Skip to content
This repository

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
  • 10 commits
  • 166 files changed
  • 0 comments
  • 2 contributors
May 21, 2012
Ray Miller Initial release. b2572d1
May 29, 2012
Ray Miller Implement user admin functions. 0d645af
Jun 15, 2012
Ray Miller Build results of bd05253 on devel bd8f89a
Jul 12, 2012
Saj sajp Implement plate and well tracking
   Implement browse interface for qc-runs
   Implement reporting framework
73e4083
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
Jul 17, 2012
Ray Miller Implement plate list and view.
   Implement well relations view.
671b8dc
Jul 19, 2012
Ray Miller Implement downloadable plate list. 16d67f9
Jul 23, 2012
Ray Miller Add support for multiple species. dcb8c7e
Jul 25, 2012
Saj 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

Showing 166 changed files with 1,643 additions and 2,908 deletions. Show diff stats Hide diff stats

  1. +0 7 .gitignore
  2. +6 1 Changes
  3. +379 0 LICENSE
  4. +239 0 MANIFEST
  5. +111 0 META.yml
  6. +13 0 README
  7. +0 12 ddl/generate-schema.sh
  8. +0 18 ddl/templates/roles.sql
  9. +0 11 ddl/templates/schema.sql
  10. +0 5 ddl/templates/test_roles.sql
  11. +0 428 ddl/templates/versions/1/audit-up.sql
  12. +0 6 ddl/templates/versions/1/fixtures.sql
  13. +0 173 ddl/templates/versions/1/up.sql
  14. +0 31 ddl/templates/versions/2/audit-up.sql
  15. +0 1  ddl/templates/versions/2/fixtures.sql
  16. +0 1  ddl/templates/versions/2/roles.sql
  17. +0 31 ddl/templates/versions/2/up.sql
  18. +0 409 ddl/templates/versions/3/audit-up.sql
  19. +0 39 ddl/templates/versions/3/fixtures.sql
  20. +0 154 ddl/templates/versions/3/up.sql
  21. +0 60 ddl/templates/versions/4/audit-up.sql
  22. +0 2  ddl/templates/versions/4/fixtures.sql
  23. +0 34 ddl/templates/versions/4/up.sql
  24. +0 643 ddl/templates/versions/5/audit-up.sql
  25. +0 105 ddl/templates/versions/5/fixtures.sql
  26. +0 219 ddl/templates/versions/5/up.sql
  27. +0 6 ddl/templates/versions/6/fixtures.sql
  28. +0 246 ddl/templates/versions/6/up.sql
  29. +0 134 ddl/templates/versions/7/audit-up.sql
  30. +0 36 ddl/templates/versions/7/fixtures.sql
  31. +0 40 ddl/templates/versions/7/up.sql
  32. +0 28 ddl/vars.tt
  33. +0 28 dist.ini
  34. +6 0 lib/LIMS2/Catalyst/Controller/REST.pm
  35. +6 0 lib/LIMS2/Model.pm
  36. +6 0 lib/LIMS2/Model/AuthDB.pm
  37. +6 0 lib/LIMS2/Model/Constants.pm
  38. +6 0 lib/LIMS2/Model/DBConnect.pm
  39. +6 0 lib/LIMS2/Model/FormValidator.pm
  40. +6 0 lib/LIMS2/Model/FormValidator/Constraint.pm
  41. +6 0 lib/LIMS2/Model/Plugin/BAC.pm
  42. +6 0 lib/LIMS2/Model/Plugin/Design.pm
  43. +6 0 lib/LIMS2/Model/Plugin/Gene.pm
  44. +6 0 lib/LIMS2/Model/Plugin/Plate.pm
  45. +6 0 lib/LIMS2/Model/Plugin/Process.pm
  46. +6 0 lib/LIMS2/Model/Plugin/QC.pm
  47. +6 0 lib/LIMS2/Model/Plugin/Species.pm
  48. +6 0 lib/LIMS2/Model/Plugin/User.pm
  49. +6 0 lib/LIMS2/Model/Plugin/Well.pm
  50. +6 0 lib/LIMS2/Model/ProcessGraph.pm
  51. +6 0 lib/LIMS2/Model/Schema.pm
  52. +6 0 lib/LIMS2/Model/Schema/Result/Assembly.pm
  53. +6 0 lib/LIMS2/Model/Schema/Result/BacClone.pm
  54. +6 0 lib/LIMS2/Model/Schema/Result/BacCloneLocus.pm
  55. +6 0 lib/LIMS2/Model/Schema/Result/BacLibrary.pm
  56. +6 0 lib/LIMS2/Model/Schema/Result/Backbone.pm
  57. +6 0 lib/LIMS2/Model/Schema/Result/Cassette.pm
  58. +6 0 lib/LIMS2/Model/Schema/Result/Chromosome.pm
  59. +6 0 lib/LIMS2/Model/Schema/Result/ColonyCountType.pm
  60. +6 0 lib/LIMS2/Model/Schema/Result/DefaultDesignOligoLocus.pm
  61. +6 0 lib/LIMS2/Model/Schema/Result/Design.pm
  62. +6 0 lib/LIMS2/Model/Schema/Result/DesignComment.pm
  63. +6 0 lib/LIMS2/Model/Schema/Result/DesignCommentCategory.pm
  64. +6 0 lib/LIMS2/Model/Schema/Result/DesignOligo.pm
  65. +6 0 lib/LIMS2/Model/Schema/Result/DesignOligoLocus.pm
  66. +6 0 lib/LIMS2/Model/Schema/Result/DesignOligoType.pm
  67. +6 0 lib/LIMS2/Model/Schema/Result/DesignType.pm
  68. +6 0 lib/LIMS2/Model/Schema/Result/GeneDesign.pm
  69. +6 0 lib/LIMS2/Model/Schema/Result/GenotypingPrimer.pm
  70. +6 0 lib/LIMS2/Model/Schema/Result/GenotypingPrimerType.pm
  71. +6 0 lib/LIMS2/Model/Schema/Result/Plate.pm
  72. +6 0 lib/LIMS2/Model/Schema/Result/PlateComment.pm
  73. +6 0 lib/LIMS2/Model/Schema/Result/PlateType.pm
  74. +6 0 lib/LIMS2/Model/Schema/Result/PrimerBandType.pm
  75. +6 0 lib/LIMS2/Model/Schema/Result/Process.pm
  76. +6 0 lib/LIMS2/Model/Schema/Result/ProcessBac.pm
  77. +6 0 lib/LIMS2/Model/Schema/Result/ProcessBackbone.pm
  78. +6 0 lib/LIMS2/Model/Schema/Result/ProcessCassette.pm
  79. +6 0 lib/LIMS2/Model/Schema/Result/ProcessCellLine.pm
  80. +6 0 lib/LIMS2/Model/Schema/Result/ProcessDesign.pm
  81. +6 0 lib/LIMS2/Model/Schema/Result/ProcessElectroporation.pm
