Version Release Notes

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Note that for each release, only major changes impacting the user are listed. (Previous release notes)


How to upgrade a local instance of ATiM

  • Merge your local ATiM source code with the last tagged ATiM source code.
    • Compare the merged local ATiM source code with the last tagged ATiM source code.
    • Validate that only differences exists on Hooks, Custom codes, .htaccess (for some installation), Core.php file and Database.php file.
  • Create a local copy (Test) of your Prod ATiM database.
    • Execute 'atim_v2.x.x_upgrade.sql' script (one to many scripts have to be loaded according to the upgrade you are working on).
 mysql -u {user} -p {atimtest} --default-character-set=utf8 < atim_v2.x.x_upgrade.sql
  • Read the release notes plus the linked 'ReadMe.txt' file(s) for the all tags linked to your upgrade.
  • Using the ATiM Developer Tools (
    • List all custom codes/hooks you developed for your local installation and review all codes that has to be validated and/or modified (based on release notes).
    • Validate the database tables structure.
    • Create the 'custom_post_2xx.sql' script with custom SQL statements you have to execute on your database. Part of the statements could be generated using the 'FormBuilder' tool.
 -- -----------------------------------------------------------------------------------------------------------------------------------
 -- SQLs 1 to ...
 -- -----------------------------------------------------------------------------------------------------------------------------------
 -- -----------------------------------------------------------------------------------------------------------------------------------
 -- SQLs 1 to ...
 -- -----------------------------------------------------------------------------------------------------------------------------------
 -- -----------------------------------------------------------------------------------------------------------------------------------
 -- Version
 -- -----------------------------------------------------------------------------------------------------------------------------------
 UPDATE versions SET branch_build_number = 'xxxxx' WHERE version_number = '2.7.1';
  • Execute 'custom_post_2xx.sql' script.
 mysql -u {user} -p {atimtest} --default-character-set=utf8 < custom_post_2xx.sql
  • Test your upgraded test version
  • Create a backup of your Prod ATiM database and source code (to keep in a safe place).
  • Migrate in Prod
    • Replace ATiM source code
    • Execute 'atim_v2.x.x_upgrade.sql' (script(s)) and 'custom_post_2xx.sql' script on your Prod ATiM database.


Release Date: September 04th, 2018 SVN: Revision: 7393

See the ReadMe.txt file before any migration efforts.

  • Fixed issues and bugs (v2.7.1 Release's issues and bugs).
  • Improved Debugkit tool:
    • Log file part for debugging the last errors and warnings.
    • SQL Ajax queries.
  • Added upload file feature.
  • Added option to record any user log into a file on the server.
  • Developed LDAP authentication.
  • New features/designs:
    • Datamart/Report
      • Added option to complete reports with charts.
    • Inventory
      • New tool to create Collections Protocols (list of collections a participant is supposed to have).
      • New feature to set default values to all nodes (samples, aliquots) of a Collection Template.
      • New Sample and aliquot controls (Stool to Protein relationship, Xeno Buffy Coat, CD138, TIL [tumor infiltrating lymphocyte]).
    • Material
      • Activated the Material tool.
    • Order:
      • Added aliquot shipment code.
    • Storage
      • New feature to scan aliquot barcodes directly into a storage (box, etc).
      • New feature to set positions of all aliquots stored into a storage (box, etc) downloading a .CSV file with all barcodes and positions.
      • Upgraded the Manage storage types tool
      • Added option to invert the X and Y coordinates of a storage type.


Release Date: September 19th, 2017 SVN: Revision: 6858 (warning: tag revs = 6858 / trunk revs = 6857)

See the ReadMe.txt file before any migration efforts.


Release Date: February 2th, 2017 SVN: Revision: 6645

See the migration details before any migration efforts.

  • Fixed issues and bugs.
  • New features/designs:
    • Diagnosis, Annotation & Treatment
      • Added ICD-0-3-Topo Categories (tissue site/category).
      • Added CAP Report "Protocol for the Examination of Specimens From Patients With Primary Carcinoma of the Colon and Rectum" (version 2016 - v3.4.0.0)
    • Inventory
      • New Sample and aliquot controls(Buffy Coat, Nail, Vaginal swab).
    • Study
      • Investigator and Funding sub-models developed and linked to study tool.
      • New autocomplete field to select a study.
      • Study Model included into the databrowser.
    • Drug
      • New autocomplete field to select drug.
    • Storage and TMA Block
      • Separated TMA Block and storage for any search with the databrowser.
      • Developed TMA slide scoring system.
      • New autocomplete field to select TMA slide immunochemistry.
    • Order
      • New code to support TMA slide shipping.
      • A shipped item can now be defiend as returned to the bank.
      • OrderLine included into the databrowser.
    • Administration
      • New password management features to ban use of previous passwords and to allow users to reset a forgotten password.
      • Revised and upgraded system to create and manage user announcements.


