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Commits on Aug 30, 2012
@sajp sajp return true when process deleted 1e923c5
@sajp sajp bugfixes, column name is id not design_id, must first delete oligo lo…
…ci before deleting oligoes themselves to avoid foreign key constraint errors
@sajp sajp add tests for design creation and deletion 4b9e2b3
@sajp sajp add tmp dir to ignore list 5a6c59b
@sajp sajp changes names of columns used to specify parent wells for second elec…
…troporation plate upload, fix csv template as well
@sajp sajp check that 2 input wells for second_electroporation process are DNA a…
…nd XEP, add tests for this
@sajp sajp fix variable names for validation of second_electroporation parent wells 85ab614
Commits on Aug 31, 2012
@sajp sajp fix links to stylesheets 0af48f1
@sajp sajp plate create test, fix parent well variable names ad01dbc
@sajp sajp throw exception if both cassette and backbone specified for a 2w gate…
…way process
@sajp sajp add test for either cassette or backbone validation on 2w gateway pro…
@sajp sajp Merge branch 'devel' into improve_test_coverage 5ff3bf4
@sajp sajp bugfix, entity_class no entity 6044f20
@sajp sajp test list candidate designs for gene on +ve strand, and for non exist…
…ant gene
@sajp sajp add search for non existant gene fdaa7cc
@sajp sajp add test for creating a plate that already exists, test list plates f…
@markquintontulloch markquintontulloch Add sponsor name at top of reports - refs #8895 9e9952a
@markquintontulloch markquintontulloch Merge branch 'allele_request_tracking' into devel 3807f28
@markquintontulloch markquintontulloch Merge branch 'devel' of into devel f9bebf3
@markquintontulloch markquintontulloch v0.014
   Fixed SEP template
   Added SEP verification
   Sponsor heading added to reports
@sajp sajp Merge branch 'devel' 52c5428
@sajp sajp v0.015
   Fixed SEP plate upload template
   Added verification for 2w gateway process
   Moved code into Util modules
   Fix links to css files in header
Commits on Sep 03, 2012
@sajp sajp add plate rename subroutine, plus tests 92f9cb1
@sajp sajp check all a plates wells for child wells before attempting to delete …
…it, if it has child wells throw error, add tests for this check
@sajp sajp work in progress, plate edit page 1073367
@af11-sanger af11-sanger Cell line drop down list created. tests added. 448ba40
@af11-sanger af11-sanger ignore .project file 176fbee
Commits on Sep 04, 2012
@sajp sajp plate report viewable test e8de79d
@sajp sajp display sponsor as part of report name if its specified, no longer pu…
…t it at top of all reports
@sajp sajp Merge branch 'devel' 07900e1
@sajp sajp v0.016
    Bugfix, well reports were not working because they did not have a sponsor.
    Moved sponsor into report name, removed from generic Report code.
    Added test to make sure Plate Reports are viewable.
Commits on Sep 05, 2012
@sajp sajp add check for existing_backbone, use this instead of existing_final_b…
…ackbone check as intermediate_backbones can be present in final vectors
@sajp sajp show a clearer message to the user when we can not find the parent we…
…ll on plate upload, add tests for new error message
@sajp sajp Merge branch 'devel' 49bdd65
@sajp sajp Merge branch 'devel' into plate_edit_page c5ac77b
@sajp sajp v0.017
    Show clearer error message on plate upload when parent well does not exist.
    Switch from final-backbone check to just backbone check.
@af11-sanger af11-sanger work in progress b2a01c0
@af11-sanger af11-sanger Merge branch 'devel' into cell_line_drop_down
@af11-sanger af11-sanger update to sponsors table 5685af2
@af11-sanger af11-sanger cell line drop down and validation added 2926395
@af11-sanger af11-sanger updated .gitignore 2d19835
@af11-sanger af11-sanger Revert "update to sponsors table"
This reverts commit 5685af2.
