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  • 348 commits
  • 286 files changed
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  • 4 contributors
This comparison is big! We're only showing the most recent 250 commits
Aug 13, 2012
Saj sajp add basic plate report for PICK plates 335b8ac
Saj sajp remove unique constraint on process_output_well table, well_id column…
…, could not use dbix class schema loader to generate schemas when this constraint was added, need to look into problem
53613e5
Saj sajp add basic plate reports for FP and POOL type plates 05d033b
Saj sajp Merge branch 'add_plate_reports' into devel e72c72c
Saj sajp add check of process output well types, tests as well 802f698
Saj sajp SEP Pick plates need a seperated report class 4c672e1
Saj sajp POOL plate types need seperate report classes 6cec998
Saj sajp Merge branch 'add_plate_reports' into devel 58155d2
Saj sajp Merge branch 'process_plate_type_check' into devel 88b1ae1
Aug 14, 2012
Saj sajp put page title in page-header class, move create user button to top o…
…f page
28084b7
Saj sajp put page title in page-header class, tidy up forms ae2a8ba
Saj sajp qc_run_id is uuid not integer 10681ac
Saj sajp remove horizontal line 9ea9446
Saj sajp standardise header format dda929e
Saj sajp standardise headers, tidy up small display issues a99cf27
Saj sajp use dl lists to nicely format qc run basic info boxes 68cd21d
Saj sajp whitespace 14a518f
Saj sajp fix fixture data well_id_seq, you can not just add rows to the fixtur…
…e data file
8a270d1
Saj sajp Merge branch 'html_tidy' into devel 6795dac
Aug 15, 2012
Saj sajp initial commit of dna status upload interface 7ed2a3d
Saj sajp add link to new dna status upload page c31ce32
Saj sajp add file_handle check and pass_or_fail check 2afe0d7
Saj sajp add post filter option to turn pass or fail into boolean 3da546a
Saj sajp checkpoint for plugin code to update a dna status values for wells on…
… a plate via csv file
e61500d
Aug 16, 2012
Saj sajp stop check_params from putting in empty values for optional params th…
…at use post_filter or rename, add tests
1507378
Saj sajp Merge branch 'devel' into dna_assay_results 0a7527d
Aug 17, 2012
Saj sajp success_msg no longer filters out html code 8954e97
Saj sajp check if well does not already have a dna status before creating one,…
… add debug message if one is created
708603e
Saj sajp add more descriptive success message 76fd800
Saj sajp moved data upload code into new util module, deal with different newl…
…ine formats, empty lines, and limes with only well names in csv files
dfdff44
Saj sajp import parse_csv_file method f1445a7
Saj sajp add delete well dna status method bf4de41
Saj sajp use correct Exception module 61b129a
Saj sajp test well dna status creationg, retrieval and deletion methods a983000
Saj sajp changed error messages for csv parsing, modify tests to reflect this …
…change
cb7efcd
Saj sajp add tests for data upload util module, moved csv parsing code here so…
… removed those tests from the plate plugin test file
c3bbde7
Saj sajp add tests for plate dna status update page cc42af5
Aug 20, 2012
Saj sajp rename pass param value to something more descriptive d10032c
Saj sajp add help text for dna status upload page, plus template file for upload a2bfa7d
Saj sajp whitespace 29201a9
Saj sajp fix html, missing < 8a5cfb9
Saj sajp add well names to plate upload template files 2c46ea0
Saj sajp Merge branch 'dna_assay_results' into devel 34e09ff
Saj sajp add well names to first electroporation plate upload template e4f1e09
Aug 21, 2012
Saj sajp initial commit of create plate util module f743f13
Saj sajp checkpoint 2fbc460
Saj sajp move check process wells code to util module e472b24
Saj sajp Implement allele request tracking.
   Add Projects and Sponsors tables.
   Implement production reports by sponsor.
   Implement plate create via csv upload form.
   Implement dna assay result loading onto plates.
ad9c8c9
Saj sajp v0.013
   Implement allele request tracking.
   Add Projects and Sponsors tables.
   Implement production reports by sponsor.
   Implement plate create via csv upload form.
   Implement dna assay result loading onto plates.
c6d766b
Aug 22, 2012
Saj sajp refactor to move most of the process creation code into the CreatePro…
…cess util module
41d6d38
Saj sajp refactor to move majority of plate create code into CreatePlate Util …
…module, add tests
8c7bc75
Saj sajp refactor to move some gene search code into GeneSearch util module fr…
…om gene plugin module
d24fbe2
Saj sajp add test to search for human genes e786cd2
Saj sajp refactor to move some create qc run code from plugin into new createq…
…c util module
2f1eaba
Saj sajp whitespace 34a2db8
Saj sajp add return statements bf4148f
Saj sajp prune files and folders from release 2e66a26
Saj sajp Build results of 2e66a26 on devel 62a5be9
Saj sajp v0.013 fd09a3a
Saj sajp Merge branch 'devel'
Conflicts:
	Changes
f5ee40b
Saj sajp Implement allele request tracking.
   Add Projects and Sponsors tables.
