mails for external submissions (Timo Wiese)
- GUIDE-671: added ability to register a ticket number via API (Timo Wiese)
- GUIDE-667: added ability to configure and run multiple dependent cluster jobs (Timo Wiese)
- GUIDE-573: Increase test coverage to 90% (Oydin Iqbal)
- GUIDE-673: increased json file size (Timo Wiese)
- GUIDE-172: added cross guide submission merging check (Timo Wiese)
- GUIDE-647: added functionality to proceed with requested values (Timo Wiese)
- GUIDE-654: added possibility to run cluster jobs (Timo Wiese)
- GUIDE-672: Provide URL to fetch originally imported JSON (Gregor Warsow)
- GUIDE-665: removed unknown values from external data export (Timo Wiese)
- GUIDE-669: added ability to import and export different properties (Timo Wiese)
- GUIDE-670: fixed project prefixes from closed projects not being found (Timo Wiese)
- GUIDE-631: simplified and cleaned up merging candidates (Timo Wiese)
- GUIDE-656: introduce OTP adapter (Timo Wiese)
- GUIDE-660: Simplify getter for baseMaterial (Oydin Iqbal)
- GUIDE-664: new mail layout (Timo Wiese)
- GUIDE-662: fixed that new samples could not have more than one species (Timo Wiese)
- GUIDE-663: Change toString method of sequencing type (Oydin Iqbal)
- GUIDE-646: Create table and GUI for newly requested values (Oydin Iqbal)
- GUIDE-657: added possibility to mark the news link with red dot (Tim Lorbacher)
- GUIDE-568: merge columns highlighted (Timo Wiese)
- GUIDE-563: Add project form link if no project is selected (Oydin Iqbal)
- GUIDE-640: Introduce logfile for mails and shorten the main logfile (Oydin Iqbal)
- GUIDE-659: fixed csv import bug (Timo Wiese)
- GUIDE-555: Show old/current parser upon editing (Tim Lorbacher)
- GUIDE-137: Check whether the selected project contains human or mouse data (Oydin Iqbal)
- GUIDE-527: adapted sorting on read only page (Timo Wiese)
- GUIDE-622: Improved CSV import (Oydin Iqbal)
- GUIDE-625: authorization for page providing users to be notified for given project is now possible via token (Gregor Warsow)
- GUIDE-652: Updated information texts for validation columns (Oydin Iqbal)
- GUIDE-655: do not send empty feedback mails (Timo Wiese)
- GUIDE-643: implemented validation level to gui and server-side validation (Timo Wiese)
- GUIDE-644: added entity cluster job (Oydin Iqbal)
- GUIDE-572: increase test coverage to 80 percent (Timo Wiese)
- GUIDE-653: made project path accessible via token (Tim Lorbacher)
- GUIDE-651: Do not send empty on-hold reminder mail (Oydin Iqbal)
- GUIDE-621: added validation level and sequencing technology to submission (Timo Wiese)
- GUIDE-599: Added information texts, mouse overs and error messages for parser feature (Oydin Iqbal)
- GUIDE-602: Make parser available for ILSe submission (Oydin Iqbal)
- GUIDE-645: adapted import and made it more robust (Timo Wiese)
- GUIDE-649: Include link to news page in header (Oydin Iqbal)
- GUIDE-626: Added reminder mail when submission is on hold for more than 48h (Oydin Iqbal)
- GUIDE-630: cleanup backend functions (Timo Wiese)
- GUIDE-634: creation of tests for metadata merging (Timo Wiese)
- GUIDE-598: terminate open submissions 90 days after external data availability (Timo Wiese)
- GUIDE-635: fixed merging warning with stopped samples (Timo Wiese)
- GUIDE-571: increase test coverage to 70 percent (Timo Wiese)
- GUIDE-619: added entity sequencing technology (Timo Wiese)
- GUIDE-557: projects not registered in otp will no longer be imported (Timo Wiese)
- GUIDE-613: improved loading speed of details pages and change of the dropdowns appearance (Timo Wiese)
- GUIDE-628: added ability to add sequencing types without displaying them (Timo Wiese)
- GUIDE-616: fixed problems after releasing external data feature (Timo Wiese)
- GUIDE-173: excluded internal columns from export (Timo Wiese)
- GUIDE-540: use Spring 5 WebClient instead of BufferedReader to read from ilse api (Timo Wiese)
- GUIDE-618: get rid of log messages for anonymous user (Timo Wiese)
- GUIDE-614: Added code documentation for Services (Oydin Iqbal)
- GUIDE-627: provide content of submission received mail for autoclosed submissions as appendix in FinallySubmittedMail (Gregor Warsow)
- GUIDE-604: make ILSe Api accessible via token (Gregor Warsow)