  82. +6 0 lib/LIMS2/Model/Schema/Result/ProcessInputWell.pm
  83. +6 0 lib/LIMS2/Model/Schema/Result/ProcessOutputWell.pm
  84. +6 0 lib/LIMS2/Model/Schema/Result/ProcessRecombinase.pm
  85. +6 0 lib/LIMS2/Model/Schema/Result/ProcessType.pm
  86. +6 0 lib/LIMS2/Model/Schema/Result/QcAlignment.pm
  87. +6 0 lib/LIMS2/Model/Schema/Result/QcAlignmentRegion.pm
  88. +6 0 lib/LIMS2/Model/Schema/Result/QcEngSeq.pm
  89. +6 0 lib/LIMS2/Model/Schema/Result/QcRun.pm
  90. +6 0 lib/LIMS2/Model/Schema/Result/QcRunSeqProject.pm
  91. +6 0 lib/LIMS2/Model/Schema/Result/QcRunSeqWell.pm
  92. +6 0 lib/LIMS2/Model/Schema/Result/QcRunSeqWellQcSeqRead.pm
  93. +6 0 lib/LIMS2/Model/Schema/Result/QcSeqProject.pm
  94. +6 0 lib/LIMS2/Model/Schema/Result/QcSeqRead.pm
  95. +6 0 lib/LIMS2/Model/Schema/Result/QcTemplate.pm
  96. +6 0 lib/LIMS2/Model/Schema/Result/QcTemplateWell.pm
  97. +6 0 lib/LIMS2/Model/Schema/Result/QcTestResult.pm
  98. +6 0 lib/LIMS2/Model/Schema/Result/Recombinase.pm
  99. +6 0 lib/LIMS2/Model/Schema/Result/RecombineeringResultType.pm
  100. +6 0 lib/LIMS2/Model/Schema/Result/Role.pm
  101. +6 0 lib/LIMS2/Model/Schema/Result/SchemaVersion.pm
  102. +6 0 lib/LIMS2/Model/Schema/Result/Species.pm
  103. +6 0 lib/LIMS2/Model/Schema/Result/SpeciesDefaultAssembly.pm
  104. +6 0 lib/LIMS2/Model/Schema/Result/User.pm
  105. +6 0 lib/LIMS2/Model/Schema/Result/UserPreference.pm
  106. +6 0 lib/LIMS2/Model/Schema/Result/UserRole.pm
  107. +6 0 lib/LIMS2/Model/Schema/Result/Well.pm
  108. +6 0 lib/LIMS2/Model/Schema/Result/WellAcceptedOverride.pm
  109. +6 0 lib/LIMS2/Model/Schema/Result/WellColonyCount.pm
  110. +6 0 lib/LIMS2/Model/Schema/Result/WellComment.pm
  111. +6 0 lib/LIMS2/Model/Schema/Result/WellDnaQuality.pm
  112. +6 0 lib/LIMS2/Model/Schema/Result/WellDnaStatus.pm
  113. +6 0 lib/LIMS2/Model/Schema/Result/WellPrimerBand.pm
  114. +6 0 lib/LIMS2/Model/Schema/Result/WellQcSequencingResult.pm
  115. +6 0 lib/LIMS2/Model/Schema/Result/WellRecombineeringResult.pm
  116. +6 0 lib/LIMS2/Model/Types.pm
  117. +6 0 lib/LIMS2/Model/Util.pm
  118. +6 0 lib/LIMS2/Model/Util/ComputeAcceptedStatus.pm
  119. +6 0 lib/LIMS2/Model/Util/PgUserRole.pm
  120. +6 0 lib/LIMS2/Model/Util/QCResults.pm
  121. +6 0 lib/LIMS2/Model/Util/WellName.pm
  122. +6 0 lib/LIMS2/Report.pm
  123. +6 0 lib/LIMS2/Report/DNAPlate.pm
  124. +6 0 lib/LIMS2/Report/DesignPlate.pm
  125. +6 0 lib/LIMS2/Report/EPPlate.pm
  126. +6 0 lib/LIMS2/Report/FinalVectorPlate.pm
  127. +6 0 lib/LIMS2/Report/FirstElectroporationProductionDetail.pm
  128. +6 0 lib/LIMS2/Report/IntermediateVectorPlate.pm
  129. +6 0 lib/LIMS2/Report/PlateList.pm
  130. +6 0 lib/LIMS2/Report/PostIntermediateVectorPlate.pm
  131. +6 0 lib/LIMS2/Report/QcRun.pm
  132. +6 0 lib/LIMS2/Report/QcRunSummary.pm
  133. +6 0 lib/LIMS2/Report/SEPPlate.pm
  134. +6 0 lib/LIMS2/Report/VectorProductionDetail.pm
  135. +6 0 lib/LIMS2/Report/VectorProductionSummary.pm
  136. +6 0 lib/LIMS2/ReportGenerator.pm
  137. +6 0 lib/LIMS2/ReportGenerator/ColonyCounts.pm
  138. +6 0 lib/LIMS2/ReportGenerator/Plate.pm
  139. +6 0 lib/LIMS2/ReportGenerator/Plate/DoubleTargeted.pm
  140. +6 0 lib/LIMS2/ReportGenerator/Plate/SingleTargeted.pm
  141. +6 0 lib/LIMS2/Test.pm
  142. +6 0 lib/LIMS2/WebApp.pm
  143. +6 0 lib/LIMS2/WebApp/Controller/API.pm
  144. +6 0 lib/LIMS2/WebApp/Controller/API/AutoComplete.pm
  145. +6 0 lib/LIMS2/WebApp/Controller/API/Design.pm
  146. +6 0 lib/LIMS2/WebApp/Controller/API/PlateWell.pm
  147. +6 0 lib/LIMS2/WebApp/Controller/API/QC.pm
  148. +6 0 lib/LIMS2/WebApp/Controller/API/Report.pm
  149. +6 0 lib/LIMS2/WebApp/Controller/Admin.pm
  150. +6 0 lib/LIMS2/WebApp/Controller/Auth.pm
  151. +6 0 lib/LIMS2/WebApp/Controller/Root.pm
  152. +6 0 lib/LIMS2/WebApp/Controller/User.pm
  153. +6 0 lib/LIMS2/WebApp/Controller/User/BrowseDesigns.pm
  154. +6 0 lib/LIMS2/WebApp/Controller/User/BrowsePlates.pm
  155. +6 0 lib/LIMS2/WebApp/Controller/User/Graph.pm
  156. +6 0 lib/LIMS2/WebApp/Controller/User/QC.pm
  157. +6 0 lib/LIMS2/WebApp/Controller/User/Report.pm
  158. +6 0 lib/LIMS2/WebApp/Controller/User/Report/Gene.pm
  159. +6 0 lib/LIMS2/WebApp/Model/AuthDB.pm
  160. +6 0 lib/LIMS2/WebApp/Model/Golgi.pm
  161. +6 0 lib/LIMS2/WebApp/Pageset.pm
  162. +6 0 lib/LIMS2/WebApp/Script/FastCGI.pm
  163. +6 0 lib/LIMS2/WebApp/View/HTML.pm
  164. +73 0 t/00-compile.t
  165. +20 0 t/author-critic.t
  166. +22 0 t/release-no-smart-comments.t
7 .gitignore
... ... @@ -1,7 +0,0 @@
1   -.build
2   -LIMS2-WebApp-*
3   -ddl/lims2_devel
4   -ddl/lims2_test
5   -ddl/lims2_test2
6   -ddl/lims2_live
7   -ddl/lims2_staging
7 Changes
... ... @@ -1,4 +1,9 @@
1   -{{$NEXT}}
  1 +0.010 2012-07-25 13:08:51 Europe/London
  2 +
  3 + Implement support for creation of EP, XEP, SEP, EP_PICK and FP plate types.
