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Commits on Nov 20, 2014
Tiago Grego tg6 retrieve_qc_run_results_fast gene name search changed to solr gene index c3442cd
Commits on Nov 21, 2014
Tiago Grego tg6 QcRunSummary uses legacy code for design based runs, and new gene by …
…gene code for crispr runs
a8c96b5
Tiago Grego tg6 v0.270
    QcRunSummary report gene symbols and support for crispr qc
f76c2d5
Tiago Grego tg6 QcRunSummary report display name updated 712dd2e
Commits on Nov 25, 2014
af11-sanger af11-sanger report caching extended to support data structures using json. starte…
…d writing recovery detail report
e2c1edc
Commits on Nov 26, 2014
af11-sanger af11-sanger use report structured data to provide dates in recovery overview page 4251993
af11-sanger af11-sanger sensible error when plate or well not found 704a9e6
af11-sanger af11-sanger implemented recovery overview to detail click throughs 3e6c6ed
Commits on Nov 27, 2014
af11-sanger af11-sanger faster better recovery detail reports 2ebd951
Tiago Grego tg6 wge_design_importer logs d389174
Commits on Dec 01, 2014
Saj sajp factor out javascript dealing with updating crispr es qc well values …
…into seperate file
96d2380
Saj sajp show values for validated and variant size to crispr es qc well values b075770
Saj sajp refactor code to add a update_crispr_well method 689eb77
Saj sajp add variant size and validated columns to crispr es qc well 617ee34
Saj sajp add validated column to crispr es qc run 9bac7d8
Commits on Dec 02, 2014
Saj sajp add comments to javascript a499a6e
Saj sajp add API method to validate a crispr es qc run 8d461fb
Saj sajp add button to validate crispr es qc run, display validated flag on qc…
… run list page
4722ecb
Saj sajp update crisprs_es_qc tables dc9c8a3
Saj sajp store variant size result for crispr es qc d0ef29e
Saj sajp delete commented out html 0fb0a87
Saj sajp hide non human reports from menu when species is set to human 2e4777c
Saj sajp make changes to the Legacy Cre KnockIn project report 775265c
Saj sajp Merge branch 'devel' into crispr_qc_variant_type a3e2d44
af11-sanger af11-sanger recovery detail report now uses structured data and includes current …
…project info
d21b9c9
af11-sanger af11-sanger fixed some bugs in crispr recovery detail reports. still not showing …
…both left and right crispr wells..
54649fc
Commits on Dec 03, 2014
Saj sajp fix perlcritic issues f6ef0e3
Saj sajp v0.271
    Update Legacy Cre KnockIn report
fc8ddca
Saj sajp Merge branch 'devel' into crispr_qc_variant_type f6345b4
Saj sajp crispr es qc should mark any well as accepted if anything other than …
…no-call is set for the variant type, only do this is the base ep well is not already marked as accepted
550709d
Saj sajp tidy up 6000c04
Saj sajp add no-call as a crispr damage type 0aa4789
Saj sajp remove validated field from crispr_es_qc_wells tables 4da287d
Saj sajp update tests for crispr es qc plugin module 04daf20
af11-sanger af11-sanger implemented project status update from recovery details report 205b8c4
af11-sanger af11-sanger fix to recovery class foreign key in projects table 5d5e5ff
af11-sanger af11-sanger v0.272
    Bugfix: recovery class foreign key added to correct column
ecb19b8
Commits on Dec 04, 2014
Saj sajp move ddl version to 79 6b3e117
Saj sajp update to version 79 dc2b0fb
Saj sajp Merge branch 'devel' into crispr_qc_variant_type b242de0
Saj sajp Merge branch 'master' into devel d0186ec
Saj sajp v0.272 32ad7c7
af11-sanger af11-sanger Merge branch 'devel' into recovery_reports 92da273