- GUIDE-608: make Fasttrack known to Guide (Tim Lorbacher)
- GUIDE-610: Inform Operator about Fasttrack Submissions (Tim Lorbacher)
- GUIDE-615: simplify originProjectsSet (Tim Lorbacher)
- GUIDE-629: do not set submission on hold if species is 'OTHER' (Gregor Warsow)
- GUIDE-620: added entity validation level (Timo Wiese)
- GUIDE-608: make Fasttrack known to Guide (Tim Lorbacher)
- GUIDE-591: fixed server validation for maximum length of PID (Gregor Warsow)
- GUIDE-522: base_material column for export (Tim Lorbacher)
- GUIDE-617: fixed broken user overview (Timo Wiese)
- GUIDE-310: registration mail for uploaded submission (Tim Lorbacher)
- GUIDE-489: implemented the feature to add or remove lines on the extended page (Timo Wiese)
- GUIDE-503: New Page for external Feature (Timo Wiese)
- GUIDE-545: fixed 'back and edit' button and otp merged samples on external data feature (Timo Wiese)
- GUIDE-546: adapted validation regexes and descriptions (Timo Wiese)
- GUIDE-425: Implemented unvalidated deletion of submissions and catching of duplicated md5-sums at TSV-Upload (Oydin Iqbal)
- GUIDE-606: disabled json extraction for auto-closed submissions (Gregor Warsow)
- GUIDE-611: Make the sending of mails asynchronous (Oydin Iqbal)
- GUIDE-600: do not use empty PID for detection of similar PIDs; also show PID and sampleType in found-similar-pid email (Gregor Warsow)
- GUIDE-612: improved loading speed of statistic page (Timo Wiese)
- GUIDE-609: fixed javascript problems and introduced eslint (Timo Wiese)
- GUIDE-368: added species to edit pages (Tim Lorbacher, Oydin Iqbal, Timo Wiese)
- GUIDE-565: import species into guide (Tim Lorbacher, Oydin Iqbal, Timo Wiese)
- GUIDE-537: excluded withdrawn samples from the merging warning (Oydin Iqbal)
- GUIDE-601: created limited pool connections to external databases (Timo Wiese)
- GUIDE-605: fixed the ON_HOLD state setting the lock user (Timo Wiese)
- GUIDE-585: added new on hold state (Timo Wiese, Oydin Iqbal, Tim Lorbacher)
- GUIDE-603: make tomcat's maxParameterCount adaptable and add properties check on startup (Timo Wiese)
- GUIDE-206: added storage overview for organizational unit (Tim Lorbacher)
- GUIDE-595: empty SeqType is regarded as a valid value in client-side validation (Gregor Warsow)
- GUIDE-569: send mail if there are similar PIDs in different projects (Timo Wiese)
- GUIDE-531: perform json extractor script for auto closed submission (Timo Wiese)
- GUIDE-554: added delete button for last Parser Field Component (Oydin Iqbal)
- GUIDE-558: added delete function for Parser (Oydin Iqbal)
- GUIDE-590: use single cell from sequencing type instead of sample (Timo Wiese)
- GUIDE-577: Changed path from /icgc/dkfzlsdf/ to /omics/odcf/ in runJsonExtractorScript (Oydin Iqbal)
- GUIDE-587: always show back&edit button when the submission is active (Tim Lorbacher)
- GUIDE-582: removed unessesary empty row at the end of tsv file (Tim Lorbacher)
- GUIDE-584: fixed project selection while uploading tsv by admins (Timo Wiese)
- GUIDE-594: Fixed read-only-page if no sequencing type is given (Oydin Iqbal)
- GUIDE-596: fixed error on details page if server side validation failed (Timo Wiese)
- GUIDE-478: get storage sizes from isilon database (Timo Wiese)
- GUIDE-588: use correct subject for json extraction / merging mails to ticket system (Gregor Warsow)
- GUIDE-580: added average feedback for feedback overview (Tim Lorbacher)
- GUIDE-501: handle proceed stop flag from GPCF (Timo Wiese)
- GUIDE-578: send mail when submission is terminated (Oydin Iqbal)
- GUIDE-515: added initial admin statistics (Timo Wiese)
- GUIDE-564: adapted otp query to handle new project fields structure (Timo Wiese)
- GUIDE-499: adapted summary page so that it hides unnecessary columns (Timo Wiese)
- GUIDE-561: fixed reset of empty submissions (Gregor Warsow)
- GUIDE-574: fixed reminder mails and overview for new unlocked state (Timo Wiese)
- GUIDE-482: trigger table merging after setting data received via GUI (Timo Wiese)
- GUIDE-568: fixed response if mails cannot send while importing (Timo Wiese)
- GUIDE-575: fix final submit mail for auto closed submissions (Timo Wiese)