  4 + Implement basic reports for new plate types.
  5 + Re-order columns in vector production summary report
  6 + Add tables for primer_band and colony_pick data
2 7
3 8 0.009 2012-07-23 12:54:21 Europe/London
4 9
379 LICENSE
... ... @@ -0,0 +1,379 @@
  1 +This software is copyright (c) 2012 by Genome Research Ltd.
  2 +
  3 +This is free software; you can redistribute it and/or modify it under
  4 +the same terms as the Perl 5 programming language system itself.
  5 +
  6 +Terms of the Perl programming language system itself
  7 +
  8 +a) the GNU General Public License as published by the Free
  9 + Software Foundation; either version 1, or (at your option) any
  10 + later version, or
  11 +b) the "Artistic License"
  12 +
  13 +--- The GNU General Public License, Version 1, February 1989 ---
  14 +
  15 +This software is Copyright (c) 2012 by Genome Research Ltd.
  16 +
  17 +This is free software, licensed under:
  18 +
  19 + The GNU General Public License, Version 1, February 1989
  20 +
  21 + GNU GENERAL PUBLIC LICENSE
  22 + Version 1, February 1989
  23 +
  24 + Copyright (C) 1989 Free Software Foundation, Inc.
  25 + 51 Franklin St, Suite 500, Boston, MA 02110-1335 USA
  26 +
  27 + Everyone is permitted to copy and distribute verbatim copies
  28 + of this license document, but changing it is not allowed.
  29 +
  30 + Preamble
  31 +
  32 + The license agreements of most software companies try to keep users
  33 +at the mercy of those companies. By contrast, our General Public
  34 +License is intended to guarantee your freedom to share and change free
  35 +software--to make sure the software is free for all its users. The
  36 +General Public License applies to the Free Software Foundation's
  37 +software and to any other program whose authors commit to using it.
  38 +You can use it for your programs, too.
  39 +
  40 + When we speak of free software, we are referring to freedom, not
  41 +price. Specifically, the General Public License is designed to make
  42 +sure that you have the freedom to give away or sell copies of free
  43 +software, that you receive source code or can get it if you want it,
  44 +that you can change the software or use pieces of it in new free
  45 +programs; and that you know you can do these things.
  46 +
  47 + To protect your rights, we need to make restrictions that forbid
  48 +anyone to deny you these rights or to ask you to surrender the rights.
  49 +These restrictions translate to certain responsibilities for you if you
  50 +distribute copies of the software, or if you modify it.
  51 +
  52 + For example, if you distribute copies of a such a program, whether
  53 +gratis or for a fee, you must give the recipients all the rights that
  54 +you have. You must make sure that they, too, receive or can get the
  55 +source code. And you must tell them their rights.
  56 +
  57 + We protect your rights with two steps: (1) copyright the software, and
  58 +(2) offer you this license which gives you legal permission to copy,
  59 +distribute and/or modify the software.
  60 +
  61 + Also, for each author's protection and ours, we want to make certain
  62 +that everyone understands that there is no warranty for this free
  63 +software. If the software is modified by someone else and passed on, we
  64 +want its recipients to know that what they have is not the original, so
  65 +that any problems introduced by others will not reflect on the original
  66 +authors' reputations.
  67 +
  68 + The precise terms and conditions for copying, distribution and
  69 +modification follow.
  70 +
  71 + GNU GENERAL PUBLIC LICENSE
  72 + TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
  73 +
  74 + 0. This License Agreement applies to any program or other work which
  75 +contains a notice placed by the copyright holder saying it may be
  76 +distributed under the terms of this General Public License. The
  77 +"Program", below, refers to any such program or work, and a "work based
  78 +on the Program" means either the Program or any work containing the
  79 +Program or a portion of it, either verbatim or with modifications. Each
  80 +licensee is addressed as "you".
  81 +
  82 + 1. You may copy and distribute verbatim copies of the Program's source
  83 +code as you receive it, in any medium, provided that you conspicuously and
  84 +appropriately publish on each copy an appropriate copyright notice and
  85 +disclaimer of warranty; keep intact all the notices that refer to this
  86 +General Public License and to the absence of any warranty; and give any
  87 +other recipients of the Program a copy of this General Public License
  88 +along with the Program. You may charge a fee for the physical act of
  89 +transferring a copy.
  90 +
  91 + 2. You may modify your copy or copies of the Program or any portion of
  92 +it, and copy and distribute such modifications under the terms of Paragraph
  93 +1 above, provided that you also do the following:
  94 +
  95 + a) cause the modified files to carry prominent notices stating that
  96 + you changed the files and the date of any change; and
  97 +
  98 + b) cause the whole of any work that you distribute or publish, that
  99 + in whole or in part contains the Program or any part thereof, either
  100 + with or without modifications, to be licensed at no charge to all
  101 + third parties under the terms of this General Public License (except
  102 + that you may choose to grant warranty protection to some or all
  103 + third parties, at your option).
  104 +
  105 + c) If the modified program normally reads commands interactively when
  106 + run, you must cause it, when started running for such interactive use
  107 + in the simplest and most usual way, to print or display an
  108 + announcement including an appropriate copyright notice and a notice
  109 + that there is no warranty (or else, saying that you provide a
  110 + warranty) and that users may redistribute the program under these
  111 + conditions, and telling the user how to view a copy of this General
  112 + Public License.
  113 +
  114 + d) You may charge a fee for the physical act of transferring a
  115 + copy, and you may at your option offer warranty protection in
  116 + exchange for a fee.
  117 +
  118 +Mere aggregation of another independent work with the Program (or its
  119 +derivative) on a volume of a storage or distribution medium does not bring
  120 +the other work under the scope of these terms.
  121 +
  122 + 3. You may copy and distribute the Program (or a portion or derivative of
  123 +it, under Paragraph 2) in object code or executable form under the terms of
  124 +Paragraphs 1 and 2 above provided that you also do one of the following:
  125 +
  126 + a) accompany it with the complete corresponding machine-readable
  127 + source code, which must be distributed under the terms of
  128 + Paragraphs 1 and 2 above; or,
  129 +
  130 + b) accompany it with a written offer, valid for at least three
  131 + years, to give any third party free (except for a nominal charge
  132 + for the cost of distribution) a complete machine-readable copy of the
  133 + corresponding source code, to be distributed under the terms of
  134 + Paragraphs 1 and 2 above; or,
  135 +
  136 + c) accompany it with the information you received as to where the
  137 + corresponding source code may be obtained. (This alternative is
  138 + allowed only for noncommercial distribution and only if you
  139 + received the program in object code or executable form alone.)