Tiago Grego tg6 QC Run Summary Report fix 27e7121
af11-sanger af11-sanger started adding extra information to recovery detail reports 3c3e70c
David Parry-Smith dparrysmith Added a public report for AlleleDump b112d82
David Parry-Smith dparrysmith Merge branch 'devel' into david_misc b1819cc
David Parry-Smith dparrysmith v0.273
    Added public report AlleleDump to generate a (compressed) csv for partner download
5331ec4
af11-sanger af11-sanger added recovery overview link to nav bar 7833c86
Commits on Dec 08, 2014
Tiago Grego tg6 changed 'crisprs constructed' field to display accepted CRISPR_V wells 1ac9baa
Commits on Dec 09, 2014
af11-sanger af11-sanger merged devel. removed debugging. perlcritic fixes. 85a190a
af11-sanger af11-sanger Merge branch 'devel' 70e91cb
af11-sanger af11-sanger v0.274
   Added recovery reports
09fbf1e
Tiago Grego tg6 pcr passes back into sub sponsor report 5d5d08f
Tiago Grego tg6 Merge branch 'devel' of github.com:htgt/LIMS2-WebApp into devel f17d877
Tiago Grego tg6 Merge branch 'devel' 1fa8835
Tiago Grego tg6 pcr passes only show up when logged in cf2883d
Tiago Grego tg6 Merge branch 'devel' 5a0085d
Tiago Grego tg6 v0.275
    Added pcp passed to sponsor sub report when user is logged in
60247c7
Commits on Dec 10, 2014
Saj sajp do not make crispr es qc well accepted to true if its parent well is …
…already accepted, add test for this
909d04e
Saj sajp Merge branch 'devel' of github.com:htgt/LIMS2-WebApp into devel 3f29a8b
Tiago Grego tg6 Merge branch 'devel' of github.com:htgt/LIMS2-WebApp into devel 30f8fa6
af11-sanger af11-sanger sort gene name lists fd272f5
af11-sanger af11-sanger added numerical ID to recovery classes so users can edit name. update…
…d forms and API accordingly
5e2397d
Commits on Dec 11, 2014
Saj sajp remove link to gene crispr es qc page, not wanted, leave page in thou…
…gh in case they want it back
9888c68
Saj sajp modify crispr qc view sub template to be more flexible in what it sho…
…ws, also if its used to update crispr es qc information or not
9d528e5
Saj sajp update links to crispr_qc_view sub template to send in correct flags …
…so correct info is shown
3e80da8
Saj sajp make multiple changes to gene summary page:
All tabs are closed by default
Reverse order of tabs, latest wells first
show additional information in crispr qc tab
8c92414
Saj sajp tidy up crispr qc title 2b51f9e
Saj sajp add a update_crispr_es_qc_run method instead of one just to validate …
…a crispr qc run
d4e2c22
Saj sajp add update crispr es qc run REST method, replaced validate method c6aa8c8
Saj sajp wip on invalidate button on crispr es qc run page a8f7338
af11-sanger af11-sanger show recovery class name in sponsor progress report 56c9986
af11-sanger af11-sanger Merge branch 'recovery_reports' into devel c5b547a
af11-sanger af11-sanger Merge branch 'add_recovery_class_id' into devel d14ae9e
af11-sanger af11-sanger v0.276
   Added ID primary key to recovery classes so names can be modified
651bd4f
Saj sajp remove surplus columns from crispr qc view on gene summary page 636fc20
David Parry-Smith dparrysmith Fixed mismatched alignment of rows between locked and scrolling regio…
…n in

extJs grid
26ea51d
David Parry-Smith dparrysmith Merge branch 'david_misc' into devel 4703ac2
af11-sanger af11-sanger bugfix: recovery classes were not displayed in sponsor report f3a1abd
af11-sanger af11-sanger Merge branch 'devel' of github.com:htgt/LIMS2-WebApp into devel 39ef667
Commits on Dec 12, 2014
Saj sajp switch from using scratch109 1ef10f6
Saj sajp Merge branch 'devel' into gene_summary_changes 19e6d03
