Changelog

v6.0.0 - Start of PanelPlex Major Update Project

DEV-262 DNAS Help Desk Portal Link in WebUI

Application Portal WebUI

• Added "Get Help" button to portal menu bar that will open DNAS Help Desk Portal in a new tab.
• Replaced mailto: support@dna... at bottom of page with DNAS Help Desk link to bottom
• Updated Copyright to 2022

v6.0.1 - BIOTYPE testing portal

DEV-212 WebUI Diagnostics Dashboard app - Application Portal WebUI

Application Portal WebUI

• Add a link from the PPngs results page to a new tab for the diagnostic content
• Created a 'Diagnostics Dashboard' page

DEV-299 Change Solution label to Design - Application Portal WebUI

Application Portal WebUI

• In the WebUI PP results interface, update terminology in the bottom table (standardize with documented terminology)

DEV-301 Make Biotype portal header

Application Portal WebUI

• Added "- for BIOTYPE development only" to portal base.xhtml header.

v6.0.2 - User input of oligo design set data

DEV-196 User input of oligo design set data - Application Portal WebUI

Application Portal WebUI

• Added new data object for oligo user input.
• Added parsers for Excel and CSV input files.
• Implemented Singleplex to Multiplex, tying it into the backend.
• Implemented design regions based on the new oligo format, tying it into the backend.
• Implemented partial junction functionality, tying the most basic form into the backend.
• Updates the UI to allow user access to the new features.

v6.0.3 - If ThermoSleuth cannot place one of the Singleplex to Multiplex primer pairs, it spoils the run

DEV-319 If ThermoSleuth cannot place one of the Singleplex to Multiplex primer pairs, it spoils the run - PanelPlex_main

PanelPlex_main

• Prevents failure, allowing solution to just drop out.

v6.0.4

DEV-314 Diagnostics Dashboard middle-layer and backend support

Project Behemoth (PanelPlex)

• Add DiagnosticsDashboardBean and Loader classes to support loading a reaction set with Hibernate
• Add a helper object for the loading/organizing/display of oligo related data
• Export oligo data as CSV

v6.0.5

DEV-205 Oligo evaluation panel in a new Diagnostics Dashboard feature

Application Portal WebUI

• Update NGS (PanelPlex) results page to pass selected reaction to the new dashboard page
• Populate dashboard page with oligo details table with basic functionality (sorting, hide columns)
• Button to download the oligo table
• Tabs (placeholders) for bimolecular/cross hybridization matrices

v6.0.6

DEV-202 Constrain designs by control oligos and control amplicons

PanelPlex_main

• Adds ability for the user to specify control oligos that will be incorporated into the PanelPlex analysis.

v6.0.7

DEV-1995 Fix more detailed issues introduced by Develop Merge

PanelPlex_main

• Fixes interamplicon generation problem caused by merge, as well as other misc merge conflicts.

v6.0.8

DEV-1992 Generate Design Set output files

PanelPlex_main

• Has PanelPlex generate output files using the DesignOligo format.

v6.0.9

DEV-200 Generate SAM design output files

PanelPlex_main

• Has PanelPlex call the Python process to create the SAM file

v6.0.10

DEV-325 Provide WebUI-PP access to SAM design output files

Application Portal WebUI

• Adds button to download SAM file

v6.0.11

DEV-1996 Update checked in template files

Infrastructure & Server Config

• Updates files

v6.0.12

DEV-1997 Have the portal call the SAM generator with all accession lengths

PanelPlex_main

• Sends all accessions and lengths to the Python SAM generator

v6.0.13

DEV-1998 Update DesignerOligo CSV format

PanelPlex_main

• Updates column names and values to latest schema

v6.0.14

DEV-1999 Add radio button to enable target regions to be run without generating new oligos

Application Portal WebUI

• Adds radio button to restrict run to controls

v6.0.15

DEV-1990 User interface for Primer and Probe vs Amplicon matrix of binding parameters

Application Portal WebUI

• Adds primer and probe vs amplicon matrix

v6.0.16

DEV-2000 Ensure that oligo names are unique

PanelPlex_main

• Updates name creation code to ensure uniqueness

v6.0.17

DEV-2001 Fix indexing for control primers

PanelPlex_main

• Ensure that primers are positioned on the correct strand

v6.0.18

DEV-2002 Make blanks wildcards for control oligos

PanelPlex_main

• Runs blank control oligos against every target

v6.0.19

DEV-2004 Indexing for the substring to cut out the amplicon region is off when creating CSV

PanelPlex_main

• Fixes indexing

v6.0.20

DEV-2003 Download Cross-Hybridization matrix and other minor fixes

Application Portal WebUI

• Activate download button (try the Primefaces DataExporter.)
• Change column headers to “ - AMPLICON” as the other oligo names.
• Center data/values in the columns
• “Cross-hybridization” (hyphenated, not one word or separate words)
• Note to users regarding "n/a" values

v6.0.21

DEV-2005 Translate ThermoSleuth indexing into Designer indexing when using TS values to replace Designer ones

PanelPlex_main

• Shifts to using correct indexing

v6.0.22

DEV-2018 PP-NGS Results page refactor

Application Portal WebUI

• Refactor the PanelPlex NGS results page, consolidating results.xhtml and batchresults.xhtml with 3 interactive tables (panels), based primarily off of ngs/results.xhtml

v6.0.23

DEV-2019 Results Reaction Sets Panel

Application Portal WebUI

• Rename the first panel/dataTable to Reaction Sets
• Rename Solution column to Reaction Set Id
• Add Number of Reaction Sets column
• Add Reaction Set Ids column

v6.0.24

DEV-2020 Results Reaction Set panel content

Application Portal WebUI

• Reaction id column
• comma separated Target Ids column
• Reaction score column

v6.0.25

DEV-2021 Results Reaction Designs Panel

Application Portal WebUI

• Rename table as 'Reaction Design Set'
• Add columns
• Design Id
• Target Id
• Total Design Score
• Remove data (redundant from Designs Dashboard)
• oligo sequences
• list of primers and probes

v6.0.26

DEV-2032 Update Oligo loader and UI to operate under new constraints

Application Portal WebUI

• Updates UI and workflow in order to enable full control functionality
• Adds explicit control for specifying Singleplex to Multiplex runs

v6.0.27

DEV-2031 Track filtering of input oligos

PanelPlex_main

• Saves logs for user oligo filtering to S3

v6.0.28

DEV-2051 Update Extension Temperature Default

Application Portal WebUI, ThermoSleuth

• Changed default TS Extension Temperature to 63C (was 72C).
• updated version

v6.0.29

DEV-2013 Migrate improved Simulator wrapper code from the Cephied branch

PanelPlex_main

• Imported improved Simulator code

v6.0.30

DEV-2012 Update Simulator wrapper to save its results matrix to a file

PanelPlex_main

• Shifts Simulator to output a full matrix to JSON.

v6.0.31

DEV-2015 Call Simulator wrapper in NGS code path

PanelPlex_main

• Make the simulator call from the PanelPlex main workflow

v6.0.32

DEV-2070 Refactor Designer calls to split generation and scoring of oligos

PanelPlex_main

• Refactors Designer wrapper into a single classes
• Splits Designer call into two versions

v6.0.33

DEV-2016 Update Design Dashboard to read from matrix file

PanelPlex_main

Application Portal WebUI

• Load Simulator run results (JSON) in PanelPlex results
• Populate the Designs Dashboard cross-hybridization matrix with simulator data
• Removed previous cross-hybridization matrix

v6.0.34

DEV-229 Generate modified oligos for design consideration

PanelPlex_main

Application Portal WebUI

• Adds call to tool to modify oligos that overlap user-specified positions accordingly.
• Saves input and output files to cloud with new more general interface.
• Fixes minor issue with an error if there was a blank in the outermost cell of the oligo import.
• Makes it so that junctions only generate the forward or reverse regions if they are not already given.