  140 +
  141 +Source code for a work means the preferred form of the work for making
  142 +modifications to it. For an executable file, complete source code means
  143 +all the source code for all modules it contains; but, as a special
  144 +exception, it need not include source code for modules which are standard
  145 +libraries that accompany the operating system on which the executable
  146 +file runs, or for standard header files or definitions files that
  147 +accompany that operating system.
  148 +
  149 + 4. You may not copy, modify, sublicense, distribute or transfer the
  150 +Program except as expressly provided under this General Public License.
  151 +Any attempt otherwise to copy, modify, sublicense, distribute or transfer
  152 +the Program is void, and will automatically terminate your rights to use
  153 +the Program under this License. However, parties who have received
  154 +copies, or rights to use copies, from you under this General Public
  155 +License will not have their licenses terminated so long as such parties
  156 +remain in full compliance.
  157 +
  158 + 5. By copying, distributing or modifying the Program (or any work based
  159 +on the Program) you indicate your acceptance of this license to do so,
  160 +and all its terms and conditions.
  161 +
  162 + 6. Each time you redistribute the Program (or any work based on the
  163 +Program), the recipient automatically receives a license from the original
  164 +licensor to copy, distribute or modify the Program subject to these
  165 +terms and conditions. You may not impose any further restrictions on the
  166 +recipients' exercise of the rights granted herein.
  167 +
  168 + 7. The Free Software Foundation may publish revised and/or new versions
  169 +of the General Public License from time to time. Such new versions will
  170 +be similar in spirit to the present version, but may differ in detail to
  171 +address new problems or concerns.
  172 +
  173 +Each version is given a distinguishing version number. If the Program
  174 +specifies a version number of the license which applies to it and "any
  175 +later version", you have the option of following the terms and conditions
  176 +either of that version or of any later version published by the Free
  177 +Software Foundation. If the Program does not specify a version number of
  178 +the license, you may choose any version ever published by the Free Software
  179 +Foundation.
  180 +
  181 + 8. If you wish to incorporate parts of the Program into other free
  182 +programs whose distribution conditions are different, write to the author
  183 +to ask for permission. For software which is copyrighted by the Free
  184 +Software Foundation, write to the Free Software Foundation; we sometimes
  185 +make exceptions for this. Our decision will be guided by the two goals
  186 +of preserving the free status of all derivatives of our free software and
  187 +of promoting the sharing and reuse of software generally.
  188 +
  189 + NO WARRANTY
  190 +
  191 + 9. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
  192 +FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
  193 +OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
  194 +PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
  195 +OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
  196 +MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
  197 +TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
  198 +PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
  199 +REPAIR OR CORRECTION.
  200 +
  201 + 10. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
  202 +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
  203 +REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
  204 +INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
  205 +OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
  206 +TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
  207 +YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
  208 +PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
  209 +POSSIBILITY OF SUCH DAMAGES.
  210 +
  211 + END OF TERMS AND CONDITIONS
  212 +
  213 + Appendix: How to Apply These Terms to Your New Programs
  214 +
  215 + If you develop a new program, and you want it to be of the greatest
  216 +possible use to humanity, the best way to achieve this is to make it
  217 +free software which everyone can redistribute and change under these
  218 +terms.
  219 +
  220 + To do so, attach the following notices to the program. It is safest to
  221 +attach them to the start of each source file to most effectively convey
  222 +the exclusion of warranty; and each file should have at least the
  223 +"copyright" line and a pointer to where the full notice is found.
  224 +
  225 + <one line to give the program's name and a brief idea of what it does.>
  226 + Copyright (C) 19yy <name of author>
  227 +
  228 + This program is free software; you can redistribute it and/or modify
  229 + it under the terms of the GNU General Public License as published by
  230 + the Free Software Foundation; either version 1, or (at your option)
  231 + any later version.
  232 +
  233 + This program is distributed in the hope that it will be useful,
  234 + but WITHOUT ANY WARRANTY; without even the implied warranty of
  235 + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
  236 + GNU General Public License for more details.
  237 +
  238 + You should have received a copy of the GNU General Public License
  239 + along with this program; if not, write to the Free Software
  240 + Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston MA 02110-1301 USA
  241 +
  242 +
  243 +Also add information on how to contact you by electronic and paper mail.
  244 +
  245 +If the program is interactive, make it output a short notice like this
  246 +when it starts in an interactive mode:
  247 +
  248 + Gnomovision version 69, Copyright (C) 19xx name of author
  249 + Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
  250 + This is free software, and you are welcome to redistribute it
  251 + under certain conditions; type `show c' for details.
  252 +
  253 +The hypothetical commands `show w' and `show c' should show the
  254 +appropriate parts of the General Public License. Of course, the
  255 +commands you use may be called something other than `show w' and `show
  256 +c'; they could even be mouse-clicks or menu items--whatever suits your
  257 +program.
  258 +
  259 +You should also get your employer (if you work as a programmer) or your
  260 +school, if any, to sign a "copyright disclaimer" for the program, if
  261 +necessary. Here a sample; alter the names:
  262 +
  263 + Yoyodyne, Inc., hereby disclaims all copyright interest in the
  264 + program `Gnomovision' (a program to direct compilers to make passes
  265 + at assemblers) written by James Hacker.
  266 +
  267 + <signature of Ty Coon>, 1 April 1989
  268 + Ty Coon, President of Vice
  269 +
  270 +That's all there is to it!
  271 +
  272 +
  273 +--- The Artistic License 1.0 ---
  274 +
  275 +This software is Copyright (c) 2012 by Genome Research Ltd.
  276 +
  277 +This is free software, licensed under:
  278 +
  279 + The Artistic License 1.0
  280 +
  281 +The Artistic License
  282 +
  283 +Preamble
  284 +
  285 +The intent of this document is to state the conditions under which a Package
  286 +may be copied, such that the Copyright Holder maintains some semblance of
  287 +artistic control over the development of the package, while giving the users of
  288 +the package the right to use and distribute the Package in a more-or-less
  289 +customary fashion, plus the right to make reasonable modifications.
  290 +
  291 +Definitions:
  292 +
  293 + - "Package" refers to the collection of files distributed by the Copyright
  294 + Holder, and derivatives of that collection of files created through
  295 + textual modification.
  296 + - "Standard Version" refers to such a Package if it has not been modified,
  297 + or has been modified in accordance with the wishes of the Copyright
  298 + Holder.
  299 + - "Copyright Holder" is whoever is named in the copyright or copyrights for
  300 + the package.
  301 + - "You" is you, if you're thinking about copying or distributing this Package.
  302 + - "Reasonable copying fee" is whatever you can justify on the basis of media
  303 + cost, duplication charges, time of people involved, and so on. (You will
  304 + not be required to justify it to the Copyright Holder, but only to the
  305 + computing community at large as a market that must bear the fee.)