Saj sajp Merge branch 'devel' into crispr_qc_run_changes 635237b
Tiago Grego tg6 sponsor All selection fix 1ac2d17
Tiago Grego tg6 Merge branch 'devel' of github.com:htgt/LIMS2-WebApp into devel 7b7b2de
Tiago Grego tg6 Merge branch 'devel' 3dd6af7
Saj sajp add invalidate button to crispr es qc run, also show validated badge dbd0d68
Tiago Grego tg6 v0.277
    Sponsor All selection fix on project efforts/recovery overview
38bf10b
Commits on Dec 15, 2014
Saj sajp if damage type no-call or mosaic then unset accepted flag 2d35fc9
Saj sajp only unset accepted flag on crispr es well if it is already accepted 18882b0
Saj sajp disable accepted flag if damage type is mosaic or no-call e86be59
Saj sajp automatically uncheck and disable accepted checkbox if damage type ch…
…anged to no-call or mosaic
a83fa25
Saj sajp add more tests for update_crispr_es_qc_well method 87272cc
David Parry-Smith dparrysmith Added WGE REST config for devel to lims2_setup.sh 5a9d46f
Commits on Dec 16, 2014
David Parry-Smith dparrysmith Added WGE REST client command for live or devel 06783d0
Tiago Grego tg6 recovery damage reporting on sponsor report f1a658a
Commits on Dec 18, 2014
Saj sajp Merge branch 'devel' into crispr_qc_run_changes 69f3ea2
Saj sajp v0.277
    Changes to crispr es qc interface
111981a
Saj sajp v0.278
    Changes to crispr es qc interface
d787dad
Tiago Grego tg6 sr displaying overview counts, ep counts can be been by clicking the …
…ep value
99f4fa1
Commits on Jan 06, 2015
af11-sanger af11-sanger can now flag genotyping primers as validated on assembly plate report ada11af
Commits on Jan 07, 2015
af11-sanger af11-sanger user can now flag crispr primers as validated too b24c9d3
af11-sanger af11-sanger validated primers now linked to qc runs via qc template wells and dis…
…played in qc results
d8debec
Commits on Jan 09, 2015
Tiago Grego tg6 sponsor report updates for staging deployment 6fbfbc9
Tiago Grego tg6 Merge branch 'devel' into sr_damages_grouped 20bd657
Tiago Grego tg6 fixed column 'info' on sponsor sub report 846863f
Commits on Jan 12, 2015
af11-sanger af11-sanger fixes for tests dd563e4
Commits on Jan 13, 2015
af11-sanger af11-sanger added missing fixtures file 92c17fa
af11-sanger af11-sanger added more barcode discard reasons 9f3028b
af11-sanger af11-sanger v0.279 af5e782
Tiago Grego tg6 sponsor report caching for staging and devel 99288d4
Commits on Jan 14, 2015
Tiago Grego tg6 merged development sponsor_sub_report_genes.tt into sponsor_sub_repor…
…t.tt
c1d3b34
Commits on Jan 16, 2015
Tiago Grego tg6 fixed path of staging cached sponsor reports c1ccf51
Commits on Jan 19, 2015
Saj sajp scratch109 is back up, switch back to using it aa31e95
Saj sajp Merge branch 'master' into devel f8dbd50
Saj sajp v0.280 55974d5
Commits on Jan 21, 2015
Tiago Grego tg6 caching of sr full reports added, several changes required on the sr …
…added
0c44bc5
Tiago Grego tg6 Merge branch 'devel' into sr_damages_grouped 4450629
Saj sajp sort public gene page results by crispy damage type, only show damage…
… type from validated runs
892df31
Saj sajp custom order for summary data on public gene summary page 45bc299
Commits on Jan 22, 2015
Saj sajp Merge branch 'devel' 64afa27
Saj sajp v0.281 9e92855
Tiago Grego tg6 latest fixes to front page sponsor report. getting ready for live 4988376
Tiago Grego tg6 forked sponsor report to allow single targeted and non crispr mouse p…
…rojects to use the old codebase
848105f
Tiago Grego tg6 Merge branch 'devel' into sr_damages_grouped 3f4ee52
Tiago Grego tg6 v0.282