v6.0.35

DEV-2076 Pre-create the oligo filtering file

PanelPlex_main

• Creates the oligo filtering file at the start of the run.

v6.0.36

DEV-2078 PP Dashboard change to Target Tm

PanelPlex_main

• Change Oligo Details Tm value to Target Tm
• Update column headers to reduce ambiguity (Tm and Fraction Bound), resize to show name

v6.0.37

DEV-2084 Create new JSON Data Objects

PanelPlex_main

• Adds new objects

v6.0.38

DEV-2088 PP Results backend support

PanelPlex_main

• Translating the data paradigm to reaction-based to enable a uniform results (page) presentation

v6.0.39

DEV-2066 PanelPlex Step 2 Refactor

Application Portal WebUI

• Move advanced settings to collapsable containers on steps 2 and 4
• Address wording a white space
• Group like settings

v6.0.40

DEV-2104 Generate and select best probe for user input Junction Oligo_sequence

PanelPlex_main

• Design probes with defined mutants for specificity

v6.0.41

DEV-2092 Integrate new JSON objects to PanelPlex workflow

PanelPlex_main

• Initial incorporation of the JSON backed storage into PanelPlex, replacing the database backing

v6.0.42

DEV-2106 Update Simulator calls to work with new JSON data structures

PanelPlex_main

• Additional fixes to make Simulator work properly with the DEV-2092 fix.

v6.0.43

DEV-2107 Reconnect PP Designs Dashboard with JSON

Application Portal WebUI

• Set the PanelPlex results page to load from the JSON schema
• Set the Designs Dashboard page to load from the JSON schema

v6.0.44

DEV-2108 Allow mix and match to provide multiple probes for a given design

PanelPlex_main

• Update the mix and match to populate designs with multiple probes.

v6.0.45

DEV-2109 Include amplicons in Cross-Hybridization tables and standardize names

PanelPlex_main

• Cleans up naming conventions, including issues that were hampering Cross-Hybridization table.

v6.0.46

DEV-861 On Hybridization Conditions page, User should be able to remove a custom kit and also be able to change the order of kits

Application Portal WebUI

• User created kits at the top of the list - starting with the newest

v6.0.47

DEV-2117 JSON generator and parser

PanelPlex_main

• Initial incorporation of JSON backed input parameters for PanelPlex workflow

v6.0.48

DEV-2123 Amplicon Fraction Bound Percent to Decimal

PanelPlex_main

• Convert Minimum Amplicon Fraction Bound (Inclusivity) from percent to fraction (decimal)

v6.0.49

DEV-2119 Implement Shared Primers in UI

Application Portal WebUI

• Adds user interface for semicolon separation and shared primers.

v6.0.50

DEV-2124 serialize JSON input

Application Portal WebUI, PanelPlex_main

• User inputs to JSON constraints, serialized

v6.0.51

DEV-2128 Export constraints JSON

Application Portal WebUI, PanelPlex_main

• Allow the user to download PanelPlex constraints for a job from the results and job pages

v6.0.52

DEV-2114 JSON input function for PanelPlex WebUI

Application Portal WebUI

PanelPlex_main

• Default PanelPlex constraints/input parameters to a single resource
• User imported PanelPlex constraints from JSON
• Reset PanelPlex input parameters to default

v6.0.53

DEV-2099 Update user input parser for advanced design constraints against target regions/positions

Application Portal WebUI

PanelPlex_main

• Update oligo- and target-related column headers in input files and web UI (Step 2 and Designs Dashboard)
• Add target-specific constraints to input file parsing, oligo output json

v6.0.54

DEV-2095 PP Example Input File

Application Portal WebUI

• New example input target file (Step 2)
• Clean up web UI instructions regarding the input file

v6.0.55

DEV-2126 Update User Input parser for Target specific constraints

Application Portal WebUI

PanelPlex_main

• Parse input target-specific constraints into input oligos

v6.0.56

DEV-2120 Implement Shared Primers in Workflow Layer

PanelPlex_main

• Update algorithm to handle cases where the primers are set to be shared

v6.0.57

DEV-2127 Apply user input target constraints over WebUI inputs

PanelPlex_main

• Apply target-specific constraints on the oligo level where applicable, overriding general job constraints

v6.0.58

DEV-2141 Allow adding multiple playlists to a playlist through the search feature at one time

PanelPlex_main

• Update the search-based playlist add feature to allow multiple playlists to be added at once

v6.0.59

DEV-2142 Fix minor errors hindering build

PanelPlex_main

Application Portal WebUI

• Fixes minor errors

v6.0.60

DEV-2143 Log key data to S3

PanelPlex_main

• Updates logging to write new Json structures to S3

v6.0.61

DEV-2144 Show S3 Logs in UI

Application Portal WebUI

• Adds link to view S3 logs in job page

v6.0.62

DEV-2145 Fix bugs in S3 log upload/download

PanelPlex_main

Application Portal WebUI

• Fixes bugs.

v6.0.63

DEV-2219 Remove comment

Application Portal WebUI

• Remove commented code captured by table exporter

v6.0.64

DEV-2230 Target Specific Primer Length Range

PanelPlex_main

• Simplify variable naming

v6.0.65

DEV-2277 Fix run status bars in results page

PanelPlex_main

• Adjust status bar to pull from new source that reflects an accurate state of the run.

v6.0.66

DEV-2221 Add Amplicon to Dashboard-Oligo Details

PanelPlex_main

• Bug fix - restore amplicon details to the Designs Dashboard - Oligo Details table

v6.0.67

DEV-2214 Change label for data download button

Application Portal WebUI

• Update - change button name for accuracy

v6.0.68

DEV-2278 Shift Consensus over to JSON based data structures

PanelPlex-Consensus_main

• Reworks Consensus workflow to use new data structures.

v6.0.69

DEV-2328 Fix failures that occur when uploading very large Fasta files

Application Portal WebUI

• Updates test condition for scanning mode to return the correct results at all times.

v6.0.70

DEV-2325 Update Consensus to use new Simulator calls

PanelPlex-Consensus_main

• Alters the calling code for Consensus to use the new Simulator code.

v6.0.71

DEV-2067 PP Step 4 refactor

Application Portal WebUI

• Update - move PanelPlex input parameters from step 4 to step 2, and rearrange for an intuitive flow.

v6.0.72

DEV-2340 Ignore ^ in NCBI feature parsing

Application Portal WebUI

• Adds ^ to the list of characters parsed out of the NCBI variation entries.

v6.0.73

DEV-665 Allow user to specify for each target: min_amplicon_gap, max_amplicon_gap, minimum nucleotides on ether side of junction

PanelPlex_main

• New feature - Add amplicon gap range (min and max) as a user input parameter on the target level

v6.0.74

DEV-2334 Update Consensus UI to pull data from JSON data structures for "Solutions" column

PanelPlex_main

• Updates "Solutions" column to take data from the new JSON data structures.

v6.0.75

DEV-2139 Target input row split on select columns

PanelPlex_main

• Updates ";" parser for the target input file to restrict 'splitting' or 'duplicating' of rows to the Shared Primers feature related columns

v6.0.76

DEV-2223 Set precision in Dashboard

PanelPlex_main

• Updates PanelPlex Dashboard oligo details precision to relevant digits

v6.0.77

DEV-2353 Update SQL creation scripts to match latest database schema

Infrastructure & Server Config

• Updates SQL scripts so that the blank database can be generated from scratch.