@sajp sajp update Sponsor and ProcessRecombinase table DBIx Schema, lims2_devel …
…was slightly different from lims2_live so these files were out of date
@af11-sanger af11-sanger Valid cell line values added to fixtures and test input data 32338fa
@sajp sajp modify layout of plate_edit page 1f3030b
@af11-sanger af11-sanger fixture data corrected c83ab19
@af11-sanger af11-sanger Merge branch 'devel' into cell_line_drop_down 69d6384
Commits on Sep 06, 2012
@sajp sajp add delete_plate controller 31bc318
@sajp sajp add delete plate button and confirm modal, re-style page 1201ef5
@sajp sajp move plate has child wells check to plate object 83f00f3
@sajp sajp only show delete button for plates without child wells 732884e
@sajp sajp Merge branch 'devel' into plate_edit_page 2500575
@sajp sajp add rename_plate controller code 2b23bb0
@sajp sajp fix rename plate form url, add hidden form fields with plate id and c…
…urrent name
@sajp sajp move check for plate id into begin subroutine, rename params f8597b2
@sajp sajp restyle plate edit page, add link to edit page from plate view page 5746a98
@sajp sajp remove extra blank line 7f2fd09
@sajp sajp add tests for plate edit page, including plate rename and plate edit ff1be06
@sajp sajp move plate edit functionality from own plate edit page to plate view …
@sajp sajp rename test file 97feed6
@sajp sajp remove controller code for edit_plate page 4c9a20b
@sajp sajp Merge branch 'devel' into improve_test_coverage
@af11-sanger af11-sanger Merge branch 'devel' da4f241
@af11-sanger af11-sanger fixed perl critic issues 0b6e010
@af11-sanger af11-sanger Merge branch 'devel' fac2a06
@af11-sanger af11-sanger v0.018
	Added cell line drop down to plate upload and validation of cell line csv input
        Added plate edit functionality
Commits on Sep 07, 2012
@sajp sajp grant usage on cell_lines_id_seq to rw_role 40b1ee9
@sajp sajp upgrade bootstrap to 2.1.1 32466f3
@sajp sajp switch to custom bootstrap files, new defaults for text size and line…
… spacing in v2.1.1 were too large
@sajp sajp switch back to black navbar, wrap login name to make it line up prope…
…rly with logout button
@sajp sajp remove extra table header column 21ecc21
@sajp sajp new styling for non editable form inputs require disabled attribute i…
…nstead of readonly, we still want input to be sent with form submit so switch to hidden fields and a span that mimics a form input
@sajp sajp move db and software version info into footer stuck at bottom of page 8587a92
@sajp sajp Merge branch 'bootstrap_upgrade' into devel a6e447b
Commits on Sep 10, 2012
@sajp sajp add user dropdown navbar component 0d2aef8
@sajp sajp clean up navbar, move admin link to user dropdown ecfdc51
@sajp sajp add new password_string check 295b0b7
@sajp sajp add change user password subroutine 343e93b
@sajp sajp hide links in navbar from users without the right privilages 513006f
@sajp sajp add change password controller and view c97d5bc
@sajp sajp add tests for new password change form d776d29
@sajp sajp add plate list api b9ad938
@sajp sajp Merge branch 'devel' into improve_test_coverage 9793dd2
@sajp sajp add missing bracket; 1de143e
@af11-sanger af11-sanger Added GRCm38 oligo loci and changed default assembly in fixtures 6b1ac7a
Commits on Sep 11, 2012
@sajp sajp Merge branch 'devel' f7db4c4
@sajp sajp v0.019
   Default assembly now GRCm38
   Improved test coverage
   Updated to twitter bootstrap 2.1.1
   Implement change password form
   Styling improvements
@af11-sanger af11-sanger add process type and field creation tests cc22d21
@af11-sanger af11-sanger added tests for create/retrieve well accepted override and well recom…
…bineering results.

fixed bug in retrieve_well_recombineering_results method.
@af11-sanger af11-sanger added create/retrieve well dna quality tests e2d3160
@af11-sanger af11-sanger added more tests for well_qc_sequencing_result methods, implemented d…
…elete and fixed bug in retrieval
Commits on Sep 12, 2012
@sajp sajp add id to as_hash method for well object 9743a1f
@sajp sajp add test_result_url and created_by to as_hash method for WellQcSequen…
@sajp sajp Merge branch 'devel' into plate_list_api 7479a61
@af11-sanger af11-sanger speed up testing by using transaction rather than reloading fixtures …
…when possible
Commits on Sep 13, 2012
@sajp sajp Add extra debugging message 751a166
@sajp sajp Add delete well qc sequencing result API b7e777b
@af11-sanger af11-sanger safer way to ensure fixtures are reloaded after webapp has been tested 94e25f0
@af11-sanger af11-sanger Merge branch 'devel' into plugin_well_tests 8e31c7a
@af11-sanger af11-sanger Merge branch 'master' into devel 72f5326
@af11-sanger af11-sanger v0.020
	Unit test speed improvement.
	Added well_qc_sequencing_result delete method to API.