  306 + - "Freely Available" means that no fee is charged for the item itself, though
  307 + there may be fees involved in handling the item. It also means that
  308 + recipients of the item may redistribute it under the same conditions they
  309 + received it.
  310 +
  311 +1. You may make and give away verbatim copies of the source form of the
  312 +Standard Version of this Package without restriction, provided that you
  313 +duplicate all of the original copyright notices and associated disclaimers.
  314 +
  315 +2. You may apply bug fixes, portability fixes and other modifications derived
  316 +from the Public Domain or from the Copyright Holder. A Package modified in such
  317 +a way shall still be considered the Standard Version.
  318 +
  319 +3. You may otherwise modify your copy of this Package in any way, provided that
  320 +you insert a prominent notice in each changed file stating how and when you
  321 +changed that file, and provided that you do at least ONE of the following:
  322 +
  323 + a) place your modifications in the Public Domain or otherwise make them
  324 + Freely Available, such as by posting said modifications to Usenet or an
  325 + equivalent medium, or placing the modifications on a major archive site
  326 + such as ftp.uu.net, or by allowing the Copyright Holder to include your
  327 + modifications in the Standard Version of the Package.
  328 +
  329 + b) use the modified Package only within your corporation or organization.
  330 +
  331 + c) rename any non-standard executables so the names do not conflict with
  332 + standard executables, which must also be provided, and provide a separate
  333 + manual page for each non-standard executable that clearly documents how it
  334 + differs from the Standard Version.
  335 +
  336 + d) make other distribution arrangements with the Copyright Holder.
  337 +
  338 +4. You may distribute the programs of this Package in object code or executable
  339 +form, provided that you do at least ONE of the following:
  340 +
  341 + a) distribute a Standard Version of the executables and library files,
  342 + together with instructions (in the manual page or equivalent) on where to
  343 + get the Standard Version.
  344 +
  345 + b) accompany the distribution with the machine-readable source of the Package
  346 + with your modifications.
  347 +
  348 + c) accompany any non-standard executables with their corresponding Standard
  349 + Version executables, giving the non-standard executables non-standard
  350 + names, and clearly documenting the differences in manual pages (or
  351 + equivalent), together with instructions on where to get the Standard
  352 + Version.
  353 +
  354 + d) make other distribution arrangements with the Copyright Holder.
  355 +
  356 +5. You may charge a reasonable copying fee for any distribution of this
  357 +Package. You may charge any fee you choose for support of this Package. You
  358 +may not charge a fee for this Package itself. However, you may distribute this
  359 +Package in aggregate with other (possibly commercial) programs as part of a
  360 +larger (possibly commercial) software distribution provided that you do not
  361 +advertise this Package as a product of your own.
  362 +
  363 +6. The scripts and library files supplied as input to or produced as output
  364 +from the programs of this Package do not automatically fall under the copyright
  365 +of this Package, but belong to whomever generated them, and may be sold
  366 +commercially, and may be aggregated with this Package.
  367 +
  368 +7. C or perl subroutines supplied by you and linked into this Package shall not
  369 +be considered part of this Package.
  370 +
  371 +8. The name of the Copyright Holder may not be used to endorse or promote
  372 +products derived from this software without specific prior written permission.
  373 +
  374 +9. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
  375 +WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
  376 +MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
  377 +
  378 +The End
  379 +
239 MANIFEST
... ... @@ -0,0 +1,239 @@
  1 +Changes
  2 +LICENSE
  3 +MANIFEST
  4 +META.yml
  5 +Makefile.PL
  6 +README
  7 +bin/final_vector_report.pl
  8 +bin/lims2_create_users.pl
  9 +bin/lims2_model_dump_schema.pl
  10 +bin/process_graph.pl
  11 +lib/LIMS2/Catalyst/Controller/REST.pm
  12 +lib/LIMS2/Model.pm
  13 +lib/LIMS2/Model/AuthDB.pm
  14 +lib/LIMS2/Model/Constants.pm
  15 +lib/LIMS2/Model/DBConnect.pm
  16 +lib/LIMS2/Model/FormValidator.pm
  17 +lib/LIMS2/Model/FormValidator/Constraint.pm
  18 +lib/LIMS2/Model/Plugin/BAC.pm
  19 +lib/LIMS2/Model/Plugin/Design.pm
  20 +lib/LIMS2/Model/Plugin/Gene.pm
  21 +lib/LIMS2/Model/Plugin/Plate.pm
  22 +lib/LIMS2/Model/Plugin/Process.pm
  23 +lib/LIMS2/Model/Plugin/QC.pm
  24 +lib/LIMS2/Model/Plugin/Species.pm
  25 +lib/LIMS2/Model/Plugin/User.pm
  26 +lib/LIMS2/Model/Plugin/Well.pm
  27 +lib/LIMS2/Model/ProcessGraph.pm
  28 +lib/LIMS2/Model/Schema.pm
  29 +lib/LIMS2/Model/Schema/Result/Assembly.pm
  30 +lib/LIMS2/Model/Schema/Result/BacClone.pm
  31 +lib/LIMS2/Model/Schema/Result/BacCloneLocus.pm