v6.0.78

DEV-2368 Fix RT Primer Functionality

PanelPlex_main, PanelPlex-Consensus_main

• Fixes RT primer calls to generate them again.

v6.0.79

DEV-2371 Update AWS Util calls to make region configurable

Project_Behemoth

• Makes the AWS region configurable.

v6.0.80

DEV-2382 Update S3 calls to make region configurable

Project_Behemoth

• Makes the AWS region configurable for S3 Calls.

v6.0.81

DEV-2369 Update Consensus UI to pull data from JSON data structures for "Options" column

PanelPlex-Consensus_main

• Updates Consensus display for exclusions and crosshybridizations.

v6.0.82

DEV-2369 Invoke user input local constraints for designer jobs

PanelPlex_main

• Update source of DesignerJob input parameters with constraints JSON

v6.0.82

DEV-2367 Fix Tail functionality

PanelPlex-Consensus_main, PanelPlex_main, Application Portal WebUI

• Re-enable the running of the tail generation step.

v6.0.83

DEV-2389 Fix rebase error in constraints calls

PanelPlex-Consensus_main, PanelPlex_main, Application Portal WebUI

• Adjust the constraint calls to use the new approach.

v6.0.84

DEV-2222 Additional metrics in Oligo Details

PanelPlex_main

• Add unimolecular metrics to the designs dashboard oligo details

v6.0.85

DEV-2290 Run setup Target Strand help text

Application Portal WebUI

• Add tooltip help text to Consensus and PanelPlex step 2 (target)

v6.0.86

DEV-2023 Consensus Input Param File update

PanelPlex-Consensus_main, Application Portal WebUI

• Include Consensus parameters to Constraints structure
• Create a Consensus default values file
• Tidy up Web UI

v6.0.87

DEV-2399 Consensus Input Param File update

Application Portal WebUI, PanelPlex-Consensus_main

• New feature - reset parameters buttons on Consensus steps 2-4
• Bug fix - preserve user input whole_target_range when uploading Consensus input file

v6.0.88

DEV-2392 Update file output for Consensus

Application Portal WebUI, PanelPlex-Consensus_main

• Links Consensus user output files to JSON data store and adds new output for PanelPlex input.

v6.0.89

DEV-2232 Ensure Interoligo Hits Matrix has correct values for all cells

Application Portal WebUI, PanelPlex-Consensus_main, PanelPlex_main

• Fixes Simulator calls to more accurately reflect the calculated situation.

v6.0.90

DEV-2276 Add init/prop outputs to results WEBUI

Application Portal WebUI

• Let Consensus call the Designs Dashboard, and make the initiation oligos toggleable in the Designs Dashboard

v6.0.91

DEV-221 Save original user target input file to S3 run folder

Application Portal WebUI

• New feature - Save the user's target input file along with other run-related files

v6.0.92

DEV-379 Add ability for user to save their primer/probe list as .csv file

Application Portal WebUI

• New feature - Download button for designs in the Oligo per line format (same as target input file format)

v6.0.93

DEV-2405 Update DataReaction scoring to include crosshybridization penalties

PanelPlex-Consensus_main, PanelPlex_main

• Adds cross-hybridization penalties to the reaction score calculation.

v6.0.94

DEV-2400 Update WebUI product words

Application Portal WebUI

• Change PanelPlex-Consensus to Consensus, PanelPlex-NGS to PanelPlex, and qPCR CopyCount to CopyCount

v6.0.95

DEV-2207 Update design and reaction scoring with gap and exclusion scores

PanelPlex-Consensus_main, PanelPlex_main, Application Portal WebUI

• Adds gap and exclusion scores, incorporating the new equation for the exclusion gap adjustment

v6.0.96

DEV-2387 Standardize retention of MP input/output files for a design run

PanelPlex-Consensus_main, PanelPlex_main

• Update temporary local working path for component input and output storage

v6.0.97

DEV-2409 Standardize retention of Designer input/output files for a Consensus run

Consensus_main,

• Bug fix - update Designer to expect targan input files in the targan component folder

v6.0.98

DEV-2411 Address null pointer errors

Consensus_main, PanelPlex_main

• Bug fix - handle optional sequence definition for an oligo as optional
• Bug fix - manage loading the local constraints for a specific oligo over the global constraints

v6.0.99

DEV-2410 Add function to "kill" a TS, PanelPlex, Consensus run in the job queue

Consensus_main, PanelPlex_main

• Updates the Java process to look for the presence of a "kill.me" file and to terminate itself if it sees it.

v6.0.100

DEV-2347 Bring forward PanelPlex run validation

PanelPlex_main

• Updates the callback functions for PanelPlex step 2 and 3 to validate parameters and submit the run at the appropriate web pages

v6.0.101

DEV-2388 Move temporary component-specific formatted input/output files for a design run to s3

PanelPlex_main

• New feature - preserve working files for debugging

v6.0.102

DEV-2416 Update Consensus to use Constraints input file

Consensus_main, Application Portal WebUI

• Exposes Constraints file via the Consensus interface, and tweaks handling of its input.

v6.0.103

DEV-2204 Add WebUI button for user to "kill" a TS, PP, Consensus run

Application Portal WebUI

• New feature - cancel a queued or currently processing PanelPlex, or Consensus run from the web UI
• Update the delete button from PanelPlex, Consensus, or ThermoSleuth jobs page to only appear on completed runs

v6.0.104

DEV-2408 Update scoring to take weights and tail penalties into account

Consensus_main, PanelPlex_main, Application Portal WebUI

• Returns the weight calculation to match the way it originally was, adjusting the data structures accordingly.

v6.0.105

DEV-2422 Implement "kill" a ThermoSleuth run with web UI button

Thermosleuth_main, Application Portal WebUI

• New feature - cancel a queued or currently processing ThermoSleuth run from the web UI

v6.0.106

DEV-2407 Update scoring to include coverage penalties

Consensus_main, PanelPlex_main

• Re-implements penalties based on the coverage statistics.

v6.0.107

DEV-2224 Change "Delete" button to "Clear" button

Application Portal WebUI

• Bug fix - 'Delete (Row)' button in PanelPlex - Step 2 deletes all targets

v6.0.108

DEV-2227 DeltaH Cross-hybridization data

PanelPlex_main

• New feature - pull Delta H data for results output

v6.0.109

DEV-2423 Code Cleanup - DesignerResults

Application Portal WebUI

• Housekeeping - code cleanup

v6.0.110

DEV-2058 Add user log messages for failed PP target designs from excessive interamplicon hits

PanelPlex_main

• Adds log messages and a file to store rejected designs, while moving all run directory uploads to unzipped

v6.0.111

DEV-2426 Move Target Strand drop down to Probe section of UI

Application Portal WebUI

• Moves dropdown and reworks style and ajax update to work in the new location

v6.0.112

DEV-2218 Bimolecular homodimer values for Designs Dashboard

Consensus_main, PanelPlex_main

• New feature - provide homodimer values in the Designs Dashboard cross-hybridizations matrices

v6.0.113

DEV-797 PP scoring should show ALL terms used in getting the final score

Application Portal WebUI

• Exposes all necessary scores required to calculate the final scores

v6.0.114

DEV-2131 Copy run logs from local OS to S3 storage run folder

Consensus_main, PanelPlex_main, Thermosleuth_main

• Uploads the server logs after every run

v6.0.115

DEV-2429 Remove deprecated DesignerTarget functions and fix the places that still used them

