Release 3.0.0

[saramonzon]

Release Note for version 3.0.0

Enhances and improvements

• Installation script improvements
• Added a proper demo system using docker compose. See in readme.
• Added custom names to db tables
• Refactor: removed "iSkyLIMS_" from modules names
• Refactor: changed camelCase to snake_case to every variable (camelCase only for class names)
• Refactor: new import sorting + relative path imports
• Record samples view have been rewrited
• Added jsonschema to the environment
• Sample projects fields can be defined using a json schema
• Improvements in Wetlab API:
  • Create sample fields defined in sample project
  • Allow to display/update laboratory information
• Resolution states now match service state
• New parameters available in config table
  • USER_CENTER_USED_FOR_NAMING_SERVICE
  • ABBREVIATION_USED_FOR_SERVICE_REQUEST
• Better table visualization using cdn tables
• Searching improvements in table allowing to search for columns
• Statistics visualization improvements.
• Possibility to request delivery information via api
• Crontab process revisited:
  • New error types added
  • Adjustments when waiting for run files included (bcl2fastq processing)
  • Crontab is now activated via web and removed from installation script
• Improvements at:
  • Login page
  • Contact page
  • Service display page

Solved issues/requests:

• Resolution states #57 Resolution states
• Service name in Requesting Services Application #70 Service name in Requesting Services Application
• Available service must have service_id #74 Available service must have service_id
• Configure the service name in DRYLAB #81 Configure the service name in DRYLAB
• If the run created in iSkyLIMS_wetlab already exists, the projects are duplicated when the run is loaded. #99 If the run created in iSkyLIMS_wetlab already exists, the projects are duplicated when the run is loaded.
• error in Modify protocol Fields  #101 error in Modify protocol Fields
• new parameter for protocol that already has records in the LibParametersValues, fails to display sample information #102 new parameter for protocol that already has records in the LibParametersValues, fails to display sample information
• Search services working as search runs with the sharing option #103 Search services working as search runs with the sharing option
• implement on wetlab API to receive a list of sample names and return the run name  #105 implement on wetlab API to receive a list of sample names and return the run name
• Run date not saved for MiSeq if run is in defined state #106 Run date not saved for MiSeq if run is in defined state
• Allow to define laboratory data from json file #107 Allow to define laboratory data from json file
• Create an API request to summarize the samples defined.  #108 Create an API request to summarize the samples defined.
• Error looking for a service #113 Error looking for a service
• Display number of samples requested for a service #114 Display number of samples requested for a service
• Can't record samples #115 Can't record samples
• Problem when 2 resolution have the same availableservices selected #116 Problem when 2 resolution have the same availableservices selected
• Possibility to request delivery information #117 Possibility to request delivery information
• /drylab/api/services/ query should have date start and date end as parameters #119 Added date start and date end to /drylab/api/services/ as parameters
• Custom contact page #121 Custom contact page
• Sequencing center grabs user center #122 Now services center is filled with the center where the user belongs in the moment is requested so it is consistent in the future
• Add iSkyLIMS_drylab.ConfigSettings to upload_tables.json #123 Added configSettings table to initial upload tables so it is included in the initial / upgrade install.
• Delivery date is auto_now_add #125 Delivery date is now autoadd
• Code cleaning #129 Code cleaning
• Try to change all iSkyLIMS to iskylims, in lower case. Check if changes in database are possible. @saramonzon #133 Changed iSkyLIMS to iskylims
• When searching a service the state select field does not show the rigth options #140 When searching a service the state select field does not show the rigth options
• Problem in sequencerDetails #173 Solved issue in sequencerDetails
• Add field name to table #184 Added field name to table in sample display
• Add excel template for download in batch samples upload #185 and Error in project definition -> batch load #183 some fixes and improvements in batch upload
• Upload files to service not working #188 fixes in upload services files
• Error in handlingLibraryPreparation #186 fixes in handlingLibrary prep
• Counseling and infrastructure requests #189 fixes in counseling and infrastructure requests
• Parameter name in pipeline error #190 fixes in pipeline definition
• Remove add crontab from installation script #192 removed add crontab from install script
• Problem with recorded runs using folder #200 fixed Problem with recorded runs using folder
• Pool table must be a jexcel table so you can select multiple samples #199 pool creation table is now a jexcel table for multiple selection
• Allow to create run (via pool data) even if run already exists #201 A pool can be created even if the run already exists
• Samples table in service should be scrollbar #202 samples table in service is has now a scroll bar
• In Add kit used in protocols "Choose a value" is a selectable option #204 Added choose value option in dropdown list for kit selection
• Unused or useless button in Add user Lot commercial kit #205 Renamed unused button in add user lot
• BUG when displaying NovaSeq Test Run #206 fixed bug when displaying novaseq test run
• Error adding options to option list in Sample Project  #207 fixed adding options to option list in project fields
• unable to fetch sample sheet files from existing runs #214 fixed retrieve sample sheets file from run
• Show the samples that could be included in sample sheet #215 Show the samples that can be included in sample sheet in library preparation
• Crontab sets directly to error when runParameters is not found #224 Added time when runParameters does not exists in crontab process

Other bugs solved:

• Check during crontab execution (When searching for new runs) if sample sheet has user_id in description

Third Party upgrades

• Bootstrap upgrade to version 5
• Jexcel upgrade to version 4
• jquery 3.4.6