  32 +lib/LIMS2/Model/Schema/Result/BacLibrary.pm
  33 +lib/LIMS2/Model/Schema/Result/Backbone.pm
  34 +lib/LIMS2/Model/Schema/Result/Cassette.pm
  35 +lib/LIMS2/Model/Schema/Result/Chromosome.pm
  36 +lib/LIMS2/Model/Schema/Result/ColonyCountType.pm
  37 +lib/LIMS2/Model/Schema/Result/DefaultDesignOligoLocus.pm
  38 +lib/LIMS2/Model/Schema/Result/Design.pm
  39 +lib/LIMS2/Model/Schema/Result/DesignComment.pm
  40 +lib/LIMS2/Model/Schema/Result/DesignCommentCategory.pm
  41 +lib/LIMS2/Model/Schema/Result/DesignOligo.pm
  42 +lib/LIMS2/Model/Schema/Result/DesignOligoLocus.pm
  43 +lib/LIMS2/Model/Schema/Result/DesignOligoType.pm
  44 +lib/LIMS2/Model/Schema/Result/DesignType.pm
  45 +lib/LIMS2/Model/Schema/Result/GeneDesign.pm
  46 +lib/LIMS2/Model/Schema/Result/GenotypingPrimer.pm
  47 +lib/LIMS2/Model/Schema/Result/GenotypingPrimerType.pm
  48 +lib/LIMS2/Model/Schema/Result/Plate.pm
  49 +lib/LIMS2/Model/Schema/Result/PlateComment.pm
  50 +lib/LIMS2/Model/Schema/Result/PlateType.pm
  51 +lib/LIMS2/Model/Schema/Result/PrimerBandType.pm
  52 +lib/LIMS2/Model/Schema/Result/Process.pm
  53 +lib/LIMS2/Model/Schema/Result/ProcessBac.pm
  54 +lib/LIMS2/Model/Schema/Result/ProcessBackbone.pm
  55 +lib/LIMS2/Model/Schema/Result/ProcessCassette.pm
  56 +lib/LIMS2/Model/Schema/Result/ProcessCellLine.pm
  57 +lib/LIMS2/Model/Schema/Result/ProcessDesign.pm
  58 +lib/LIMS2/Model/Schema/Result/ProcessElectroporation.pm
  59 +lib/LIMS2/Model/Schema/Result/ProcessInputWell.pm
  60 +lib/LIMS2/Model/Schema/Result/ProcessOutputWell.pm
  61 +lib/LIMS2/Model/Schema/Result/ProcessRecombinase.pm
  62 +lib/LIMS2/Model/Schema/Result/ProcessType.pm
  63 +lib/LIMS2/Model/Schema/Result/QcAlignment.pm
  64 +lib/LIMS2/Model/Schema/Result/QcAlignmentRegion.pm
  65 +lib/LIMS2/Model/Schema/Result/QcEngSeq.pm
  66 +lib/LIMS2/Model/Schema/Result/QcRun.pm
  67 +lib/LIMS2/Model/Schema/Result/QcRunSeqProject.pm
  68 +lib/LIMS2/Model/Schema/Result/QcRunSeqWell.pm
  69 +lib/LIMS2/Model/Schema/Result/QcRunSeqWellQcSeqRead.pm
  70 +lib/LIMS2/Model/Schema/Result/QcSeqProject.pm
  71 +lib/LIMS2/Model/Schema/Result/QcSeqRead.pm
  72 +lib/LIMS2/Model/Schema/Result/QcTemplate.pm
  73 +lib/LIMS2/Model/Schema/Result/QcTemplateWell.pm
  74 +lib/LIMS2/Model/Schema/Result/QcTestResult.pm
  75 +lib/LIMS2/Model/Schema/Result/Recombinase.pm
  76 +lib/LIMS2/Model/Schema/Result/RecombineeringResultType.pm
  77 +lib/LIMS2/Model/Schema/Result/Role.pm
  78 +lib/LIMS2/Model/Schema/Result/SchemaVersion.pm
  79 +lib/LIMS2/Model/Schema/Result/Species.pm
  80 +lib/LIMS2/Model/Schema/Result/SpeciesDefaultAssembly.pm
  81 +lib/LIMS2/Model/Schema/Result/User.pm
  82 +lib/LIMS2/Model/Schema/Result/UserPreference.pm
  83 +lib/LIMS2/Model/Schema/Result/UserRole.pm
  84 +lib/LIMS2/Model/Schema/Result/Well.pm
  85 +lib/LIMS2/Model/Schema/Result/WellAcceptedOverride.pm
  86 +lib/LIMS2/Model/Schema/Result/WellColonyCount.pm
  87 +lib/LIMS2/Model/Schema/Result/WellComment.pm
  88 +lib/LIMS2/Model/Schema/Result/WellDnaQuality.pm
  89 +lib/LIMS2/Model/Schema/Result/WellDnaStatus.pm
  90 +lib/LIMS2/Model/Schema/Result/WellPrimerBand.pm
  91 +lib/LIMS2/Model/Schema/Result/WellQcSequencingResult.pm
  92 +lib/LIMS2/Model/Schema/Result/WellRecombineeringResult.pm
  93 +lib/LIMS2/Model/Types.pm
  94 +lib/LIMS2/Model/Util.pm
  95 +lib/LIMS2/Model/Util/ComputeAcceptedStatus.pm
  96 +lib/LIMS2/Model/Util/PgUserRole.pm
  97 +lib/LIMS2/Model/Util/QCResults.pm
  98 +lib/LIMS2/Model/Util/WellName.pm
  99 +lib/LIMS2/Report.pm
  100 +lib/LIMS2/Report/DNAPlate.pm
  101 +lib/LIMS2/Report/DesignPlate.pm
  102 +lib/LIMS2/Report/EPPlate.pm
  103 +lib/LIMS2/Report/FinalVectorPlate.pm
  104 +lib/LIMS2/Report/FirstElectroporationProductionDetail.pm
  105 +lib/LIMS2/Report/IntermediateVectorPlate.pm
  106 +lib/LIMS2/Report/PlateList.pm
  107 +lib/LIMS2/Report/PostIntermediateVectorPlate.pm
  108 +lib/LIMS2/Report/QcRun.pm
  109 +lib/LIMS2/Report/QcRunSummary.pm
  110 +lib/LIMS2/Report/SEPPlate.pm
  111 +lib/LIMS2/Report/VectorProductionDetail.pm
  112 +lib/LIMS2/Report/VectorProductionSummary.pm
  113 +lib/LIMS2/ReportGenerator.pm
  114 +lib/LIMS2/ReportGenerator/ColonyCounts.pm
  115 +lib/LIMS2/ReportGenerator/Plate.pm
  116 +lib/LIMS2/ReportGenerator/Plate/DoubleTargeted.pm
  117 +lib/LIMS2/ReportGenerator/Plate/SingleTargeted.pm
  118 +lib/LIMS2/Test.pm
  119 +lib/LIMS2/WebApp.pm
  120 +lib/LIMS2/WebApp/Controller/API.pm
  121 +lib/LIMS2/WebApp/Controller/API/AutoComplete.pm
  122 +lib/LIMS2/WebApp/Controller/API/Design.pm
  123 +lib/LIMS2/WebApp/Controller/API/PlateWell.pm
  124 +lib/LIMS2/WebApp/Controller/API/QC.pm
  125 +lib/LIMS2/WebApp/Controller/API/Report.pm
  126 +lib/LIMS2/WebApp/Controller/Admin.pm
  127 +lib/LIMS2/WebApp/Controller/Auth.pm
  128 +lib/LIMS2/WebApp/Controller/Root.pm
  129 +lib/LIMS2/WebApp/Controller/User.pm
  130 +lib/LIMS2/WebApp/Controller/User/BrowseDesigns.pm
  131 +lib/LIMS2/WebApp/Controller/User/BrowsePlates.pm
  132 +lib/LIMS2/WebApp/Controller/User/Graph.pm
  133 +lib/LIMS2/WebApp/Controller/User/QC.pm
  134 +lib/LIMS2/WebApp/Controller/User/Report.pm
  135 +lib/LIMS2/WebApp/Controller/User/Report/Gene.pm
  136 +lib/LIMS2/WebApp/Model/AuthDB.pm
  137 +lib/LIMS2/WebApp/Model/Golgi.pm