Consensus_main, PanelPlex_main

• Fixes exclusion code to look at the right values, and updates the target functions to pull from the oligo data

v6.0.116

DEV-2412 Update file management to decouple components and workflows

Consensus_main, PanelPlex_main

• Consolidate file management handlers to a consistent standard

v6.0.117

DEV-2424 Apply new storage configs to legacy EC2

Consensus_main, PanelPlex_main, Thermosleuth_main

• Update config references

v6.0.118

DEV-2421 Make fast-compare the default option

Consensus_main, Application Portal WebUI

• Update - change default aligner for Consensus to FastCompare

v6.0.119

DEV-2226 Delta H cross-hybridization table

Consensus_main, Application Portal WebUI

• New feature - display DeltaH cross-hybridizations in the Designs Dashboard

v6.0.120

DEV-2425 Change statuses to "Completed"

Consensus_main, Application Portal WebUI

• New Feature - For Consensus and PanelPlex runs that complete without results, the status is set to "Completed"

v6.0.121

DEV-2337 Update example Target Input file

Application Portal WebUI

• Update - update probe coordinates to realistic values

v6.0.122

DEV-2444 Updates to enable E1 DEV pipeline

ThermoSleuth_main, Consensus_main, PanelPlex_main

• Update - add console logs related to file management with AWS S3

v6.0.123

DEV-2444 Updates to enable E1 DEV pipeline

ThermoSleuth_main, Consensus_main, PanelPlex_main

• Update - playlist file path correction for AWS S3 objects

v6.0.124

DEV-2444 Updates to enable E1 DEV pipeline

ThermoSleuth_main, Consensus_main, PanelPlex_main, Application Portal WebUI

• Update - playlist file path correction for AWS S3 objects, add playlist status logging
• Restore genome viewer for ThermoSleuth webUI

v6.0.125

DEV-2444 Updates to enable E1 DEV pipeline

ThermoSleuth_main

• Update - adding thermosleuth logging

v6.0.126

DEV-2444 Updates to enable E1 DEV pipeline

ThermoSleuth_main, Consensus_main, PanelPlex_main

• Update - remove server logging

v6.0.127

DEV-2445 Workflow run tracking

ThermoSleuth_main, Consensus_main, PanelPlex_main

• Update - store tracking information with the run data

v6.0.128

DEV-2437 Tidy up user target input file ingestion

PanelPlex_main, Application Portal WebUI

• Update - clean up code relating to loading a target input file
• New feature - expand a target junction oligo to target region oligos
• New feature - display junction(s) and related target region oligos in step 2
• New feature - add probe_primer_overlap_limit, junction_padding_minimum, and primer_design_range_minimum to webUI, constraints
• New feature - Recalculate target design regions on button click, run submission

v6.0.129

DEV-2446 Add Intelliqube data format parser to CopyCount

CopyCount_Workflow

• Adds Intelliqube data processor

v6.0.130

DEV-2440 Combine targets logic

CopyCount_Workflow

• Update - implement new calculations to determine which junctions should be combined, if any

v6.0.131

DEV-2451 Fix Intelliqube parser to handle ROX data

CopyCount_Workflow

• Adds extra filters to ignore unused channels

v6.0.132

DEV-2105 Update Thermosleuth product WebUI to accept modified nucleotides in input seqs

Application Portal WebUI

• Loosens checks on valid sequences to allow bracket codes
• Updates ThermoSleuth query length calculations to count nucleotides instead of characters
• Minor fix to file output where strand type could be output incorrectly

v6.0.133

DEV-2450 Fix bug in combine targets logic

CopyCount_Workflow

• Bug fix - separate combined target design regions and shared target feature
• Bug fix - update the user-facing list of targets

v6.0.134

DEV-2238 Code Cleanup - billing services

Application Portal WebUI

• Housekeeping - code cleanup

v6.0.135

DEV-2206 Add new scoring rule for fluorophore

Consensus_main, PanelPlex_main

• Adds new scoring term for Taqman cleaving at the five prime end

v6.0.136

DEV-2396 Consensus design range param for junctions

Consensus_main

• Fixes data flow and misc bugs preventing Consensus from running successfully

v6.0.137

DEV-2461 Add UI Components for Fluorophore Taqman Cleaving penalty

Application Portal WebUI

• Adds output displaying the penalty, as well as the weight sliders, for the Fluorophore Taqman Cleaving penalty

v6.0.138

DEV-2460 Maintain tiling feature

Application Portal WebUI, PanelPlex_main

• Fixes regressions in the Tiling code due to v6
• Fixes regression in coverage calculations when there are multiple options for coverage
• Makes FAILED default for no-result jobs, but allows COMPLETED to be set if it did get to the end

v6.0.139

DEV-2238 Develop portal signin and product access check from new user license objects

Application Portal WebUI

• Update - switch login service to api
• Housekeeping - remove deprecated code

v6.0.140

DEV-2238 Develop portal signin and product access check from new user license objects

Application Portal WebUI, PanelPlex_main, Consensus_main

• Debug - decouple deprecated fields

v6.0.141

DEV-2481 Fix problems in Controls and Predesigns

Application Portal WebUI, PanelPlex_main

• Fixes regressions preventing PanelPlex from running Control/Predesign jobs.

v6.0.142

DEV-2365 Invalid double quote symbol throws error

Consensus_main, PanelPlex_main

• Replaces invalid double quote symbol with generic escaped one.

v6.0.143

DEV-199 Store JBoss log

Consensus_main, PanelPlex_main, ThermoSleuth_main

• Reactivates storage of server log to new location.

v6.0.144

DEV-2459 Clarify status of runs

Consensus_main, PanelPlex_main, Application Portal WebUI

• Makes "Completed" and "Done" display differently to the user.
• Cleans up the Results column on the results page.

v6.0.145

DEV-2384 Add product page header with institution AWS hours used/remaining

Application Portal WebUI

• Update portal user to match user access api, display processing hours usage
• Update Consolidate end user permissions

v6.0.146

DEV-2384 Add product page header with institution AWS hours used/remaining

Application Portal WebUI

• Bug fix - Display when not viewing a specific product

v6.0.147

DEV-2486 Fix error in mix and match thin-out code

Consensus_main, PanelPlex_main

• Calculates overlap correctly

v6.0.148

DEV-2487 Fix errors discovered while investigating bug in thin-out code

Consensus_main, PanelPlex_main

• Fixes bug preventing playlist creation
• Fixes bug using probes as input oligos
• Fixes bug where control input oligos would not make it past the UI checks
• Fixes bug where empty columns could generate Null Pointer exceptions before giving a proper error

v6.0.149

DEV-778 Maintain filter to force all designs to have either FP or RP end at the junction position

Consensus_main, PanelPlex_main

• Fixes bug in amplicon gap calculation affecting endpoint junction calculation.

v6.0.150

DEV-2238 Develop portal signin and product access check from new user license objects

Application Portal WebUI

• Bug fix - update junit tests to latest API version

v6.0.151

DEV-2492 Add check to prevent lockout spiral in License Manager

Application Portal WebUI

• Does not perform license checks on logged out user

v6.0.152

DEV-2493 Remove API-referencing unit test

Application Portal WebUI

• Removes the module

v6.0.153

DEV-2484 Remove API-referencing unit test

Application Portal WebUI

• Bug fix - navigation and error handling
• Bug fix - update links to configured addresses
• Bug fix - login attempt messages
• Bug fix - PanelPlex values do not auto-reset

v6.0.154

DEV-2494 Fix Consensus runs that use exclusivity playlists

Consensus_main

• Fixes file paths and temporarily deactivates individual FastCompare score for oligos

v6.0.155

DEV-2338 Update validation of input target design regions

Application Portal WebUI

• Adds new validation checks and tweaks the text for existing ones
• Updates minor predesign check to no longer require five prime and three prime coordinates

v6.0.156

DEV-276 Misleading instructions ("or") on the Consensus web portal

Application Portal WebUI

• Removes incorrect Consensus controls UI

v6.0.157

DEV-2057 Add error message for target designs outside user input amplicon size constraints

