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Commits on May 21, 2012
Ray Miller Initial release. b2572d1
Commits on May 29, 2012
Ray Miller Implement user admin functions. 0d645af
Commits on Jun 15, 2012
Ray Miller Build results of bd05253 on devel bd8f89a
Commits on Jul 12, 2012
@sajp sajp Implement plate and well tracking
   Implement browse interface for qc-runs
   Implement reporting framework
73e4083
Commits on Jul 13, 2012
Ray Miller Tighten up LIMS2::Model::FormValidator::Constraint::integer.
   Don't display the welcome paragarph in an alert div.
c8dcda2
Ray Miller Bugfix LIMS2::Model::software_version(). daeb081
Commits on Jul 17, 2012
Ray Miller Implement plate list and view.
   Implement well relations view.
671b8dc
Commits on Jul 19, 2012
Ray Miller Implement downloadable plate list. 16d67f9
Commits on Jul 23, 2012
Ray Miller Add support for multiple species. dcb8c7e
Commits on Jul 25, 2012
@sajp sajp Implement support for creation of EP, XEP, SEP, EP_PICK and FP plate…
… types.

   Implement basic reports for new plate types.
   Re-order columns in vector production summary report
   Add tables for primer_band and colony_pick data
0b4301f
Commits on Jul 26, 2012
@markquintontulloch markquintontulloch New table for sponsors 3d1adfb
Ray Miller Implement electroporation detail and summary reports.
   Bugfix mouse gene retrieval; resolves #8713.
04ec611
@markquintontulloch markquintontulloch Merge branch 'devel' into allele_request_tracking 8c2f129
@markquintontulloch markquintontulloch Added targeting_type, mutation_type, final_cassette_function tables d97bf86
Commits on Jul 30, 2012
Ray Miller The beginnings of the allele request factory 8dec4d2
Ray Miller Merged changes to test data from devel branch 7326d81
Ray Miller Add as_string() method and overload stringification f1f3840
Ray Miller Allow allele_request() to take single (hasref) argument or list of ke…
…y/value pairs
bcdfc3e
Ray Miller Refactor tests to reduce code duplication f9b1fbf
Ray Miller Implement code to retrieve vector wells satisfying cassette/recombina…
…se requirement
84abce0
Ray Miller Don't re-implement the graph traversal, use depth_first_traversal() a…
…nd take the performance hit of querying ancestors rather than tracking state as the graph is traversed
960ad79
@markquintontulloch markquintontulloch Deleted unwanted db tables 19f3de0
@markquintontulloch markquintontulloch Merge changes from upstream 7100679
@markquintontulloch markquintontulloch Addition of electroporation well methods to allele request code 515972b
Ray Miller Add 'conditional' column to cassettes table b34a0f2
Ray Miller The SEP wells we are interested in are in the intersection of first a…
…llele descendants and second allele descendants
d89513d
Ray Miller Factor out cassette function checks into helper module and add more f…
…unction types
991a9cb
Commits on Jul 31, 2012
Ray Miller Tidy code 3c547aa
Ray Miller Strip extraneous comments c183cfa
Ray Miller More tests, and an outline of tests required b538e05
Commits on Aug 01, 2012
Ray Miller Refactor all report filesystem access into LIMS2::Report so the work …
…dir only needs to be specified once
7c7af5e
Ray Miller Merge branch 'devel' of github.com:htgt/LIMS2-WebApp into devel 80a9945
Ray Miller Bugfix: retrieve all matching cache rows 58f2ed3
Ray Miller v0.012
   Implement cacheing for slow-to-generate reports.