@af11-sanger af11-sanger add ddl template to create fixture_md5 table for test db e51bb31
@af11-sanger af11-sanger added tests for compute_accepted_status b553195
Commits on Sep 14, 2012
@sajp sajp Add news tests for clone_pool and freeze process creations 3647948
@sajp sajp whitespace removal a7b446c
@sajp sajp add test for process plate types 8743cd9
@sajp sajp Merge branch 'create_process_util' into devel 2d46f26
@sajp sajp add grants to allow new db to have tests run against it d0a1db0
Commits on Sep 18, 2012
@sajp sajp initial commit of code to generate lab electroporation report ce29d7e
@sajp sajp add dna_wells attribute to allele request object 3c66aa8
Commits on Sep 19, 2012
@sajp sajp move download button next to report title to free up more space for t…
…he report
@sajp sajp Add links to genes to electroporate report 1163327
Commits on Sep 20, 2012
@sajp sajp Split DNA wells on report into first and second allele, then into
promoter driven and promoterless cassettes
@sajp sajp initial commit of sponsor gene report fd57896
@sajp sajp renamed report 7cefff2
@sajp sajp make new reports work when no sponsor specified 2e63780
@sajp sajp no longer need second report, push data from here in to Genes To Elec…
…troporate report
@sajp sajp modify layout of report to place all wells of certain type in one col…
…umn, also only print FEP / SEP plate names
@sajp sajp show parent dna well for ep wells ec742e9
@sajp sajp whitespace cd78ca6
Commits on Sep 24, 2012
@sajp sajp Merge branch 'electroporation-report' into devel 707786e
Commits on Sep 25, 2012
@sajp sajp Add pick wells to allele request objects 618f65b
@sajp sajp add report for front page sponsor progress; 3945a7e
@sajp sajp incorporate new sponsor progress report into front page 64f5d36
Commits on Sep 26, 2012
@sajp sajp only show progress report if we can get a cached version of it 6962ac0
@sajp sajp remove debug code, rename column heading 0a3c7db
Commits on Oct 01, 2012
@sajp sajp use LIMS2::ReportGenerator::Plate d5d60d2
@sajp sajp make cache last 22 hours 3f9f8f4
@sajp sajp wrap gene symbol lookup in try block to catch errors in solr lookup f748ef1
Commits on Oct 02, 2012
@sajp sajp Merge branch 'devel' 4ee0658
@sajp sajp change front page report heading d36c429
@sajp sajp Merge branch 'devel' 9ccd0e9
@sajp sajp v0.021
    Added front page report
    Added genes to electroporate report
    Implemented more tests for process creation
@af11-sanger af11-sanger Added QC job submission form 88c6100
Commits on Oct 03, 2012
@af11-sanger af11-sanger Added QC job progress pages. Added plate map request to submit new qc…
… form (but not yet implemented)
@af11-sanger af11-sanger Fix to avoid error when listing qc run that has just started 88448ee
@af11-sanger af11-sanger Implemented plate map generation 7e00b86
Commits on Oct 04, 2012
@sajp sajp new qc_run fixture data to test against 4ae0934
@af11-sanger af11-sanger Modules for fetching lastest QC info from file system moved to HTGT-Q…
Commits on Oct 05, 2012
@sajp sajp bugfix, check file format exists e8b1ed9
@sajp sajp add tests for retrieval of qc run results b0678b7
Commits on Oct 08, 2012
@af11-sanger af11-sanger Merge branch 'devel' into submit_qc dd4831d
@af11-sanger af11-sanger fixed perlcritic issues b91bf8a
@af11-sanger af11-sanger Merge branch 'devel' f680219
@af11-sanger af11-sanger v0.022
	Added QC job submission form
	Added lastest QC jobs view
Commits on Oct 09, 2012
@sajp sajp add tests for QcResults Util module f1099a3
@sajp sajp Merge branch 'qc-tests' into devel 3c09ac3
Commits on Oct 11, 2012
@sajp sajp REST authentication no longer done using http basic auth, pass in use…
…rname and password through request params
@sajp sajp get authenticated mech through login form, not thorugh HTTP Basic Auth 42e9cb2
@sajp sajp use pre authenticated mech for tests 85981ea
@sajp sajp Merge branch 'devel' 23e60a4
@sajp sajp v0.023 e98d13e
Commits on Oct 12, 2012
@sajp sajp if no strand set then do not return oligo fasta files in design as_ha…
…sh method
@sajp sajp use authenticated mech 8bc83d3
@sajp sajp Merge branch 'devel' of into devel ea513a3
Commits on Oct 16, 2012
@af11-sanger af11-sanger Improved QC submission error reporting fc66ec2
@af11-sanger af11-sanger Remove qc_template_well name format check 80c38ce
@af11-sanger af11-sanger update schema version to 11 6832b32
Commits on Oct 17, 2012
@af11-sanger af11-sanger Initial work on generating EngSeq params 00209ee
Commits on Oct 18, 2012
@af11-sanger af11-sanger well plugin generate_well_eng_seq_params now complete (needs better t…
…est coverage)
Commits on Oct 22, 2012
@af11-sanger af11-sanger fixed find_process so it does not return empty resultsets 809700a
@af11-sanger af11-sanger fixed perlcritic issues f1c17a4
@af11-sanger af11-sanger arrayref constraint not needed. use well mehtods instead of ProcessGr…
…aph methods. more tests
@af11-sanger af11-sanger add test for allele engseq params 4a123ca