Application Portal WebUI

• Adds an extra validation error message, and refines existing message

v6.0.158

DEV-2428 Display ThermoSleuth Cart

Application Portal WebUI

• Bug fix - display ThermoSleuth Cart

v6.0.159

DEV-2497 Put run logs and processor logs in different subdirectories

Consensus_main, PanelPlex_main

• Splits the server logs and run logs into two non-nested directories

v6.0.160

DEV-2496 Add the run_id (runDirectoryId) to product Job Lists

Application Portal WebUI

• New feature - add the run_ID to PanelPlex, Consensus, ThermoSleuth results list (jobs.xhtml) pages

v6.0.161

DEV-620 Add user name and email to the Stack Trace

Application Portal WebUI

• Update - hide the stack trace from the user

v6.0.162

DEV-620 Add user name and email to the Stack Trace

Application Portal WebUI, PanelPlex_main

• Update - remove link to deprecated output file

v6.0.163

DEV-2404 Add link to confluence software docs into Portal WebUI

Application Portal WebUI

• New feature - add a link to DNAS (all) product documentation

v6.0.164

DEV-2498 Debug logout of the application web portal

Application Portal WebUI

• Bug fix - forward and redirect for relative and absolute page paths

v6.0.165

DEV-2501 Remove Completed Status

Consensus_main, PanelPlex_main

• Removes Completed status
• Tidies up logging

v6.0.166

DEV-2491 Develop web UI to reset user password

Application Portal WebUI

• Update - switch password reset service to api

v6.0.167

DEV-2506 Allow ThermoSleuth owner and admins to view a run

ThermoSleuth_main, Application Portal WebUI

• Bug fix - load ThermoSleuth results

v6.0.168

DEV-2503 Reattach FastCompare and Targan runs and statistics to Consensus

Consensus_main

• Adjusts the Consensus workflow to use the FastCompare generated runs
• Fixes the Targan file generation to offset for subregions

v6.0.169

DEV-2511 Debug transaction error to persist password reset request

Application Portal WebUI

• Bug fix - track password reset requests

v6.0.170

DEV-2502 Ensure all Consensus design solutions are included in output PCR_designs.csv

Application Portal WebUI, Consensus_main

• Fixes indexing errors in the CSV creation and the amplicon calculation
• Removes old code for result file recalculation

v6.0.171

DEV-2507 Allow Designer run owner and admin to view results

Application Portal WebUI, Consensus_main, PanelPlex_main

• Bug fix - load Designer results

v6.0.172

DEV-2512 Turn off multiplex for batch singleplex mode in panelplex

Application Portal WebUI, PanelPlex_main

• Removes unnecessary checks from Multiplex and batch singleplex, allowing partial results
• Fixes other minor issues preventing batch singleplex from running

v6.0.173

DEV-2427 Add warning column in reaction sets table for uncovered targets

Application Portal WebUI

• Adds column alerting user to any targets that the multipick reaction set does not cover

v6.0.174

DEV-2505 Address null InputStream for S3 object creation

Application Portal WebUI, Consensus_main, PanelPlex_main, ThermoSleuth_main

• Replaces null value with input stream on S3 cancellation call
• Replaces old timeout code with new job cancellation call

v6.0.175

DEV-2509 Remove deprecated download buttons

Application Portal WebUI

• Remove "Download Temporary Fasta File" and "Download Reaction Designs" from the PanelPlex results view

v6.0.176

DEV-2495 Add Fluorophore and quencher on TaqMan Probe selection

Application Portal WebUI

• Updates UI to properly display flourophores and quenchers

v6.0.177

DEV-2275 Implement feature access controls in WebUI

Application Portal WebUI

• Updates UI and processor server queue management to consider new license model on specific features

v6.0.178

DEV-2508 Address error on constraints file upload

Application Portal WebUI

• Update location of user's custom global_constraints for Designer projects to Step 2/target definition
• Update input parameters preview in results view for Designer projects

v6.0.179

DEV-2508 Address error on constraints file upload

Application Portal WebUI

• Housekeeping - code cleanup

v6.0.180

DEV-2508 Address error on constraints file upload

Application Portal WebUI, Consensus_main

• Update move maxPrimerPairDepth to global_constraints

v6.0.181

DEV-2540 Change PP results view IDs to names from user

Application Portal WebUI, Consensus_main, PanelPlex_main

• Replaces ids with user-parsable names

v6.0.182

DEV-2554 Fix oligo names

Application Portal WebUI, Consensus_main, PanelPlex_main

• Fixes ingestion of target names and updates oligo name generation to construct it from the base oligo

v6.0.183

DEV-2525 Ensure PanelPlex WebUI constraint field values

Application Portal WebUI, PanelPlex_main

• Bug fix - Store all PanelPlex Step 2 input field values on update
• New Feature - on updates to fields relating to junction target region calculation, allow user to use recalculate targets feature
• Update default PanelPlex values (detection_mode, primer_design_range_minimum)
• Update - reorganize fields in PanelPlex Step 2 with updated labels and tooltip text
• Update - user-facing labels, messages in web UI

v6.0.184

DEV-2548 Ensure PanelPlex WebUI constraint field values

Application Portal WebUI

• Update main and CopyCount landing pages' navigation paths to distinct tiles

v6.0.185

DEV-2538 Fix ingestion and display of modified nucleotides in ThermoSleuth WebUI

Application Portal WebUI

• Removes number removal, and loads run info in ThermoSleuth jobs

v6.0.186

DEV-2550 Subtract 1 from gap calculation in exclusion scoring

Consensus_main, PanelPlex_main

• Adjusts the gap calculation

v6.0.187

DEV-2556 Fix Consensus crash when loading ThermoSleuth job

Thermosleuth_main

• Adds check for sub-ThermoSleuth jobs

v6.0.188

DEV-2563 Remove 'view errors' hyperlink from Status column

Application Portal WebUI

• Remove hyperlink from Failed status for both Consensus and PanelPlex

v6.0.189

DEV-2519 Update Raw Design Sets to Include IDs

Application Portal WebUI

• New Feature - the Download Raw Design Set Data in PanelPlex results now includes reaction data

v6.0.190

DEV-2390 Export amplicon details

Application Portal WebUI

• Bug fix - display amplicon coordinates and sense in the Designs Dashboard

v6.0.191

DEV-2573 Debug parsing local constraints

PanelPlex_main

• Debug - persist local constraints downstream

v6.0.192

DEV-2537 Replace deprecated code in Consensus iteration feature

Consensus_main

• Fixes Consensus iteration feature

v6.0.193

DEV-2559 Add outstanding Consensus constraints to global_constraints object

Consensus_main, PanelPlex_main

• Add ThermoSleuth load throttle config value to constraints ("candidate_oligo_search_limit")

v6.0.194

DEV-2566 Update Step 2 page on constraints upload for Consensus

Application Portal WebUI

• Debug - update form values on custom global_constraints selection

v6.0.195

DEV-2579 Implement candidate oligo search limit parameter for component ThermoSleuth runs

Consensus_main, PanelPlex_main

• Adds logic to inclusivity analysis to respect the candidate_oligo_search_limit parameter

v6.0.196

DEV-2560 Re-add probe_modifications to global_constraints object

Consensus_main, PanelPlex_main

• Adds probe modifications to exported global_constraints

v6.0.197

DEV-2585 Sort before ThermoSleuth cut

Consensus_main

• Sorts the candidate designs before running ThermoSleuth to only grab from the best designs

v6.0.198

DEV-2527 Update target_name for junctions and probes when PanelPlex combines target junctions