5e2c51d
Ray Miller Implement cacheing for slow-to-generate reports. 8f2edbf
@markquintontulloch markquintontulloch Development of tests for allele request 31ced46
@markquintontulloch markquintontulloch Moved version to 9 9ebb7fa
@markquintontulloch markquintontulloch Merge devel 6e31b9e
@markquintontulloch markquintontulloch Fixed CachedReport.pm d7a6502
@markquintontulloch markquintontulloch Initial checkin of SingleTargted code for allele request d19388b
Ray Miller Projects and sponsors tables 5224ac7
Ray Miller Add support for filtering production reports by sponsor 0548bbf
Commits on Aug 03, 2012
@markquintontulloch markquintontulloch Sponsor breakdown for vector and electroporation detail and summary r…
…eports - refs #8769
787bdc5
Commits on Aug 06, 2012
@sajp sajp add list process types sub 5acec35
@sajp sajp add plate to navigation bar, whitespace tidy up 16e2441
@sajp sajp add initial plate upload controller and template files f183e6f
Commits on Aug 07, 2012
@sajp sajp add psgi conf file to gitignore b9e88ce
@sajp sajp add process plate types hash to constants module 52b9e20
@sajp sajp specify values as well as field names so can generate select lists c0db317
@sajp sajp add functions to get custom fields for given process, as well as plat…
…e types linked to a process
dc3aa20
@sajp sajp show stashed variables in form, means users do not have to reenter da…
…ta for validation errors
bb7d472
@sajp sajp initial commit util module for process creation 5c21d60
@sajp sajp checkpoint code e7b9a26
@sajp sajp add some styling to upload plate complete page 0309eb2
@sajp sajp remove next button, submit form when dropdown list changes 926b095
@sajp sajp disable submit button once clicked db955a7
Commits on Aug 08, 2012
@sajp sajp tidy up html e882672
@sajp sajp check plate type is set 18013a4
@sajp sajp when creating a plate check it does not already exist
process plate data merges plate process data with the well process data
parse csv file with Text::CSV_XS
1c2ef1a
@sajp sajp rework way process specific fields are set and displayed to give more…
… control
093df52
@markquintontulloch markquintontulloch Sponsor selection holding page for reports - resolves #8767, EP Picks…
… in Gene Reports - resolves #8773
3338ad4
@sajp sajp form tweaks 95ef0c4
Commits on Aug 09, 2012
@sajp sajp add create_plate_csv_upload method to model that calls create_plate d…
…irectly, do not need to send plate data hash back to controller and have it call plate create
0cb35a1
@sajp sajp minor refactor of form flow, upon creation of plate forward to view_p…
…late page
485230a
@sajp sajp wrap parsing of csv file in try catch block, check for empty well dat…
…a array
a3551e4
@sajp sajp add returns to subroutines, check for existance of step param 1bf494e
@sajp sajp add tests for plate upload forms 80a6ae2
@sajp sajp delete newly created plate, makes repeating this test quicker, no nee…
…d to reload fixture data
31e0475
@sajp sajp add titles for each test to make output clearer 50d9785
@sajp sajp added tests for plate creation via csv upload functions 2f085cb
@sajp sajp move process specific fields hash into constants module, create plate…
…_help_info function that returns information that will help a user understand the process types and plates
9f7e718
@sajp sajp add template files for plate upload c396fcf
Commits on Aug 10, 2012
@sajp sajp add information about using the plate create forms to each page a911a7d
@sajp sajp wrongly named parameter for qc_template retrieval, added extra check …
…to make sure search of qc_templates is not done without a name or a id
277f89f
@sajp sajp remove cassette from recombinase process test d71db0c
@sajp sajp bugfix, test for unknown values when doing parameter validation, do n…
…ot just ignore them, add tests for this and the ignore_unknown flag
faa40e0
@sajp sajp Merge branch 'ignore_unknown_bugfix' into devel 283557d
@sajp sajp has checking only for undef, not empty string, which does need to be …
…replaced, added test for this case
2bdd21b
@sajp sajp add tmp dir to gitignore 21bdde7
@sajp sajp Merge branch 'plate_upload' into devel
Conflicts:
	.gitignore
7c59025
@sajp sajp search for more specific content, remove test for non existance of Ce…
…ll Line, it appears in help text now
8c91fed
@sajp sajp add unique constraint to well_id table in process_output_well table, …
…basically this means a output well can only belong to one process, so a well can only be created by one process, added extra fixture data and modified current tests to stop them failing from duplicate key violations brought on by this constraint
b916fae
Commits on Aug 13, 2012
@sajp sajp moved extra process test fixture data into main fixture data file 84e0354
@sajp sajp add basic plate report for PICK plates 335b8ac
@sajp 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
@sajp sajp add basic plate reports for FP and POOL type plates 05d033b
@sajp sajp Merge branch 'add_plate_reports' into devel e72c72c
@sajp sajp add check of process output well types, tests as well 802f698
@sajp sajp SEP Pick plates need a seperated report class 4c672e1
@sajp sajp POOL plate types need seperate report classes 6cec998
@sajp sajp Merge branch 'add_plate_reports' into devel 58155d2
@sajp sajp Merge branch 'process_plate_type_check' into devel 88b1ae1
Commits on Aug 14, 2012
@sajp sajp put page title in page-header class, move create user button to top o…
…f page
28084b7
@sajp sajp put page title in page-header class, tidy up forms ae2a8ba
@sajp sajp qc_run_id is uuid not integer 10681ac
@sajp sajp remove horizontal line 9ea9446
@sajp sajp standardise header format dda929e