Release Date: March 8th, 2016


  • Fixed issues and bugs.
  • New features/designs:
    • Display all batchsets in sub-lists to replace the 'filter' option: Temporary batchset, private batchsets, group batchsets and public batchsets
    • Participant message:
      • Batch creation
      • Migrate message's type list values to 'Dropdown List Configuration' tool
    • Data browser
      • Be able to search on either the TMA blocks used to create these slides or storages that contain these one from a TMA slides node


Release Date: October 20th, 2015


  • Fixed issues and bugs.
  • New features/designs:
    • Export storage layout in CSV
    • New batch action to create one internal use to apply to many aliquots
    • Order tool:
      • Order line optional and option configurable
      • Use 'addGrid' feature to create order lines and order items
      • Changed shipment creation re-directions
      • Added 'Order' object to databrowser
    • TMA
      • Use 'addGrid' feature to create TMA slide
      • Link TMA slide to study
    • Added an 'In Stock and Storage Data Update' form to complete data once and apply them to all used 'parent' aliquots in following batch actions:


Release Date: June 29th, 2015


  • Fixed issues and bugs.
  • New code to:
    • To customize new link between a study and type of record in a easy way (see function StudySummary.listAllLinkedRecords())
    • Allow users to link a study to a either participant identifier or a participant consent
  • New sample type : Xenograft derivatives (tissue, blood collected from animal plus all created derivatives (dna, rna, etc))


Release Date: March 16th, 2015


  • Fixed issues and bugs.
  • New code to:
    • Export ICD code description in CSV file
    • Limit the number of elements that could be processed in batch
    • Allow users to create treatment in batch and to display them in a detailed index view (as event)
    • Generate a report listing the number of elements (of a batchset or a databrowser node) per patient
    • Display any consent in Patient Chronology Form
    • Create drugs in batch
    • Display date of realiquoting and derivative creation in collection content tree view
  • New sample type : Xenograft and cord blood


Release Date: July 1st, 2014


  • Fixed issues and bugs.
  • Migrated to CakePhp 2.4.10.


Release Date: April 23th, 2014


  • Fixed issues and bugs.


Release Date: April 4th, 2014


  • Fixed issues and bugs.


Release Date: February 24th, 2014


In addition to bug fixes this version includes:

  • Clinical Annotation
    • Support for adding annotation events and family history records in batch
    • Display treatment precision (Drugs, surgical procedures) from diagnosis tree view
  • Inventory
    • New sample types: CSF and Saliva
    • User can now view aliquot uses from the collection tree view
  • Storage
    • New tool to allow users to create custom storage types (ex: new box format, etc)
  • Databrowser, Reports and Batch Sets
    • Add support for browsing on children and parent data (ex: List all DNA created from a particular tissue sample, list all primary diagnoses from a list of metastasis, etc)
    • Ability to browse on treatment precisions as chemotherapy drugs, surgical procedures
    • Format dates to be Excel compliant for any data export
    • Display the browsing steps (search criteria) for any 'Saved Browsing' query
    • Ability to launch data browsing or create a new batch set from report result set
    • New function to list differences between 2 batch sets or data browser node contents
    • New report to list all child storage entities contained within a storage entity (ex: all boxes, racks, shelves of one freezer)
    • New report to list all linked diagnosis events (primary, secondary, recurrence, etc) from one event of this diagnosis
    • Display main headers when joining many data browser nodes or exporting data to Excel
    • Allow user to add elements to a batch set even though the number of elements of the batch set is higher than the display limit
    • Allow user to launch some batch actions even if the number of elements of a batch set is higher than the display limit
  • Administration
    • Custom drop down lists are now grouped by category
    • New feature to block user or IP address after a set number of failed login attempts
    • Added configurable validation for password creation
    • Option to set time period after which user credentials will expiry and require a password update
  • Other Tools
    • Protocol - Add option to sort on protocol extend list
    • Study/Projects - Now able to view all records (aliquots, orders, shipments) linked to a study or project


Release Date: March 19th, 2013


  • Fixed issues and bugs.