PanelPlex_main

• Updates the target name for junctions

v6.0.199

DEV-2558 Fix multiple probe feature validation when generated from overlapping junction design regions

PanelPlex_main

• Debug - correctly apply license control on combined junction regions with probes

v6.0.200

DEV-2557 Misc one line WebUI fixes

Application Portal WebUI

• Center product tiles on welcome page
• Display product name on results page
• Debug Gray-out "Next" button if unlicensed features are attempted

v6.0.201

DEV-2527 Update target_name for junctions and probes when PanelPlex combines target junctions

PanelPlex_main

• Updates oligo names

v6.0.202

DEV-2562 Provide download link for target input file

Application Portal WebUI

• New feature - download the user's target input file from the PanelPlex results page (Input Parameters tab)

v6.0.203

DEV-2571 Fix null pointers found during v6 testing

Consensus_main, PanelPlex_main

• Fix various errors that led to Null Pointer exceptions in Consensus and PanelPlex

v6.0.204

DEV-2551 Add "Reporter Email" field to portal WebUI bug encountered page

Application Portal WebUI

• New feature - new field in the error report for a user to supply their email

v6.0.205

DEV-2561 Display playlists used in webUI (Consensus and PanelPlex)

Consensus_main, PanelPlex_main

• New feature - display playlists used in Consensus and PanelPlex

v6.0.206

DEV-2555 Debug reload function for PanelPlex design target regions

PanelPlex_main

• Debug target input file reload

v6.0.207

DEV-2587 Generate broken down json files from run_results.json

Consensus_main, PanelPlex_main

• Adds code for reaction-only interoligo hit json files

v6.0.208

DEV-2583 Revert TS to use genome viewer

ThermoSleuth_main

• Debug restore genome viewer and structure viewer in ThermoSleuth

v6.0.209

DEV-2580 Remove amplicons from columns of Design Dashboard cross-hyb tables

Consensus_main, PanelPlex_main, Application Portal WebUI

• Removes amplicon data from columns of interoligo matrix data storage
• Updates web UI to accept the asymmetric matrix

v6.0.210

DEV-2584 Solve AWS TLS 1.2 errors in webserver

Consensus_main, PanelPlex_main

• Updates portal to request TLS 1.2 usage when it sends mail

v6.0.211

DEV-2588 Separate Consensus setup step 3 RESET button from "Back" button

Application Portal WebUI

• Updates button placement at the top of Consensus and PanelPlex products for consistency

v6.0.212

DEV-2587 Generate broken down json files from run_results.json

Consensus_main, PanelPlex_main

• Alters the save functionality to remove the independent upload for the interoligo matricies

v6.0.213

DEV-2591 Fix Null Pointer Exception in ThermoSleuth emails

Thermosleuth_main

• Bug fix - load run_info

v6.0.214

DEV-2593 Fix Json load error

Consensus_main, PanelPlex_main, Application Portal WebUI

• Fixes load issue in Json
• Fixes null pointer error when not giving a probe region to a probe design
• Fixes missing forward and reverse labels for no-probe designs
• Makes the order of the tabs in the playlist selection consistent between Consensus and PanelPlex

v6.0.215

DEV-2592 Load reaction crosshyb on dashboard load

Consensus_main, PanelPlex_main, Application Portal WebUI

• Updates the Designs Dashboard to only load the needed interoligo matricies on Dashboard view

v6.0.216

DEV-2552 In ThermoSleuth add Forward Primer DG and Reverse Primer DG columns to amplicons.csv file

Thermosleuth_main

• New feature - export forward primer DG and reverse primer DG to amplicon output

v6.0.217

DEV-2598 Fix Null Pointer Exception in Consensus results page

Application Portal WebUI

• Fixes null pointer

v6.0.218

DEV-2567 Fix PP junction variant probe feature

Application Portal WebUI, PanelPlex_main

• Adds link between probe regions and their junctions
• Removes mutant probes from inclusivity thermoblast, uses more accurate Designer data instead
• Removes mutant oligo sequence from cloned forward primer, reverse primer and probe regions

v6.0.219

DEV-2543 Sort Consensus design results in WebUI by "solution score" to be consistent with PCR_designs file

Application Portal WebUI, Consensus_main

• Bug fix - Default view in Consensus results now sorted properly by Total Score

v6.0.220

DEV-2457 Update rules for negative amplicon gaps to include

Thermosleuth_main

• Debug - filter ThermoSleuth results to remove overlapping primers (negative amplicon gap)

v6.0.221

DEV-2568 Add specific run log for designer failures

Application Portal WebUI, Thermosleuth_main, PanelPlex_main, Consensus_main

• Improves logging and error handling to give better information about status and errors

v6.0.222

DEV-2603 Refine selection of second+ inclusivity sequence to increase Consensus Inclusivity Coverage

Application Portal WebUI, Consensus_main

• Fixes error in iterative keystone selection
• Fixes associated null pointer errors
• Adds extra logging and cleans up target names

v6.0.223

DEV-2611 Update Oligo Name and appearance in Consensus Designs Dashboard

Application Portal WebUI, PanelPlex_main, Consensus_main

• Updates the design, amplicon and oligo names to match requirements
• Sorts designs dashboard crosshyb tables so that the amplicon oligos are on the bottom

v6.0.224

DEV-2595 Debug Tiling Mode

Application Portal WebUI, PanelPlex_main, Consensus_main

• Bug fix - tiling mode
• Load default values based on Design Mode selection

v6.0.225

DEV-2602 Fix off-by-one coordinate errors in ThermoSleuth v6 Product

Application Portal WebUI, Thermosleuth_main

• New feature - update coordinate reporting to both ends in the industry standard
• Update - increase width of primer selector

v6.0.226

DEV-2620 Update pom resource specification to explicitly load entire resources directory

Project_Behemoth

• Makes the base resource directory for the processor pom explicit

v6.0.227

DEV-2609 Rounding of numbers needed in Thermodynamic details pages

Application Portal WebUI, Consensus_main

• Update - reduce precision of thermodynamic values in Consensus

v6.0.228

DEV-2610 Update name of Consensus oligo_details.csv with "PanelPlex" in the name

Application Portal WebUI, Consensus_main

• Bug fix - Correct product name in generated filename download

v6.0.229

DEV-2581 Ensure only shared designs are produced in PP results

PanelPlex_main

• Fixes bug in the loading of designs for the pruning multipick run
• Adjusts filtering of interamplicon exclusions to allow for shared primer restrictions

v6.0.230

DEV-2612 Add reaction tracking info to top of design dashboard

Application Portal WebUI, Consensus_main, PanelPlex_main

• Add project, reaction set, and reaction information to the Designs Dashboard

v6.0.231

DEV-2614 Update Consensus k-mer analysis validation

Consensus_main

• Update validation messages related to Target Characteristics

v6.0.232

DEV-2626 Ensure values in Consensus results downloads are not object references

Consensus_main

• Bug fix - export exclusion oligo sequences in coverage output csv

v6.0.233

DEV-2623 Remove partition percent bound result

Thermosleuth_main

• Update - remove Partition Percent Bound from ThermoSleuth results page

v6.0.234

DEV-2628 Update Exclusion Score for consistency

Consensus_main

• Bug fix - export false amplicon score in the Consensus coverage csv

v6.0.235

DEV-2630 Update tiling validation

PanelPlex_main

• Bug fix - catch error when tiling design region is too small
• Bug fix - apply default values on design mode selection

v6.0.236

DEV-2594 Differentiate Predesigns from Controls

PanelPlex_main, Application Portal WebUI

• Runs grouping feature whenever there is only one design for all multiplex targets
• Fixes oligo names and numbering
• Don't penalize predesigns for not being in non-existent regions
• Fixes problem with predesigns in designs dashboard
• Fixes bug where empty input file rows could crash input reading
• Fixes wildcard functionality
• Don't accept user-defined primers outside the region designated for them

v6.0.237

DEV-2632 Fix inconsistencies and errors in false amplicon calculation

PanelPlex_main, Consensus_main

• Fixes several interrelated bugs that were causing inconsistencies in the false amplicon report

v6.0.238

DEV-2633 Fix Null Pointer Exception in Playlist emails

Application Portal WebUI

• Passes run info through so that the Playlist creation and edit emails can use it

v6.0.239

DEV-2631 Fix Show Initiation filter

Application Portal WebUI

• Updates Show Initiation button to call a specific reload function

v6.0.240

DEV-2635 Make target file validation fail predesigns with accessions not in inclusivity