  138 +lib/LIMS2/WebApp/Pageset.pm
  139 +lib/LIMS2/WebApp/Script/FastCGI.pm
  140 +lib/LIMS2/WebApp/View/HTML.pm
  141 +root/favicon.ico
  142 +root/lib/navigation.tt
  143 +root/lib/pagination.tt
  144 +root/lib/wrapper.tt
  145 +root/site/admin/create_user.tt
  146 +root/site/admin/index.tt
  147 +root/site/admin/update_user.tt
  148 +root/site/auth/login.tt
  149 +root/site/user/browsedesigns/index.tt
  150 +root/site/user/browsedesigns/list_designs.tt
  151 +root/site/user/browsedesigns/view_design.tt
  152 +root/site/user/browseplates/index.tt
  153 +root/site/user/browseplates/view.tt
  154 +root/site/user/error.tt
  155 +root/site/user/graph/index.tt
  156 +root/site/user/index.tt
  157 +root/site/user/qc/index.tt
  158 +root/site/user/qc/view_qc_alignment.tt
  159 +root/site/user/qc/view_qc_result.tt
  160 +root/site/user/qc/view_qc_run.tt
  161 +root/site/user/report/await_report.tt
  162 +root/site/user/report/gene_report.tt
  163 +root/site/user/report/simple_table.tt
  164 +root/static/bootstrap/css/bootstrap.css
  165 +root/static/bootstrap/css/bootstrap.min.css
  166 +root/static/bootstrap/img/glyphicons-halflings-white.png
  167 +root/static/bootstrap/img/glyphicons-halflings.png
  168 +root/static/bootstrap/js/bootstrap.js
  169 +root/static/bootstrap/js/bootstrap.min.js
  170 +root/static/css/lims2.css
  171 +root/static/images/btn_120x50_built.png
  172 +root/static/images/btn_120x50_built_shadow.png
  173 +root/static/images/btn_120x50_powered.png
  174 +root/static/images/btn_120x50_powered_shadow.png
  175 +root/static/images/btn_88x31_built.png
  176 +root/static/images/btn_88x31_built_shadow.png
  177 +root/static/images/btn_88x31_powered.png
  178 +root/static/images/btn_88x31_powered_shadow.png
  179 +root/static/images/catalyst_logo.png
  180 +root/static/images/spinner-circle.gif
  181 +root/static/jquery/css/ui-lightness/images/ui-bg_diagonals-thick_18_b81900_40x40.png
  182 +root/static/jquery/css/ui-lightness/images/ui-bg_diagonals-thick_20_666666_40x40.png
  183 +root/static/jquery/css/ui-lightness/images/ui-bg_flat_10_000000_40x100.png
  184 +root/static/jquery/css/ui-lightness/images/ui-bg_glass_100_f6f6f6_1x400.png
  185 +root/static/jquery/css/ui-lightness/images/ui-bg_glass_100_fdf5ce_1x400.png
  186 +root/static/jquery/css/ui-lightness/images/ui-bg_glass_65_ffffff_1x400.png
  187 +root/static/jquery/css/ui-lightness/images/ui-bg_gloss-wave_35_f6a828_500x100.png
  188 +root/static/jquery/css/ui-lightness/images/ui-bg_highlight-soft_100_eeeeee_1x100.png
  189 +root/static/jquery/css/ui-lightness/images/ui-bg_highlight-soft_75_ffe45c_1x100.png
  190 +root/static/jquery/css/ui-lightness/images/ui-icons_222222_256x240.png
  191 +root/static/jquery/css/ui-lightness/images/ui-icons_228ef1_256x240.png
  192 +root/static/jquery/css/ui-lightness/images/ui-icons_ef8c08_256x240.png
  193 +root/static/jquery/css/ui-lightness/images/ui-icons_ffd27a_256x240.png
  194 +root/static/jquery/css/ui-lightness/images/ui-icons_ffffff_256x240.png
  195 +root/static/jquery/css/ui-lightness/jquery-ui-1.8.21.custom.css
  196 +root/static/jquery/js/jquery-ui-1.8.21.custom.min.js
  197 +root/static/js/jquery-1.7.2.min.js
  198 +root/static/js/poller.js
  199 +script/lims2_webapp_cgi.pl
  200 +script/lims2_webapp_create.pl
  201 +script/lims2_webapp_fastcgi.pl
  202 +script/lims2_webapp_server.pl
  203 +script/lims2_webapp_test.pl
  204 +t/00-compile.t
  205 +t/10-dbconnect.t
  206 +t/10-lims2-test.t
  207 +t/20-form-validator.t
  208 +t/50-model-plugin-bac.t
  209 +t/50-model-plugin-design.t
  210 +t/50-model-plugin-gene.t
  211 +t/50-model-plugin-plate.t
  212 +t/50-model-plugin-process.t
  213 +t/50-model-plugin-qc.t
  214 +t/50-model-plugin-user.t
  215 +t/50-model-plugin-well.t
  216 +t/80-login.t
  217 +t/80-qc.t
  218 +t/author-critic.t
  219 +t/data/2w_gateway_process.yaml
  220 +t/data/3w_gateway_process.yaml
  221 +t/data/cre_bac_recom_process.yaml
  222 +t/data/create_di_process.yaml
  223 +t/data/dna_prep_process.yaml
  224 +t/data/int_recom_process.yaml
  225 +t/data/plate.yaml
  226 +t/data/qc_run.yaml
  227 +t/data/qc_seq_reads.yaml
  228 +t/data/qc_template.yaml
  229 +t/data/rearray_process.yaml
  230 +t/data/recombinase_process.yaml
  231 +t/data/well.yaml
  232 +t/fixtures/00-clean-db.sql
  233 +t/fixtures/10-users-roles.sql
  234 +t/fixtures/20-constrained-vocab.sql
  235 +t/fixtures/30-bacs.sql
  236 +t/fixtures/30-designs.sql
  237 +t/fixtures/40-qc.sql
  238 +t/fixtures/50-plate-wells.sql
  239 +t/release-no-smart-comments.t
111 META.yml
... ... @@ -0,0 +1,111 @@
  1 +---
  2 +abstract: 'Catalyst based application'
  3 +author:
  4 + - 'Wellcome Trust Sanger Institute'
  5 +build_requires:
  6 + English: 0
  7 + File::Find: 0
  8 + File::Temp: 0
  9 + HTTP::Request::Common: 0
  10 + Test::More: 0.88
  11 + Test::Most: 0
  12 +dynamic_config: 0
  13 +generated_by: 'Dist::Zilla version 4.300014, CPAN::Meta::Converter version 2.120921'
  14 +license: perl
  15 +meta-spec:
  16 + url: http://module-build.sourceforge.net/META-spec-v1.4.html
  17 + version: 1.4
  18 +name: LIMS2-WebApp
  19 +requires:
  20 + Bio::Seq: 0
  21 + Bio::SeqIO: 0
  22 + CHI: 0
  23 + Carp: 0