    Added new front page sponsor report
ed3410e
Tiago Grego tg6 count misplacement fixed 3e897e0
Commits on Jan 23, 2015
Tiago Grego tg6 front page report recovery class cleanup, damages ordering standardized ad43ba7
Tiago Grego tg6 Added well_genotyping_info_search error page a50e22e
Tiago Grego tg6 hidden Date Report from gene summary search cae4e6a
Commits on Jan 26, 2015
af11-sanger af11-sanger started refactoring of primer generation code from LIMS2-Scripts b4a0804
af11-sanger af11-sanger combined primer generate methods for single and paired 6cdaa5b
Commits on Jan 27, 2015
Tiago Grego tg6 Removed unclassified variant calls a8c7585
Tiago Grego tg6 Added variant size to Public Gene Report Page 28a0885
Tiago Grego tg6 well_genotyping_info changes 80d6fc2
Tiago Grego tg6 vep and vcf files hidden by default in well_genotyping_info b1d2202
Commits on Jan 28, 2015
David Parry-Smith dparrysmith Allow ambiguous base calls in the trace viewer
Corrects issue wih traces not displaying in CRISPR ES QC when there are
multiple calls for a specific location. This resolution may not be ideal
but permits the valid trace to be viewed even if the base calling is not
ideal.
d1d12b3
David Parry-Smith dparrysmith Merge branch 'master' into devel 67e20c2
David Parry-Smith dparrysmith v0.283
    Corrected behaviour of trace viewer to deal with ambiguous base calls for CRISPR ES QC
60ea0a3
af11-sanger af11-sanger now using LIMS2::Util::QcPrimers to generate crispr pair primers 9837cdd
af11-sanger af11-sanger crispr primers now generated for single or pair c6785a5
Tiago Grego tg6 Gene page Pre-Injection QCs renamed to Secondary QC 6768e7b
Commits on Jan 29, 2015
Tiago Grego tg6 Merge branch 'devel' of github.com:htgt/LIMS2-WebApp into devel f1a5140
Tiago Grego tg6 Merge branch 'devel' c40830a
Tiago Grego tg6 v0.284
    Changes to the clones page and well genotyping info page
78e62cd
af11-sanger af11-sanger genotyping primers now generated but not checked against existing script c3c4366
Commits on Jan 30, 2015
Tiago Grego tg6 unitialized variable bug fix e368cbf
Tiago Grego tg6 Updated colony count uploads 22177c5
Commits on Feb 02, 2015
af11-sanger af11-sanger added crispr pcr primer generation (needs further testing) 0554239
Commits on Feb 04, 2015
af11-sanger af11-sanger added group_crispr_assembly process and supporting code 63c4862
af11-sanger af11-sanger perlcritic fixes ebf16bc
af11-sanger af11-sanger display crispr group primers on assembly plate report 3425310
af11-sanger af11-sanger genoverse_primer_view now displays crispr group crisprs 9fb524f
af11-sanger af11-sanger genoverse now displays crispr group crisprs and primers 176c452
af11-sanger af11-sanger ignore perlcritic subroutine complexity complaint 7f04286
af11-sanger af11-sanger Merge branch 'devel' into primer_generation 7cf005c
af11-sanger af11-sanger added some shortcut methods to Crisprs, Groups and Pairs so they can …
…all be used in the same way when persisting crispr primers etc
84beb0f
Commits on Feb 05, 2015
af11-sanger af11-sanger added group primer generation settings 98b5a61
af11-sanger af11-sanger removed unique constraints from crispr_primers table and updated code…
… to handle this
7f19ebb
af11-sanger af11-sanger changes to persist crispr pcr primers 784c22e
Tiago Grego tg6 fixed qc_template_plate_template.csv 183604d
af11-sanger af11-sanger v0.285
   Added group_crispr_assembly process
598d6ec
Commits on Feb 06, 2015
David Parry-Smith dparrysmith Added Genoverse button to Intermediate plates
Shows design and ensembl tracks only at the moment.