Application Portal WebUI

• Makes target file validation more restrictive

v6.0.241

DEV-2629 Correct INIT/PROP Amplicon coordinates

PanelPlex_main, Application Portal WebUI

• Update naming of, coordinates, sequence splicing of the gap for amplicons Ref_Fragment and Prop_Amplicon
• Update SAM file management and download to a zipped file

v6.0.242

DEV-2636 Flatten "playlist of playlist" import

Application Portal WebUI

• Removes playlist-of-playlist linking in the data structure
• Makes playlist-of-playlist import UI put the accessions directly into the main playlist

v6.0.243

DEV-2638 Replace duplicate removal comparison with hash comparison

Application Portal WebUI

• Moves ambiguity tally to sequence creation
• Creates md5 digest hash for sequence at creation
• Checks for duplicate sequences based on digest hash rather than direct comparison

v6.0.244

DEV-2641 Update wrapper to read new Multipick grouping output format

PanelPlex_main, Application Portal WebUI

• Updates the multipick wrapper code to parse new information from the multipick executable
• Removes reaction set total penalties in PanelPlex UI, renames the panel/interpanel penalties

v6.0.245

DEV-2642 Fix primer/probe Target_Accession in Consensus Designs Dashboard-Design Oligos table

PanelPlex_main, Consensus_main, Application Portal WebUI

• Switches Target_Accession in the designs dashboard to the hit value

v6.0.246

DEV-2596 Fix positioning of reverse sense primer/probe modifications and mutations

PanelPlex_main

• Update input parameters to the sequence tools to modify oligos
• Update interpretation of results from the sequence tools to modify oligos

v6.0.247

DEV-2646 Remove 3-prime metrics from Consensus results WebUI

Application Portal WebUI

• Removes unused columns from result page

v6.0.248

DEV-2651 Fix array out of bounds error

PanelPlex_main, Consensus_main

• Sets the correct minimum value for the genomic slicing

v6.0.249

DEV-2645 Remove 3-prime NET Score and k-mer score (FC) from Design Total Score

PanelPlex_main, Consensus_main, Application Portal WebUI

• Relegates the 3 prime NET score and k-mer scores to the earlier heuristic score value
• Fixes bug in playlist load code

v6.0.250

DEV-2521 Re-Develop microservice for getting institution active products

Application Portal WebUI

• Update processor server spooling from user-based to institution-based
• Added API and JSON utilities

v6.0.251

DEV-2652 Remove extra character string from Consensus amplion fasta files

Consensus_main

• Removes extraneous string

v6.0.252

DEV-2267 Display release notes in web UI

Application Portal WebUI

• Update release notes page to display formatted markdown files

v6.0.253

DEV-2655 Fix cancel requests executed while generating modified oligos

PanelPlex_main, Consensus_main

• Fixes cancel request

v6.0.254

DEV-2656 Fix amplicon len off by one error in Consensus results

Consensus_main

• Debug amplicon length value in Consensus results

v6.0.255

DEV-2653 Include target input oligo_name in name of primer/probe candidates

PanelPlex_main, Consensus_main

• Update primer and probe candidate names to include the target input oligo_name

v6.0.256

DEV-2657 Add a note in the WEB UI file upload limit

PanelPlex_main, Consensus_main

• Update - inform users on file upload limit

v6.0.257

DEV-2658 Fix PP modified oligos functionality

PanelPlex_main, Consensus_main

• Bug fix - remove obfuscating double quote characters from modifier input csv file
• Bug fix - use oligo name instead of oligo id

v6.0.258

DEV-2660 Filter junction probes to force junction overlap

PanelPlex_main, Consensus_main

• Adds filter to force probes to overlap junction
• Fixes error in Excel input of region files
• Removes incorrect failure on no results found

v6.0.259

DEV-2653 Include target input oligo_name in name of primer/probe candidates

PanelPlex_main, Consensus_main

• Bug fix - use oligo_function abbreviation in oligo_name

v6.0.260

DEV-2662 Fix error writing zeroes in Json

PanelPlex_main, Consensus_main

• Changes Jackson settings to no longer strip zeroes

v6.0.261

DEV-2663 Fix prefiltering and sorting in mix and match

PanelPlex_main, Consensus_main

• Removes positional filtering for probes prior to mix and match
• Sorts Reverse and RT primers by their five prime end for mix and match

v6.0.262

DEV-2665 Create oligos from modified sequences early

PanelPlex_main, Consensus_main

• Bug fix - add modified sequences to compete with generated candidates

v6.0.263

DEV-2666 Fix Null Pointer Exception in Oligo name creation

Consensus_main

• Alters Consensus naming to use the proper data it has access to

v6.0.264

DEV-2669 Change "Target Strand" to "Probe binds to"

Application Portal WebUI

• Update wording of the label for which strand a probe binds to

v6.0.265

DEV-2648 Set weight to zero for "Off-target-hits" penalty

Application Portal WebUI

• Changes the default scoring weight for the raw off-target hits

v6.0.266

DEV-2667 Consensus cross-hyb table missing primer/probe Tms

PanelPlex_main, Consensus_main

• Bug fix - report two-state melting temperature in the Designs Dashboard

v6.0.267

DEV-2670 Store Consensus-specific settings

PanelPlex_main, Consensus_main

• Bug fix - port remaining Consensus input parameters to the new structure for import

v6.0.268

DEV-2671 Fix Consensus Coverage:Alignment sequences displayed and used for stats

Consensus_main

• Bug fix - correct offset error in Consensus coverage display for alignment

v6.0.269

DEV-2572 Ensure that runs fail gracefully after database connection loss

PanelPlex_main, Consensus_main, Thermosleuth_main, Application Portal WebUI

• Forces a run to a failed state if it failed unable to do so from the processor
• Adds extra logging for mix-and-match
• Removes last vestiges of the old error reporting code

v6.0.270

DEV-2678 Fix attempt to get run directory from ThermoSleuth sub-jobs

Application Portal WebUI

• Prevents the failure check from loading ThermoSleuth sub-jobs

v6.0.271

DEV-2676 Adjust TS amplicon sequence displayed

Thermosleuth_main, Application Portal WebUI

• Bug fix - show exact sequence of the amplicon in export functions and genome viewer

v6.0.272

DEV-2680 Fix evaluation for whether controls are in targets

PanelPlex_main

• Fixes coordinate checking for whether control oligos are in a given target

v6.0.273

DEV-2677 Fix Design Dashboard DG, DH values

Application Portal WebUI

• Adjusts DH table to pull from the correct data

v6.0.274

DEV-2679 Ensure PP tiling run can start multiple jobs

PanelPlex_main

• Bug fix - preserve user's contact email throughout tiling runs

v6.0.275

DEV-2050 Update portal with new v6 EULA

Application Portal WebUI

• Update - add latest EULA and policy policies
• Bug fix - fix 'not forwarding' bug