Release Date: February 11th, 2013


  • Fixed issues and bugs.
  • Merged protocol details and extend forms.
  • Upgrade collection template creation to fix bugs.
  • Add tab labels in structure formats.
  • Cast search on participant identifiers to decimal when user search on range.


Release Date: September 13th, 2012


  • Fixed issues and bugs.


Release Date: August 17th, 2012


  • Fixed issue where a system error was displayed after deletion of a storage entity.
  • Fixed a bug where the user was unable to delete a collection to participant link.


Release Date: August 7th, 2012


This release contains over 200 improvements, bug fixes and changes from ATiM v2.4.3A. Highlights for this version include:

Bug Fixes

  • Fixed a bug where an ATIM install in the webroot folder would not allow the user to expand tree view child nodes or use coding tools.
  • Errors generated during re-aliquoting are now displayed correctly
  • Fixed issue where disabled sample types were still accessible through collection templates
  • Inactive collection templates will not be available for use by the user
  • Fixed an issue where date accuracy fields were not being set during batch actions
  • Date/time fields with 0 minutes will now save correctly
  • Fixed an issue where reproductive history records were unable to be deleted
  • Fixed how revision (audit trail) data is saved for master/detail tables
  • Improved/fixed specific styling issues with Internet Explorer and Firefox
  • Prevented a case where the user could click submit quickly many times and multiple rows would be created

New Features/Enhancements

  • New function to merge participant data and merge collections
  • Ability to create a batch set of aliquots from the shipping module
  • New export to CSV option where a 1..N relationship is present
  • Improved performance for views by optimizing queries
  • Added a main menu warning for all collections without linked consents
  • When mouse-over on an index line the row will now be highlighted
  • Automatic rebuild of language files and clear existing cache when ATiM updated
  • On session timeout, re-display any previously entered data after user unlocks application
  • Track date aliquot is moved from one storage entity to another
  • Any permission changes are now effective on save rather than logout/login
  • A CSV file can be generated for use with external barcoding software. Accessible from collection, samples, and aliquots


Release Date: March 19th, 2012


  • Added help bubbles to some inventory date fields.
  • Aliquot type is now properly displayed in storage tree view.
  • Fixed an issue where copy pasting in batch functions could affect the parents fields sur as “in_stock”.
  • Fixed coding_icd automagic where searching for a string will automatically search for relevant codes.

Important note concerning release 2.4.3: The upgrade script for 2.4.3A must be ran against a 2.4.2 installation, not 2.4.3. Release 2.4.3 has been removed from our servers because it contained the new sample type "purified RNA". This sample type has been removed from 2.3.4A as this is not a new sample type, but simply a purification method. If you have already installed 2.3.4, it's up to you to keep "purified RNA" as a sample type or remove it from there.


Release Date: December 8th, 2011


  • Tweaked CSV export
  • Fixed an error triggered when deleting a treatment not linked to any extend data.
  • Fixed an error triggered when adding a specimen review.


Release Date: November 22nd, 2011


  • Fixed detailed search screens.
  • Fixed an issue where for some IE8 users, search forms having time fields would prevent the form from working.


Release Date: November 14th, 2011


  • It’s now possible to drag items from storage to storage, in the storage layout page.
  • In tree views, non available aliquots are now displayed in grey.
  • Major changes to the diagnosis module. For help, see use the diagnosis section.
  • CAP reports moved from the diagnosis module to the annotation module.
  • A warning for expired and undone messages/reminders will be displayed in the main page.
  • New “unmatched parents” option in the databrowser will create a node with the elements of the parent node that were not used for the current node.
  • Added manageable permission presets.
  • Added a user search screen.
  • Added collection template. They allow to design what a data entry must be and chain forms one after the other, removing the need to manually browse collections to add items one by one.
  • System managed identifiers can now be recycled when used accidentally.
  • In shipments, added a contact list.
  • It’s now possible to run multiple searches in different tabs at the same time.
  • Specimens’ aliquots now have reception to storage spent time field, and derivatives’ aliquots now have creation to storage spent time field.
  • Added a relationship field to participant contacts.
  • Search results are now loaded directly beneath search parameters, which gives a better performance and eases parameters modification.
  • Search results now use a detail form when possible. If a generic form is used, an info bubble is displayed.
  • Added an option to copy a collection form, its links to participant, diagnosis and consent.