   Implement production reports by sponsor.
   Implement plate create via csv upload form.
   Implement dna assay result loading onto plates.
3a218ca
Saj sajp v0.013
   Implement allele request tracking.
   Add Projects and Sponsors tables.
   Implement production reports by sponsor.
   Implement plate create via csv upload form.
   Implement dna assay result loading onto plates.
ec78a5d
Aug 29, 2012
Saj sajp remove commented code 4ed64ca
Saj sajp add tests for multiple constraint checks 0c550d3
Saj sajp add tests for list bac libraries, fix type in subroutine name d00c384
Aug 30, 2012
Saj sajp return true when process deleted 1e923c5
Saj 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
fb5834c
Saj sajp add tests for design creation and deletion 4b9e2b3
Saj sajp add tmp dir to ignore list 5a6c59b
Saj sajp changes names of columns used to specify parent wells for second elec…
…troporation plate upload, fix csv template as well
393e9d8
Saj sajp check that 2 input wells for second_electroporation process are DNA a…
…nd XEP, add tests for this
c6b26dd
Saj sajp fix variable names for validation of second_electroporation parent wells 85ab614
Aug 31, 2012
Saj sajp fix links to stylesheets 0af48f1
Saj sajp plate create test, fix parent well variable names ad01dbc
Saj sajp throw exception if both cassette and backbone specified for a 2w gate…
…way process
7cf4a0e
Saj sajp add test for either cassette or backbone validation on 2w gateway pro…
…cess
ef70c3b
Saj sajp Merge branch 'devel' into improve_test_coverage 5ff3bf4
Saj sajp bugfix, entity_class no entity 6044f20
Saj sajp test list candidate designs for gene on +ve strand, and for non exist…
…ant gene
c98b883
Saj sajp add search for non existant gene fdaa7cc
Saj sajp add test for creating a plate that already exists, test list plates f…
…unction
e8c517d
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 github.com:htgt/LIMS2-WebApp into devel f9bebf3
markquintontulloch markquintontulloch Fixed SEP template
   Added SEP verification
   Sponsor heading added to reports
045624a
markquintontulloch markquintontulloch v0.014
   Fixed SEP template
   Added SEP verification
   Sponsor heading added to reports
0b92f0a
Saj sajp Merge branch 'devel' 52c5428
Saj 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
76fc8d6
Saj sajp Fixed SEP plate upload template
   Added verification for 2w gateway process
   Moved code into Util modules
   Fix links to css files in header
e49b715
Sep 03, 2012
Saj sajp add plate rename subroutine, plus tests 92f9cb1
Saj 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
271425f
Saj 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
Sep 04, 2012
Saj sajp plate report viewable test e8de79d
Saj sajp display sponsor as part of report name if its specified, no longer pu…
…t it at top of all reports
411be3f
Saj sajp Merge branch 'devel' 07900e1
Saj 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.
314bc52
Saj sajp Bugfix, well reports were not working because they did not have a sp…
…onsor.

    Moved sponsor into report name, removed from generic Report code.
    Added test to make sure Plate Reports are viewable.
62576a1
Sep 05, 2012
Saj sajp add check for existing_backbone, use this instead of existing_final_b…
…ackbone check as intermediate_backbones can be present in final vectors
3ad841d
Saj 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
3f776dd
Saj sajp Merge branch 'devel' 49bdd65
Saj sajp Merge branch 'devel' into plate_edit_page c5ac77b
Saj 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.
bf24343
Saj sajp Show clearer error message on plate upload when parent well does not…
… exist.

    Switch from final-backbone check to just backbone check.
7593fe9
af11-sanger af11-sanger work in progress b2a01c0
af11-sanger af11-sanger Merge branch 'devel' into cell_line_drop_down
Conflicts:
	dist.ini
81fbf89
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.
b2bc955
Saj sajp update Sponsor and ProcessRecombinase table DBIx Schema, lims2_devel …
…was slightly different from lims2_live so these files were out of date
9d635aa
af11-sanger af11-sanger Valid cell line values added to fixtures and test input data 32338fa
Saj 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
Sep 06, 2012
Saj sajp add delete_plate controller 31bc318
Saj sajp add delete plate button and confirm modal, re-style page 1201ef5
Saj sajp move plate has child wells check to plate object 83f00f3
Saj sajp only show delete button for plates without child wells 732884e
Saj sajp Merge branch 'devel' into plate_edit_page 2500575
Saj sajp add rename_plate controller code 2b23bb0
Saj sajp fix rename plate form url, add hidden form fields with plate id and c…
…urrent name
85b8df1
Saj sajp move check for plate id into begin subroutine, rename params f8597b2
Saj sajp restyle plate edit page, add link to edit page from plate view page 5746a98
Saj sajp remove extra blank line 7f2fd09
Saj sajp add tests for plate edit page, including plate rename and plate edit ff1be06
Saj sajp move plate edit functionality from own plate edit page to plate view …
…page
b20a274
Saj sajp rename test file 97feed6
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 Added QC template plate views
        Added optional cassette and backbone overrides to create template form
9f53151