- GUIDE-509: prevented that admins and users can write data at the same time (Timo Wiese)
- GUIDE-562: Added final submit user to finally-submitted-mail (Oydin Iqbal)
- GUIDE-567: renamed reset button for ilse submissions (Timo Wiese)
- GUIDE-486: improved submission overview loading time and made it asynchronous (Timo Wiese)
- GUIDE-427: implemented the possibility to import from midterm (Timo Wiese)
- GUIDE-502: added imprint to footer (Oydin Iqbal)
- GUIDE-559: adapt link to ABT registration in OTP (Oydin Iqbal)
- GUIDE-560: prevented injection of illegal projects via tsv upload (Timo Wiese)
- GUIDE-365: Parser in Guide (Oydin Iqbal)
- GUIDE-446: Add parseIdentifier to Sample (Oydin Iqbal)
- GUIDE-514: Add parser tables to the database (Oydin Iqbal)
- GUIDE-516: Parser Overview for Admins (Oydin Iqbal)
- GUIDE-517: Adding of Information Page for Parsers (Oydin Iqbal)
- GUIDE-518: GUI page for admins to add a new Parser (Oydin Iqbal)
- GUIDE-519: GUI page for admins to edit a Parser (Oydin Iqbal)
- GUIDE-520: Add functionality to apply parser on a submission (Oydin Iqbal)
- GUIDE-551: added project import aliases to unknown project detection (Timo Wiese)
- GUIDE-549: Handle saving of Index Type correctly (Oydin Iqbal)
- GUIDE-402: implemented check if sample data from guide and gpcf has inconsistency (Timo Wiese)
- GUIDE-403: expanded fastq file name to absolute path (Timo Wiese)
- GUIDE-529: updated expected path to new path logic and fixed antibody target issue (Timo Wiese)
- GUIDE-525: do not show xenograft value for sample data from OTP (Timo Wiese)
- GUIDE-544: Handle empty sequencing type on the read only page correctly (Oydin Iqbal)
- GUIDE-543: Bug fix - Finally Submitted page was shown even when the submission was not finished yet (Oydin Iqbal)
- GUIDE-456: changed fastq file name to fastq file path (Timo Wiese)
- GUIDE-534: Prevented reopening a submission by clicking back and edit (Timo Wiese)
- GUIDE-539: Preventing the final submit of a submission in another state than VALIDATED (Timo Wiese)
- GUIDE-538: Fixed that some ilse api data was lost when saving via the gui (Timo Wiese)
- GUIDE-506: Merging Warning for external feature (Oydin Iqbal)
- GUIDE-500: Split submission into subclasses (Oydin Iqbal)
- GUIDE-528: Highlight columns on read-only page (Timo Wiese)
- GUIDE-536: Add 'proceed' from ILSe Api to known fields (Timo Wiese)
- GUIDE-524: disabled user sorting on the summary page (Timo Wiese)
- GUIDE-532: fixed bug which showed an error page after resetting a submission although reset ran through correctly (Gregor Warsow)
- GUIDE-523: merging warning did not work for xenograft samples (Gregor Warsow)
- added more documentation (Timo Wiese)
- GUIDE-428: export and import function for extended table (Timo Wiese)
- GUIDE-330: it is now ensured that all ssh errors are reported correctly (Timo Wiese)
- GUIDE-465: added regex to fastq filename (Timo Wiese)
- GUIDE-487: Improvement of merging warning (Oydin Iqbal)
- GUIDE-479: added read lengths from ilse api and use them to decide if paired or single (Timo Wiese)
- GUIDE-504: all non ILSe submissions are now unresettable (Timo Wiese)
- GUIDE-512: reminder mails were not sent out (Gregor Warsow)
- added code style tool ktlint (Timo Wiese)
- GUIDE-511: make metadata folder group-writable (Gregor Warsow, Timo Wiese)
- GUIDE-237: Add GPCF Name(s) to SeqType (Oydin Iqbal)
- GUIDE-472: write out tsv to core filestructure (Gregor Warsow)
- GUIDE-505: handled invalide mail adresses and send the mail to all other recipients (Timo Wiese)
- fixed error page to display code and message (Timo Wiese)
- GUIDE-179: added data security statement (Timo Wiese)
- GUIDE-396: LibPrepKit and IndexType not editable for "samples" (Oydin Iqbal)
- GUIDE-421: Added Guide User for submitters without AD-account (Oydin Iqbal)
- GUIDE-450: Adapt Index Type for usage (Oydin Iqbal)
- GUIDE-451: md5 sum is now the anchor for files and no longer the name (Timo Wiese)
- GUIDE-469: increase test coverage to >40% (Timo Wiese)
- GUIDE-477: Implement API to Isilon (Oydin Iqbal)
- GUIDE-481: disabled regex check for reset, terminate and finished externally buttons (Timo Wiese)
- GUIDE-443: added new logo (Timo Wiese)
- introduce auto generation of changelog