Release Date: September 27th, 2011


  • Fixed validation issues on masters models.


Release Date: September 19th, 2011


  • Fixed an issue where in the aliquot edit form it was impossible to remove the aliquot from storage.
  • Fixed an issue where Internet Explorer would use cached data instead of refreshing it.
  • Fixed an issue where detail models would not validate properly when more than a detail of the same master was loader.
  • It’s now possible to activate/deactivate users.
  • Fixed an issue where in the aliquot use screen, the parent aliquots editable fields were not working.
  • Fixed the collection link found in the participant > chronology view.
  • Fixed an issue where it was impossible to delete an empty group.


Release Date: September 1st, 2011


  • Fixed an issue where it was impossible to delete a Treatment Extend.
  • Fixed an issue where specimen reception date couldn’t be properly recorded.
  • Fixed an issue where it was impossible to delete diagnosis.
  • Fixed an issue where once a date was recorded, it was impossible to delete it.
  • Fixed an issue where trying to export a too big browser result to a csv would cause the application to run out of memory.


Release Date: August 9th, 2011


  • Renames age accuracy field to prevent them from being treated as date accuracy.
  • Alters v2.3.2 sql update file to v2.3.2.1. to prevent data loss.

Note: If you updated your installation to v2.3.2 with the 2.3.2 tag, you'll need to restore your age accuracy from your pre 2.3.2 sql backup file. To verify that, go to the version listing page. If in your versions history you have v2.3.2 with build 3335, you are concerned by this. If you have v2.3.2.1 with build 3370, you can ignore this note. If this applies to you, the fields you need to restore are diagnosis_masters.age_at_dx_precision, family_histories.age_at_dx_precision, reproductive_histories.age_at_menopause_precision, reproductive_histories.age_at_menarche_precision, reproductive_histories.hysterectomy_age_precision, reproductive_histories.age_at_first_parturition_precision and reproductive_histories.age_at_last_parturition_precision. Note that those fields names have changed in v2.3.3 so their previous match have a slightly different name.


Release Date: August 1st, 2011

SVN: -- removed --

  • Fixed an issue where saving data on a model having dates without specifying them would clear them.
  • Fixed an issue where defining an aliquot source for a derivative was possible.
  • Fixed an issue where it was not possible to delete a consent nor a clinical collection link.


Release Date: July 15th, 2011


  • Added a button to create derivatives from aliquot detail page.
  • Fixed various issues related to aliquots batch functions.
  • Fixed an issue where the databrowser would display a blank screen when there is too many results.
  • Fixed an issue where custom queries would not work properly when one of the fields refer to a datetime supporting accuracy.


Release Date: July 8th, 2011


  • Databrowser and batch set data is now sortable.
  • Submit button is now on the right of the screen, and action buttons on the left.
  • New batch processes.
    • Add quality control
    • Create derivatives both from samples and aliquots
    • Add internal uses
  • Storage can now be configured to ignore, warn or generate an error when two items are placed into the same cell space.
  • A warning is displayed on the login page if there is a time discrepancy between the server. Time discrepancy can shorten session duration.
  • Added ability to start browsing from a batch set.
  • Passwords now have a minimal length of 6 characters.
  • Added an interface to custom lists to allow to define items order and to specify if values should be displayed everywhere, only in search structures or never.
  • Added detail button to participant chronology view.
  • Text area values will now wrap when not in input mode.
  • Multi-choice action buttons can now be scrolled using a mouse wheel.
  • Hemolysis was moved from sample to aliquot level.
  • Added a button to collection indexes to reach the matching participant index tree view.
  • When viewing pages of a participant collection not having an obtained consent, a warning is displayed. A warning is also displayed when in an order containing an aliquot related to such collections.
  • Added a link to the wiki in the top menu.
  • Within menus, whole lines can now be clicked (instead of only the label).
  • Added auto accuracy. (Every date/datetime now support accuracy.)
  • Study selection have been moved from order to order line. Order now has a “default study” field which will make a study selected by default when adding a line.
  • Added paste on all lines of all sections button to pages having many grids.
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