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  • 477 commits
  • 314 files changed
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  • 5 contributors
This comparison is big! We're only showing the most recent 250 commits
Sep 06, 2012
Saj sajp remove controller code for edit_plate page 4c9a20b
Saj sajp Merge branch 'devel' into improve_test_coverage
Conflicts:
	t/50-model-plugin-plate.t
6eeeb1f
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
2eb2a11
af11-sanger af11-sanger Build results of fac2a06 on master fc82a2d
Sep 07, 2012
Saj sajp grant usage on cell_lines_id_seq to rw_role 40b1ee9
Saj sajp upgrade bootstrap to 2.1.1 32466f3
Saj sajp switch to custom bootstrap files, new defaults for text size and line…
… spacing in v2.1.1 were too large
8891f95
Saj sajp switch back to black navbar, wrap login name to make it line up prope…
…rly with logout button
3e84c2f
Saj sajp remove extra table header column 21ecc21
Saj 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
3de1892
Saj sajp move db and software version info into footer stuck at bottom of page 8587a92
Saj sajp Merge branch 'bootstrap_upgrade' into devel a6e447b
Sep 10, 2012
Saj sajp add user dropdown navbar component 0d2aef8
Saj sajp clean up navbar, move admin link to user dropdown ecfdc51
Saj sajp add new password_string check 295b0b7
Saj sajp add change user password subroutine 343e93b
Saj sajp hide links in navbar from users without the right privilages 513006f
Saj sajp add change password controller and view c97d5bc
Saj sajp add tests for new password change form d776d29
Saj sajp add plate list api b9ad938
Saj sajp Merge branch 'devel' into improve_test_coverage 9793dd2
Saj sajp add missing bracket; 1de143e
af11-sanger af11-sanger Added GRCm38 oligo loci and changed default assembly in fixtures 6b1ac7a
Sep 11, 2012
Saj sajp Merge branch 'devel' f7db4c4
Saj sajp v0.019
   Default assembly now GRCm38
   Improved test coverage
   Updated to twitter bootstrap 2.1.1
   Implement change password form
   Styling improvements
9e88c8f
Saj sajp Default assembly now GRCm38
   Improved test coverage
   Updated to twitter bootstrap 2.1.1
   Implement change password form
   Styling improvements
24284a9
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.
2d7ec15
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
c2de821
Sep 12, 2012
Saj sajp add id to as_hash method for well object 9743a1f
Saj sajp add test_result_url and created_by to as_hash method for WellQcSequen…
…cingResult
358ccd1
Saj 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
4bc6113
Sep 13, 2012
Saj sajp Add extra debugging message 751a166
Saj 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.
94ff07c
af11-sanger af11-sanger Unit test speed improvement.
	Added well_qc_sequencing_result delete method to API.
f60dc78
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
Sep 14, 2012
Saj sajp Add news tests for clone_pool and freeze process creations 3647948
Saj sajp whitespace removal a7b446c
Saj sajp add test for process plate types 8743cd9
Saj sajp Merge branch 'create_process_util' into devel 2d46f26
Saj sajp add grants to allow new db to have tests run against it d0a1db0
Sep 18, 2012
Saj sajp initial commit of code to generate lab electroporation report ce29d7e
Saj sajp add dna_wells attribute to allele request object 3c66aa8
Sep 19, 2012
Saj sajp move download button next to report title to free up more space for t…
…he report
631f7fe
Saj sajp Add links to genes to electroporate report 1163327
Sep 20, 2012
Saj sajp Split DNA wells on report into first and second allele, then into
promoter driven and promoterless cassettes
ae743d5
Saj sajp initial commit of sponsor gene report fd57896
Saj sajp renamed report 7cefff2
Saj sajp make new reports work when no sponsor specified 2e63780
Saj sajp no longer need second report, push data from here in to Genes To Elec…
…troporate report
9d55c4e
Saj sajp modify layout of report to place all wells of certain type in one col…
…umn, also only print FEP / SEP plate names
f2a23bf
Saj sajp show parent dna well for ep wells ec742e9
Saj sajp whitespace cd78ca6
Sep 24, 2012
Saj sajp Merge branch 'electroporation-report' into devel 707786e
Sep 25, 2012
Saj sajp Add pick wells to allele request objects 618f65b
Saj sajp add report for front page sponsor progress; 3945a7e
Saj sajp incorporate new sponsor progress report into front page 64f5d36
Sep 26, 2012