@sajp sajp standardise headers, tidy up small display issues a99cf27
@sajp sajp use dl lists to nicely format qc run basic info boxes 68cd21d
@sajp sajp whitespace 14a518f
@sajp sajp fix fixture data well_id_seq, you can not just add rows to the fixtur…
…e data file
8a270d1
@sajp sajp Merge branch 'html_tidy' into devel 6795dac
Commits on Aug 15, 2012
@sajp sajp initial commit of dna status upload interface 7ed2a3d
@sajp sajp add link to new dna status upload page c31ce32
@sajp sajp add file_handle check and pass_or_fail check 2afe0d7
@sajp sajp add post filter option to turn pass or fail into boolean 3da546a
@sajp sajp checkpoint for plugin code to update a dna status values for wells on…
… a plate via csv file
e61500d
Commits on Aug 16, 2012
@sajp sajp stop check_params from putting in empty values for optional params th…
…at use post_filter or rename, add tests
1507378
@sajp sajp Merge branch 'devel' into dna_assay_results 0a7527d
Commits on Aug 17, 2012
@sajp sajp success_msg no longer filters out html code 8954e97
@sajp sajp check if well does not already have a dna status before creating one,…
… add debug message if one is created
708603e
@sajp sajp add more descriptive success message 76fd800
@sajp 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
@sajp sajp import parse_csv_file method f1445a7
@sajp sajp add delete well dna status method bf4de41
@sajp sajp use correct Exception module 61b129a
@sajp sajp test well dna status creationg, retrieval and deletion methods a983000
@sajp sajp changed error messages for csv parsing, modify tests to reflect this …
…change
cb7efcd
@sajp sajp add tests for data upload util module, moved csv parsing code here so…
… removed those tests from the plate plugin test file
c3bbde7
@sajp sajp add tests for plate dna status update page cc42af5
Commits on Aug 20, 2012
@sajp sajp rename pass param value to something more descriptive d10032c
@sajp sajp add help text for dna status upload page, plus template file for upload a2bfa7d
@sajp sajp whitespace 29201a9
@sajp sajp fix html, missing < 8a5cfb9
@sajp sajp add well names to plate upload template files 2c46ea0
@sajp sajp Merge branch 'dna_assay_results' into devel 34e09ff
@sajp sajp add well names to first electroporation plate upload template e4f1e09
Commits on Aug 21, 2012
@sajp sajp initial commit of create plate util module f743f13
@sajp sajp checkpoint 2fbc460
@sajp sajp move check process wells code to util module e472b24
@sajp 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
@sajp 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
Commits on Aug 22, 2012
@sajp sajp refactor to move most of the process creation code into the CreatePro…
…cess util module
41d6d38
@sajp sajp refactor to move majority of plate create code into CreatePlate Util …
…module, add tests
8c7bc75
@sajp sajp refactor to move some gene search code into GeneSearch util module fr…
…om gene plugin module
d24fbe2
@sajp sajp add test to search for human genes e786cd2
@sajp sajp refactor to move some create qc run code from plugin into new createq…
…c util module
2f1eaba
@sajp sajp whitespace 34a2db8
@sajp sajp add return statements bf4148f
@sajp sajp prune files and folders from release 2e66a26
@sajp sajp Build results of 2e66a26 on devel 62a5be9
@sajp sajp v0.013 fd09a3a
@sajp sajp Merge branch 'devel'
Conflicts:
	Changes
f5ee40b
@sajp 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
@sajp 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
Commits on Aug 29, 2012
@sajp sajp remove commented code 4ed64ca
@sajp sajp add tests for multiple constraint checks 0c550d3
@sajp sajp add tests for list bac libraries, fix type in subroutine name d00c384
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
fb5834c
@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
393e9d8
@sajp sajp check that 2 input wells for second_electroporation process are DNA a…
…nd XEP, add tests for this
c6b26dd
@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
7cf4a0e
@sajp sajp add test for either cassette or backbone validation on 2w gateway pro…
…cess
ef70c3b
@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
c98b883
@sajp sajp add search for non existant gene fdaa7cc
@sajp 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
@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
76fc8d6
@sajp 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
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
271425f
@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
411be3f
@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.
314bc52
@sajp 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
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
3ad841d
@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
3f776dd
@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.
bf24343
@sajp 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
@sajp 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
@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
85b8df1
@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 …
…page
b20a274
@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
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
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
8891f95
@sajp sajp switch back to black navbar, wrap login name to make it line up prope…
…rly with logout button
3e84c2f
@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
3de1892
@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 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 Default assembly now GRCm38
   Improved test coverage
   Updated to twitter bootstrap 2.1.1
   Implement change password form
   Styling improvements
24284a9