Commits on Oct 23, 2012
@af11-sanger af11-sanger methods and interface to create qc template plate from plate or csv u…
@af11-sanger af11-sanger refactored template generation methods. added interface tests d080e71
Commits on Oct 24, 2012
@af11-sanger af11-sanger added autocomplete to template plate field a4adddc
@af11-sanger af11-sanger qc_template_well can now store the source well id 6b8ff93
@af11-sanger af11-sanger Merge branch 'devel' 7d1aead
@af11-sanger af11-sanger v0.024
	Added interface to create new template plates
Commits on Oct 25, 2012
@af11-sanger af11-sanger added views for qc templates, including download of genbank files for…
… qc template wells
Commits on Oct 29, 2012
@af11-sanger af11-sanger template plate creation accepts user overrides for cassette, backbone…
… and recombinases
Commits on Oct 30, 2012
@af11-sanger af11-sanger Merge branch 'devel' 6f592a1
@af11-sanger af11-sanger v0.025
	Added QC template plate views
        Added optional cassette and backbone overrides to create template form
Commits on Oct 31, 2012
@af11-sanger af11-sanger sensible error message if no design_oligo_loci found for design dd76be3
@af11-sanger af11-sanger Add option to create new plates from QC results (work in progress) 4fac84f
Commits on Nov 01, 2012
@af11-sanger af11-sanger report caller subroutine when throwing invalid parameter error 4e48815
@af11-sanger af11-sanger Plate creation from QC results now working (improvements and tests st…
…ill needed
@af11-sanger af11-sanger adding 20aa2af
Commits on Nov 05, 2012
@af11-sanger af11-sanger plates can now be renamed during plate creation from QC e102b5a
@af11-sanger af11-sanger added plate creation from QC interface tests 7289a95
Commits on Nov 08, 2012
@af11-sanger af11-sanger plate creation from QC - tidied up and added more tests 0c6608e
@af11-sanger af11-sanger intermediate backbones allowed in qc templates 94f892d
Commits on Nov 12, 2012
@sajp sajp split creation of design oligos into seperate subroutine f4a13a8
@sajp sajp add test for new create design oligo subroutine 30fe9eb
@sajp sajp add rest api for creation of design oligoes 324656c
Commits on Nov 13, 2012
@sajp sajp factor out creation of design oligo loci into seperate subroutine, ad…
…d retrieve design oligo method, add tests for both
@sajp sajp add rest api to retrieve design oligo and to create design oligo locus 253d164
@pm9-sanger pm9-sanger set location for oligo and oligo_locus e0779e8
Commits on Nov 14, 2012
@sajp sajp can now retrieve design oligo by id, added test for this 9c0d40e
@sajp sajp we do not have a GET for design oligo locus so return status no content 68aa6d4
@dparrysmith dparrysmith Fixed backbone in QC test 998ebbd
@dparrysmith dparrysmith Fixed backbone test in plugin_well and yaml 8346a4b
@sajp sajp Merge branch 'create_design_oligos' into devel b8e85ce
@dparrysmith dparrysmith Merge branch 'devel' 2d2a820
@dparrysmith dparrysmith v0.026
    Added plate creation from QC results
Commits on Nov 15, 2012
@dparrysmith dparrysmith Added test for QcRun primers 128ee9d
Commits on Nov 19, 2012
@dparrysmith dparrysmith Added gene_name column to the template browser table 18121ad
@dparrysmith dparrysmith Removed hard tab at end of line 111 (perlcritic) 7aa83a1
@af11-sanger af11-sanger Added phase matched cassettes to template creation e6f9972
@dparrysmith dparrysmith Added tests for phased cassette retrieval method 0895bf4
Commits on Nov 20, 2012
@dparrysmith dparrysmith v0.027
    Added gene name to QC template view
    Added phase matched cassettes to template creation
@dparrysmith dparrysmith v0.028 641b301
@dparrysmith dparrysmith Merge branch 'devel' 6f24dc7
@dparrysmith dparrysmith v0.029
	Re-attempt release of v0.027
Commits on Nov 21, 2012
@af11-sanger af11-sanger Adding table for well genotyping results b354609
@af11-sanger af11-sanger updated test fixture data to include new tables 7a674d7
Commits on Nov 22, 2012
@dparrysmith dparrysmith Updated schema to include overall well genotyping results tables 463c0d4
@dparrysmith dparrysmith Added tests for targeting_pass and chromosome_fail for well genotypin…
…g results
@af11-sanger af11-sanger added util module to provide ranking of genotyping QC result values 463e55a
Commits on Nov 23, 2012
@dparrysmith dparrysmith Added update_or_create methods to targeting_pass and chromosome_fail …
…genotyping QC
Commits on Nov 28, 2012
@dparrysmith dparrysmith Intermediate commit 2fcccea
@dparrysmith dparrysmith Shifted schema version numbers 13 and 14 to 14 and 15
This is to allow interpolation of a schema modification at higher
@pm9-sanger pm9-sanger API change: Added rest api for colony_picks and primer_bands fdb3d52
@pm9-sanger pm9-sanger Merge branch 'devel' fe82764
@pm9-sanger pm9-sanger v0.030
    Added to the API to allow well_clone_picks and well_primer_bands to be created through the API
@pm9-sanger pm9-sanger Revert "v0.030"
This reverts commit 8575c20.