bfc6f38
David Parry-Smith dparrysmith Merge branch 'devel' into david_misc 31ccc3a
Commits on Feb 09, 2015
Tiago Grego tg6 Added reporting filter to the EP/CRISPR_EP wells b894fda
Tiago Grego tg6 Merge branch 'devel' of github.com:htgt/LIMS2-WebApp into devel a00a50d
Tiago Grego tg6 Merge branch 'devel' 58f2020
Tiago Grego tg6 perlcritic issue 272f101
Tiago Grego tg6 Merge branch 'devel' 6b89912
Tiago Grego tg6 v0.286
    Added reporting filter to the EP/CRISPR_EP wells
    Added Genoverse button to Intermediate plates
785775f
Tiago Grego tg6 removed colonies_picked counts from sponsor report 265b0fc
af11-sanger af11-sanger try generating primers for nonsense crisprs 351c5ad
af11-sanger af11-sanger remove requirement for design id when getting primers a7071ef
af11-sanger af11-sanger merged latest devel changes 28a1a66
Commits on Feb 10, 2015
af11-sanger af11-sanger can now persist genotyping primers 230ee93
af11-sanger af11-sanger started work on user interface to primer generation ac8ed05
Commits on Feb 11, 2015
af11-sanger af11-sanger interface to generate primers and display results c87f7dd
af11-sanger af11-sanger primer generation now runs in child process e1dc2d0
Commits on Feb 12, 2015
af11-sanger af11-sanger minor changes to primer generation interface 305d298
Commits on Feb 13, 2015
Tiago Grego tg6 default sponsor report changed from simple to full mode e916fb4
Tiago Grego tg6 reverted last commit... testing required 7d45e98
Tiago Grego tg6 default sponsor report changed from simple to full mode 8e9eb7c
Commits on Feb 16, 2015
Tiago Grego tg6 to_report well flag toggle fix 7600540
Tiago Grego tg6 reverted default sponsor. need to change cache generation 5f3678e
af11-sanger af11-sanger primer generation interface bug fixes and improvements; 0bfdc74
Commits on Feb 17, 2015
Saj sajp switch EngSeqParams util module to use custom fixture data ad4e20a
Saj sajp eng seq param generation should throw error when encountering a nonse…
…nse design
9281f81
Saj sajp new relationship maps for nonsense related work 912b109
Saj sajp add new nonsense design info to static test data ce2741d
Saj sajp make db changes to allow storing of nonsense crisprs and designs a7758a5
Saj sajp design info module throws error when faced with nonsense type design,…
… added tests
cd3266f
Commits on Feb 18, 2015
Tiago Grego tg6 front page cached report defaulted to full report, fixed bug in csv d…
…ownload, atempted to fix browser cache to provide text file instead of displaying the cached html
582ae66
Tiago Grego tg6 Merge branch 'devel' 43b79f4
Tiago Grego tg6 v0.287
    front page cached report defaulted to full report, fixed bug in csv download
    atempted to fix browser cache to provide html instead of text file sometimes
3a1af7b
Commits on Feb 19, 2015
Tiago Grego tg6 atempt 2 to fix browser cache to provide html instead of text file so…
…metimes
bfdb77e
Saj sajp FarmJobRunner module is not in WebAppCommon 8746582
Saj sajp add new nonsense crispr column to create crispr method ec3b8f3
Tiago Grego tg6 Added frameshift clones count to CrisprEPDetail report adbf465
Tiago Grego tg6 Added chromosome to front page sponsor sub report 4a6d21e
Tiago Grego tg6 removed the show_all option from find_gene, adapted retrieve_gene f9079b8
Tiago Grego tg6 CrisprEPDetail perlcritic d94f2b6
Tiago Grego tg6 missing , in sponsor report... 6fc7b36
af11-sanger af11-sanger option to generate primers for short arm designs. option to run bwa o…
…n farm. primer generation files now written in LIMS2_PRIMER_DIR
ba9d2bb