Saj sajp only show progress report if we can get a cached version of it 6962ac0
Saj sajp remove debug code, rename column heading 0a3c7db
Oct 01, 2012
Saj sajp use LIMS2::ReportGenerator::Plate d5d60d2
Saj sajp make cache last 22 hours 3f9f8f4
Saj sajp wrap gene symbol lookup in try block to catch errors in solr lookup f748ef1
Oct 02, 2012
Saj sajp Merge branch 'devel' 4ee0658
Saj sajp change front page report heading d36c429
Saj sajp Merge branch 'devel' 9ccd0e9
Saj sajp Added front page report
    Added genes to electroporate report
    Implemented more tests for process creation
5df771a
Saj sajp v0.021
    Added front page report
    Added genes to electroporate report
    Implemented more tests for process creation
82825db
af11-sanger af11-sanger Added QC job submission form 88c6100
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)
6a285b0
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
Oct 04, 2012
Saj 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…
…C-Common
cdcf66e
Oct 05, 2012
Saj sajp bugfix, check file format exists e8b1ed9
Saj sajp add tests for retrieval of qc run results b0678b7
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
529e88f
af11-sanger af11-sanger Added QC job submission form
	Added lastest QC jobs view
50a7a63
Oct 09, 2012
Saj sajp add tests for QcResults Util module f1099a3
Saj sajp Merge branch 'qc-tests' into devel 3c09ac3
Oct 11, 2012
Saj sajp REST authentication no longer done using http basic auth, pass in use…
…rname and password through request params
c1f74f3
Saj sajp get authenticated mech through login form, not thorugh HTTP Basic Auth 42e9cb2
Saj sajp use pre authenticated mech for tests 85981ea
Saj sajp Merge branch 'devel' 23e60a4
Saj sajp Build results of 23e60a4 on master ba49b7d
Saj sajp v0.023 e98d13e
Oct 12, 2012
Saj sajp if no strand set then do not return oligo fasta files in design as_ha…
…sh method
2fdb565
Saj sajp use authenticated mech 8bc83d3
Saj sajp Merge branch 'devel' of github.com:htgt/LIMS2-WebApp into devel ea513a3
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
Oct 17, 2012
af11-sanger af11-sanger Initial work on generating EngSeq params 00209ee
Oct 18, 2012
af11-sanger af11-sanger well plugin generate_well_eng_seq_params now complete (needs better t…
…est coverage)
8026a95
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
6d77656
af11-sanger af11-sanger add test for allele engseq params 4a123ca
Oct 23, 2012
af11-sanger af11-sanger methods and interface to create qc template plate from plate or csv u…
…pload
d3fae5f
af11-sanger af11-sanger refactored template generation methods. added interface tests d080e71
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
368d608
af11-sanger af11-sanger Added interface to create new template plates 474a677
Oct 25, 2012
af11-sanger af11-sanger added views for qc templates, including download of genbank files for…
… qc template wells
be7ee60
Oct 29, 2012
af11-sanger af11-sanger template plate creation accepts user overrides for cassette, backbone…
… and recombinases
35c6d34
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
5d1e30b
af11-sanger af11-sanger Added QC template plate views
        Added optional cassette and backbone overrides to create template form
9f53151
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
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
b4322c7
af11-sanger af11-sanger adding create_plates.tt 20aa2af
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
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
Nov 12, 2012
Saj sajp split creation of design oligos into seperate subroutine f4a13a8
Saj sajp add test for new create design oligo subroutine 30fe9eb
Saj sajp add rest api for creation of design oligoes 324656c
Nov 13, 2012
Saj sajp factor out creation of design oligo loci into seperate subroutine, ad…
…d retrieve design oligo method, add tests for both
cba3f75
Saj 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
Nov 14, 2012
Saj sajp can now retrieve design oligo by id, added test for this 9c0d40e
Saj 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
Saj sajp Merge branch 'create_design_oligos' into devel b8e85ce
dparrysmith dparrysmith Merge branch 'devel' 2d2a820
dparrysmith dparrysmith Added plate creation from QC results b19da14
dparrysmith dparrysmith v0.026
    Added plate creation from QC results
0357768
Nov 15, 2012
dparrysmith dparrysmith Added test for QcRun primers 128ee9d