@pm9-sanger pm9-sanger v0.030
    Change to API to allow clone_picks and primer_bands to be added through the API
@dparrysmith dparrysmith Added boolean flag for virtual plates and interface support for highl…
…ighting virtual plates
@dparrysmith dparrysmith Attended to 1 perlcritic message 78a21bd
@dparrysmith dparrysmith Merge branch 'devel' into vplate_flag 0c3c7d2
Commits on Nov 29, 2012
@dparrysmith dparrysmith Merge branch 'devel' f258960
@dparrysmith dparrysmith v0.031
	Added virtual plate support
@af11-sanger af11-sanger addede extjs grid to view and update genotyping results (update funct…
…ionality not yet complete)
@af11-sanger af11-sanger Merge branch 'genotyping_results' of int…
…o genotyping_results
@af11-sanger af11-sanger fixed syntax error 7973e0c
Commits on Dec 03, 2012
@af11-sanger af11-sanger bug fix to plate_genotyping_qc_GET b7688b6
@dparrysmith dparrysmith Added Mark Plate as Virtual button to browse plates page 3d8f266
@pm9-sanger pm9-sanger Include cre knock in logic in design_for and cassette function subrou…
Commits on Dec 04, 2012
@pm9-sanger pm9-sanger Merge branch 'master' into devel 6a1c9b5
@af11-sanger af11-sanger Store cassette, backbone and recombinase override s for qc template w…
@pm9-sanger pm9-sanger fix reference spelling mistake 3e61f0b
@pm9-sanger pm9-sanger Merge branch 'amend_front_page_report' into devel 8676fe3
@af11-sanger af11-sanger use reagent combination infer process type when creating plates from QC 374f72d
Commits on Dec 05, 2012
@af11-sanger af11-sanger inferred processs type for template now shown in interface 14a2f3f
@pm9-sanger pm9-sanger BUG bad naming: gene -> allele bfda928
@pm9-sanger pm9-sanger Merge branch 'amend_front_page_report' into devel 021896b
@af11-sanger af11-sanger ExtJS update of well_targeting_pass now working 6be8322
Commits on Dec 06, 2012
@af11-sanger af11-sanger test and fixture data updated. perlcritic issues fixed a4ca89d
@af11-sanger af11-sanger Merge branch 'devel' into qc_template_process_types c19aad7
@af11-sanger af11-sanger merged devel into genotyping_results b3cddaa
@af11-sanger af11-sanger fixed perlcritic issues. removed tests for well_genotyping_results me…
…thods as work on these is ongoing
Commits on Dec 07, 2012
@pm9-sanger pm9-sanger add cre boolean to cassette table 7d45de3
@pm9-sanger pm9-sanger fix picks accepted validation ced1a02
@dparrysmith dparrysmith Added virtual plate checkbox to Plate Upload interface - Model TODO 6b7118d
Commits on Dec 10, 2012
@af11-sanger af11-sanger update to schema to allow genotyping results values to be null a77ce7a
@dparrysmith dparrysmith Added virtual plate checkbox to plate upload for rearray process d7fad75
@dparrysmith dparrysmith Attended to percritic issues 115536f
@dparrysmith dparrysmith Merge branch 'devel' into vplate_flag a46c4bc
Commits on Dec 11, 2012
@dparrysmith dparrysmith Added tests for virtual plate creation ec89f00