Commits on Feb 20, 2015
Saj sajp fix typo e4cfef1
Saj sajp typo fix and relax nonsense crispr id constraint efecb3e
Tiago Grego tg6 final changes to include chr on front page sub report cadc225
Tiago Grego tg6 perlcritic CrisprEPDetail report 5d94656
Tiago Grego tg6 v0.288
    Added chromosome to front page sponsor sub report
    Added frameshift clones count to CrisprEPDetail report
38da454
Tiago Grego tg6 chromosome not hidden on simple sponsor sub report 54384fc
Tiago Grego tg6 Merge branch 'devel' 7ec5166
Tiago Grego tg6 chromosome not hidden on simple sponsor sub report 55473e2
Tiago Grego tg6 Merge branch 'devel' e7d5413
Tiago Grego tg6 v0.289
    chromossome shown always at the simple sponsor sub report
732090f
Tiago Grego tg6 Pathogen Group 3 mouse project for sponsor sub report 3086d83
Commits on Feb 23, 2015
Saj sajp add nonsense crispr info to crispr view ea1a01b
Saj sajp update design view page to show nonsense crispr details 08dfdb0
Saj sajp add linked_nonsense_crisprs method 26d4a72
Saj sajp data for crispr view 92aea44
Saj sajp modify design info module to work with nonsense designs instead of ju…
…st dieing
30286dc
Saj sajp Add new nonsense oligo to hash of oligo colours for genome browser cf30e15
Tiago Grego tg6 sponsor sub report colony counts fixed f2fc48d
Saj sajp make more attributes type Maybe[Int] because nonsense designs 00ec532
Saj sajp add tests for nonsense designs with DesignInfo module a1fc1a1
Tiago Grego tg6 v0.290
    Sponsor sub report colonu_counts fix
    Mouse project Pathogen Group 3 added
d2a3bfb
Saj sajp Merge branch 'devel' into nc_work 4b1f03a
Saj sajp update crispr and design resultset sets with new columns 6f9ae7c
Tiago Grego tg6 added gene id and name to crispr plate view when no design ids are av…
…ailable
be79764
Commits on Feb 24, 2015
Saj sajp Merge branch 'devel' into nc_work 5bef48d
Saj sajp Merge branch 'master' into devel 38c85c0
af11-sanger af11-sanger added error capture for primer generation for each well 35b2b35
Commits on Feb 25, 2015
af11-sanger af11-sanger merge latest devel changes and fix schema numbering clash 1ceb9e9
af11-sanger af11-sanger fixed naming of crispr primer generation method/project name adb1738
af11-sanger af11-sanger store design gene strand in cache for output to csv d88a46d
Tiago Grego tg6 Added crispr information to Well Genotyping Info 275f347
Tiago Grego tg6 smart comments removed a40e8ac
af11-sanger af11-sanger primer file download now uses job_id and file name instead of file path 8422c22
af11-sanger af11-sanger perlcritic fixes 5fe91c7
Commits on Feb 26, 2015
af11-sanger af11-sanger added fixtures file 04ca35a
Tiago Grego tg6 spacing fix at well_genotyping_info 9342afd
af11-sanger af11-sanger last minute fixes 464b30e
af11-sanger af11-sanger Merge branch 'devel' of github.com:htgt/LIMS2-WebApp into devel bf477d5
Saj sajp bugfix, we were hiding reverse alignments if there was no forward ali…
…gnments
cae01be
Tiago Grego tg6 removed parent POSTINT, added parent FINAL data on FinalPickVectorPla…
…te view
3b54779
Tiago Grego tg6 Merge branch 'devel' of github.com:htgt/LIMS2-WebApp into devel d8cb1f9
Commits on Feb 27, 2015
Tiago Grego tg6 gene name search on public_gene_report changed to find_gene 3f5672e
Tiago Grego tg6 changed default appends on crispr order sheet from u6 to t7 (v1, barry) 500a7b8
Commits on Mar 02, 2015
Saj sajp type fix 29f60ef
af11-sanger af11-sanger identify crispr groups linked to design 545e6b8
af11-sanger af11-sanger Merge branch 'devel' of github.com:htgt/LIMS2-WebApp into devel ad6c501