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
Nov 20, 2012
dparrysmith dparrysmith Added gene name to QC template view
    Added phase matched cassettes to template creation
10d332f
dparrysmith dparrysmith v0.027
    Added gene name to QC template view
    Added phase matched cassettes to template creation
91713cc
dparrysmith dparrysmith v0.028 641b301
dparrysmith dparrysmith Build results of 91713cc on master 40c34f2
dparrysmith dparrysmith Merge branch 'devel' 6f24dc7
dparrysmith dparrysmith Re-attempt release of v0.027 e7ff924
dparrysmith dparrysmith v0.029
	Re-attempt release of v0.027
b3cb33a
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
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
59f6b19
af11-sanger af11-sanger added util module to provide ranking of genotyping QC result values 463e55a
Nov 23, 2012
dparrysmith dparrysmith Added update_or_create methods to targeting_pass and chromosome_fail …
…genotyping QC
c1fa831
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
priority.
7850a28
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
8575c20
pm9-sanger pm9-sanger Revert "v0.030"
This reverts commit 8575c20.
b62efae
pm9-sanger pm9-sanger v0.030
    Change to API to allow clone_picks and primer_bands to be added through the API
aed548b
pm9-sanger pm9-sanger Change to API to allow clone_picks and primer_bands to be added thro…
…ugh the API
c767448
dparrysmith dparrysmith Added boolean flag for virtual plates and interface support for highl…
…ighting virtual plates
14660cb
dparrysmith dparrysmith Attended to 1 perlcritic message 78a21bd
dparrysmith dparrysmith Merge branch 'devel' into vplate_flag 0c3c7d2
Nov 29, 2012
dparrysmith dparrysmith Merge branch 'devel' f258960
dparrysmith dparrysmith v0.031
	Added virtual plate support
6cf83d1
dparrysmith dparrysmith Added virtual plate support 1ca3ac8
af11-sanger af11-sanger addede extjs grid to view and update genotyping results (update funct…
…ionality not yet complete)
4187754
af11-sanger af11-sanger Merge branch 'genotyping_results' of github.com:htgt/LIMS2-WebApp int…
…o genotyping_results
f8f76cb
af11-sanger af11-sanger fixed syntax error 7973e0c
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…
…tines
c5e9cea
Dec 04, 2012
pm9-sanger pm9-sanger Merge branch 'master' into devel 6a1c9b5
pm9-sanger pm9-sanger Added cre_knockin support for sponsor_report ed7c910
pm9-sanger pm9-sanger v0.032
    Added cre_knockin support for sponsor_report
ba19f0d
af11-sanger af11-sanger Store cassette, backbone and recombinase override s for qc template w…
…ells
43d7eb4
pm9-sanger pm9-sanger fix reference spelling mistake 3e61f0b
pm9-sanger pm9-sanger Merge branch 'amend_front_page_report' into devel 8676fe3
pm9-sanger pm9-sanger Merge branch 'devel' 5fdffc3
pm9-sanger pm9-sanger Added design_type for cre_knockins d7c0db5
pm9-sanger pm9-sanger v0.033
    Added design_type for cre_knockins
d7c89b8
af11-sanger af11-sanger use reagent combination infer process type when creating plates from QC 374f72d
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
pm9-sanger pm9-sanger Merge branch 'amend_front_page_report' ba6f7a7
pm9-sanger pm9-sanger Merge branch 'devel' ac8d1cd
pm9-sanger pm9-sanger v0.034
    Amended Single_Targeted model
e49cc34
pm9-sanger pm9-sanger Amended Single_Targeted model cc2ec57
af11-sanger af11-sanger ExtJS update of well_targeting_pass now working 6be8322
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
6e2cecf
af11-sanger af11-sanger Merge branch 'devel' e473231
af11-sanger af11-sanger v0.035
	Added cassette, backbone and recombinase parameters to QC template wells
        Plate creation from QC infers process type from QC template wells
	Added tables to store well genotyping result data (upload/update interface work in progress)
eba1330
af11-sanger af11-sanger Added cassette, backbone and recombinase parameters to QC template w…
…ells

        Plate creation from QC infers process type from QC template wells
	Added tables to store well genotyping result data (upload/update interface work in progress)
b3d6494
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
pm9-sanger pm9-sanger Merge branch 'devel' 8aa0ae3
Dec 10, 2012
af11-sanger af11-sanger update to schema to allow genotyping results values to be null a77ce7a
pm9-sanger pm9-sanger v0.036
    Fixed sponsor report bugs. Report should now report the correct numbers.