v6.0.276

DEV-2590 Debug EULA acceptance API call

Application Portal WebUI

• Bug fix - update API call
• Bug fix - remove out-dated reference links

v6.0.277

DEV-2681 Update probe filtering during Mixnmatch

PanelPlex_main, Consensus_main

• Adds positional short circuiting for probes
• Makes probe junction filtering use correct overlap padding
• Fixes error in positional sort
• Allows cancelling job during mix-and-match

v6.0.278

DEV-2590 Debug EULA acceptance API call

Application Portal WebUI

• Bug fix - extract policy version from file name

v6.0.279

DEV-2688 Address null pointer error when checking predesign parent oligo

PanelPlex_main

• Bug fix - Predesign probes are not generated from a junction input

v6.0.280

DEV-2694 Fix creation of amplicon string for negative sense runs

PanelPlex_main, Consensus_main

• Correct the creation of the amplicon strings on negative sense runs
• Fix null pointer exception running with no probes

v6.1.0

DEV-2691 Update pipeline for v6.1.0 release

Application Portal WebUI

• Update policies and documentation

Changelog

v5.0.25

DEV-2080 Fix error where ThermoSleuth results improperly pruned

ThermoSleuth

• Adjusts code to remove incorrectly applied pruning.

v5.0.26

DEV-2082 Fix race condition in playlist saving

Sequence Playlists

• Removes race condition.

v5.0.27

DEV-2091 Update Portal to use latest version of EUtils

Sequence Playlists

• Updates library.

Changelog

v5.0.23

DEV-209 Incorporate updated primer-dimer prediction algorithm

Targan

• Makes enzyme homodimer check conditional on initial target strand type.

v5.0.24

DEV-1993 Fix CopyCount to handle GOI and control in the same channel

CopyCount

• Update CopyCount to distinguish between GOI and control even in the same channel.

Changelog

v5.0.22

DEV-320 Update Targan to use new playlist format

Targan

• Adds the ability to index the new Playlist format on the fly for Targan usage

Changelog

v5.0.13

DEV-297 Add missing queries to update MySQL scripts

Application Portal WebUI

• Added new tables and update existing tables to support 4.6.0 and 5.0.0 functionality in the SQL migration files, thus avoiding a manual work-around

v5.0.14

DEV-306 Interamplicon test in PanelPlex is Broken

PanelPlex_main

• Updated the temporary playlist generation code to properly interface with ThermoSleuth, and made the amplicon gap generation key off of the keystone alone

v5.0.15

DEV-277 Doxygen code documentation trial

Project_Behemoth

• Added initial documentation (via Doxygen) with config file.

v5.0.16

DEV-302 Clean up Behemoth with .gitignore

Infrastructure & Server Config, Project Behemoth

• Consolidated and updated .gitignore for IDE related files. Cleaned up files that should have been ignored

v5.0.17

DEV-303 Replace source of percent bound result

ThermoSleuth

• Gets PB from TS
• Altered PB from TS (/100) and limiting it to 4 decimal places
• Changed all methods which access percent Bound to Two State Fraction Bound
• Changed DB column name from PercentBound to TwoStateFractionBound

v5.0.18

BHM-2905 Filter out and ignore improbable (e.g. low percent bound) TB hits.

ThermoSleuth

• Updates code to use the new MaxHitsPerOligo parameter

v5.0.19

DEV-315 Have ThermoSleuth run multiple primers and probes in a single execution.

ThermoSleuth

• ThermoSleuth runs will now run multiple primers/probes at a time.

v5.0.20

DEV-316 Update release notes for 5.0.20 release

Infrastructure & Server Config

• Updates release notes.

v5.0.21

DEV-317 Fix default for number of PanelPlex results

PanelPlex_main

• Sets the default number of multipick solutions to the lesser of panels+1 or a configurable number.

Version 5.0.12

February 2022

Changes made to Playlist Creation:

• Users will be provided with options regarding letters other than IUPAC and agct's in playlist preperation.
• Remove slashes from playlist name.
• Fix playlist creation table lock issue.

Changes made to PanelPlex™-NGS:

• Regions .csv will have all the amplicons, synchronized the code block.
• Checks for null pointers on PanelPlex file.
• Fixes race condition that was resulting in missing amplicon data in PanelPlex CSV output.

Changes made to PanelPlex™-Consensus:

• Removes checks against Ns in region, and adds them for Ns in amplicon instead.
• Corrects update of 3' and 5' positions for control primers from inclusivity run.
• Improves coverage penalties in solutions with multiple primer pairs, so that the penalty is not overly excessive.
• Don't prohibit ambiguity codes if using FastCompare.

Changes made to ThermoBLAST-CE:

• Remove the empty sequence and notify the user.
• Updates ThermoBLAST to ThermoSleuth

Changes made to qPCR CopyCount:

• Users will be able to delete managed assays.
• Fixes error in CopyCount CNV channel selection.
• Improves CNV channel defaults.

Changes made to Infrastructure:

• Don't simply return least loaded server if there are no available servers with enough capacity.
• Updates to make the code compatible with newer MySQL versions.
• Adds config variable that can set a webserver to not check for jobs to forward to a processor server.

Version 4.1.1

September 2018

Changes made to qPCR CopyCount since the previous (4.0) release:

• Added QuantStudio 3 Data processor

Changes made to PanelPlex™-NGS since the previous (4.0) release:

• Added performance and efficiency enhancements.
• Updated the NGS input format to specify a junction range instead of a single position.

Version 4.0

May 2018

Added new product: PanelPlex™-NGS

• Allows for multiplexes up to 50plex (later versions will increase this limit)

Changes made to PanelPlex-MDx since the previous (3.2.1) release:

• Changed name of product from PanelPlex to PanelPlex-MDx. Clarifies that this product is for the consensus design of molecular diagnostics for infectious diseases.
• Added functionality to save all the input parameters for a given run. This allows accurate documentation of how each run was performed.
• Added functionality to run PP-MDx using the input parameters file. This allows runs to be repeated exactly with minimal opportunities for user input error.
• Improved default settings in PP-MDx.
• Scoring weight for G-quartet penalty increased.
• Added functionality to download all results as a .zip file.
• Page load times improved.
• Improved layout of Next and Back buttons on each page.
• Genomes with lower case letters (such as Zika virus) now correctly shown in the Coverage section of the output.
• Improved automatic keystone selection

Changes made to ThermoBLAST-CE since the previous (3.2.1) release:

• Increased number of CPU cores devoted to ThermoBLAST jobs from 14 to 33. Resulting in runtime improvement.
• Fix ability to add and remove accessions from an existing ThermoBLAST playlist
• Fixed issue where downloaded amplicon had 1 extra nucleotide on the 5’-end and was missing 2 nucleotides at the 3’-end.
• Functionality for automatic detection and deletion of duplicate accessions.
• Fixed functionality for combining pre-existing playlists.
• Increased memory limits to allow for larger playlists to be handled.
• Amplicon detection algorithm improved to both go faster and also to detect more amplicons. In the previous version some weak binding primers would not be detected as amplicons.
• Minor bug fixes and optimizations
• Several new playlists added (e.g. Vaginal microbiome, GEBA).
• Known remaining issue: Within the “View Playlist” page if you try to edit the playlist then the program terminates. Workaround: Log back in and edit the playlist from the “Playlists you created” page.

Changes made to qPCR CopyCount since the previous (3.2.1) release:

• Added support for MJ Research data format.
• Non-permanence of data implemented for CNV
• At rest encryption added for CNV data