bf94290
pm9-sanger pm9-sanger Fixed sponsor report bugs. Report should now report the correct numb…
…ers.
d05eb1c
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
Dec 11, 2012
dparrysmith dparrysmith Added tests for virtual plate creation ec89f00
dparrysmith dparrysmith Merge branch 'devel' c577671
dparrysmith dparrysmith v0.037
	Added virtual plate checkbox to plate upload interface
f8a0d4c
dparrysmith dparrysmith Added virtual plate checkbox to plate upload interface 9d393cb
Dec 17, 2012
af11-sanger af11-sanger plate relation graph - a first attempt 251c625
Dec 18, 2012
pm9-sanger pm9-sanger add recombinase upload fbdcc44
Dec 19, 2012
af11-sanger af11-sanger graph drawing moved to module. condensed plates with very similar names 02dc32f
Dec 20, 2012
Saj sajp bugfix, called next instead of return 8cb5d20
Saj sajp Merge branch 'devel' 089e542
Saj sajp Bugfix, Genes To Electroporate report. 419022c
Saj sajp v0.038
    Bugfix, Genes To Electroporate report.
a27d511
Dec 21, 2012
Saj sajp fix another next instead of return bug 2075b71
Saj sajp Merge branch 'master' into devel 1c16669
Saj sajp v0.039
    Another bugfix to Genes To Electroporate report.
343822a
Saj sajp Another bugfix to Genes To Electroporate report. bc6d950
pm9-sanger pm9-sanger added colony count upload c19d191
pm9-sanger pm9-sanger add well data to navigation bar 7e78050
pm9-sanger pm9-sanger add help for colony counts 701bba9
Jan 02, 2013
Saj sajp code review 34c624e
Jan 04, 2013
pm9-sanger pm9-sanger Code review corrections 561ed88
Jan 07, 2013
af11-sanger af11-sanger show list of plate names on condensed nodes 2971dff
Jan 08, 2013
pm9-sanger pm9-sanger Tests 099bbd2
Jan 09, 2013
af11-sanger af11-sanger plate relation option added to well relation view page e2405d5
af11-sanger af11-sanger Merge branch 'devel' into plate_graph 24b427d
af11-sanger af11-sanger perlcritic fixes 75bd093
af11-sanger af11-sanger Merge branch 'devel' 28097b7
pm9-sanger pm9-sanger added tests to improved test coverage c5c4672
af11-sanger af11-sanger v0.040
	Added plate relation view
766e815
af11-sanger af11-sanger Added plate relation view df40433
pm9-sanger pm9-sanger Merge branch 'devel' into add_dre_recominbase_process_to_EPs 550f45c
pm9-sanger pm9-sanger Merge branch 'master' into devel 1445aad
pm9-sanger pm9-sanger Added forms to append recombinase to a process attached to a well an…
…d add colony counts to a well.
ac7ccd3