  24 + Catalyst: 0
  25 + Catalyst::Controller: 0
  26 + Catalyst::Controller::REST: 0
  27 + Catalyst::Devel: 0
  28 + Catalyst::Model::Adaptor: 0
  29 + Catalyst::Model::DBIC::Schema: 0
  30 + Catalyst::Model::Factory::PerRequest: 0
  31 + Catalyst::Plugin::Authorization::Roles: 0
  32 + Catalyst::Plugin::Session::State::Cookie: 0
  33 + Catalyst::Plugin::Session::Store::FastMmap: 0
  34 + Catalyst::Plugin::Static::Simple: 0
  35 + Catalyst::Runtime: 5.80
  36 + Catalyst::Script::FastCGI: 0
  37 + Catalyst::View::TT: 0
  38 + Class::Data::Inheritable: 0
  39 + Config::Any: 0
  40 + Const::Fast: 0
  41 + Crypt::SaltedHash: 0
  42 + DBIx::Class::Core: 0
  43 + DBIx::Class::Schema: 0
  44 + DBIx::Class::Schema::Loader: 0
  45 + DBIx::Connector: 0
  46 + DBIx::RunSQL: 0
  47 + Data::Compare: 0
  48 + Data::Dump: 0
  49 + Data::FormValidator: 0
  50 + Data::Pageset: 0
  51 + Data::UUID: 0
  52 + DateTime: 0
  53 + DateTime::Format::ISO8601: 0
  54 + DateTime::Format::Pg: 0
  55 + DateTime::Format::Strptime: 0
  56 + EngSeqBuilder: 0
  57 + Exporter: 0
  58 + File::stat: 0
  59 + FindBin: 0
  60 + Getopt::Long: 0
  61 + GraphViz2: 0
  62 + HTGT::QC::Config: 0
  63 + HTGT::QC::Util::Alignment: 0
  64 + HTGT::QC::Util::CigarParser: 0
  65 + HTTP::Status: 0
  66 + Hash::MoreUtils: 0
  67 + IO::Pipe: 0
  68 + IO::String: 0
  69 + Iterator::Simple: 0
  70 + JSON: 0
  71 + LIMS2::Exception: 0
  72 + LIMS2::Exception::Database: 0
  73 + LIMS2::Exception::Implementation: 0
  74 + LIMS2::Exception::System: 0
  75 + LIMS2::Exception::Validation: 0
  76 + LIMS2::Util: 0
  77 + LIMS2::Util::EnsEMBL: 0
  78 + LIMS2::Util::Solr: 0
  79 + List::MoreUtils: 0
  80 + List::Util: 0
  81 + Log::Log4perl: 0
  82 + Log::Log4perl::Catalyst: 0
  83 + Module::Pluggable::Object: 0
  84 + Moose: 0
  85 + Moose::Role: 0
  86 + MooseX::ClassAttribute: 0
  87 + MooseX::Log::Log4perl: 0
  88 + MooseX::MarkAsMethods: 0
  89 + MooseX::NonMoose: 0
  90 + MooseX::Types: 0
  91 + MooseX::Types::Path::Class: 0
  92 + Path::Class: 0
  93 + Scalar::Util: 0
  94 + Sub::Exporter: 0
  95 + Template::AutoFilter: 0
  96 + Term::ReadPassword: 0
  97 + Test::More: 0
  98 + Test::WWW::Mechanize::Catalyst: 0
  99 + Text::CSV: 0
  100 + Try::Tiny: 0
  101 + TryCatch: 0
  102 + URI: 0
  103 + URI::QueryParam: 0
  104 + YAML::Any: 0
  105 + base: 0
  106 + namespace::autoclean: 0
  107 + overload: 0
  108 + strict: 0
  109 + utf8: 0
  110 + warnings: 0
  111 +version: 0.010
13 README
... ... @@ -0,0 +1,13 @@
  1 +
  2 +
  3 +This archive contains the distribution LIMS2-WebApp,
  4 +version 0.010:
  5 +
  6 + Catalyst based application
  7 +
  8 +This software is copyright (c) 2012 by Genome Research Ltd.
  9 +
  10 +This is free software; you can redistribute it and/or modify it under
  11 +the same terms as the Perl 5 programming language system itself.
  12 +
  13 +
12 ddl/generate-schema.sh
... ... @@ -1,12 +0,0 @@
1   -#!/bin/bash
2   -
3   -DBNAME="$1"
4   -
5   -if test -z "$DBNAME"; then
6   - echo "Usage: $0 DBNAME" >&2
7   - exit 1
8   -fi
9   -
10   -exec ttree --plugin_base=LIMS2::Template::Plugin --recurse --lib . --pre_process vars.tt \
11   - --src templates --dest "$DBNAME" --define dbname="$DBNAME"
12   -
18 ddl/templates/roles.sql
... ... @@ -1,18 +0,0 @@
1   -CREATE ROLE "[% admin_role %]" NOLOGIN NOINHERIT;
2   -CREATE ROLE "[% rw_role %]" NOLOGIN NOINHERIT;
3   -CREATE ROLE "[% ro_role %]" NOLOGIN NOINHERIT;
4   -CREATE ROLE "[% inter_role %]" NOLOGIN NOINHERIT IN ROLE "[% admin_role %]";
5   -CREATE ROLE "[% webapp_role %]" WITH ENCRYPTED PASSWORD '[% webapp_passwd %]' LOGIN NOINHERIT IN ROLE "[% ro_role %]";
6   -CREATE ROLE "[% webapp_ro_role %]" WITH ENCRYPTED PASSWORD '[% webapp_ro_passwd %]' LOGIN INHERIT IN ROLE "[% ro_role %]";
7   -CREATE ROLE "[% task_role %]" WITH ENCRYPTED PASSWORD '[% task_passwd %]' LOGIN INHERIT IN ROLE "[% rw_role %]";
8   -
9   -[%- FOR u IN webapp_users %]
10   -GRANT "[% rw_role %]" TO "[% u %]";
11   -GRANT "[% u %]" TO "[% webapp_role %]";
12   -[%- END %]
13   -
14   -[%- FOR u IN system_users %]
15   - [%- FOR r IN [ admin_role ro_role rw_role ] %]
16   -GRANT "[% r %]" TO "[% u %]";
17   - [%- END %]
18   -[%- END %]
11 ddl/templates/schema.sql
... ... @@ -1,11 +0,0 @@
1   -DROP SCHEMA IF EXISTS public CASCADE;
2   -CREATE SCHEMA public AUTHORIZATION "[% admin_role %]";
3   -REVOKE ALL ON SCHEMA public FROM PUBLIC;
4   -GRANT USAGE ON SCHEMA public TO "[% rw_role %]";
5   -GRANT USAGE ON SCHEMA public TO "[% ro_role %]";
6   -
7   -DROP SCHEMA IF EXISTS audit CASCADE;
8   -CREATE SCHEMA audit AUTHORIZATION "[% admin_role %]";
9   -REVOKE ALL ON SCHEMA audit FROM PUBLIC;
10   -GRANT USAGE ON SCHEMA audit TO "[% rw_role %]";
11   -GRANT USAGE ON SCHEMA audit TO "[% ro_role %]";
5 ddl/templates/test_roles.sql
... ... @@ -1,5 +0,0 @@
1   -CREATE ROLE "[% test_admin_role %]" WITH NOLOGIN NOINHERIT;
2   -CREATE ROLE "[% test_role %]" WITH ENCRYPTED PASSWORD '[% test_passwd %]' LOGIN INHERIT IN ROLE "[% rw_role %]";
3   -
4   -GRANT "[% test_admin_role %]" TO "[% test_role %]";
5   -GRANT "[% admin_role %]" TO "[% test_admin_role %]";
428 ddl/templates/versions/1/audit-up.sql
... ... @@ -1,428 +0,0 @@
1   -CREATE TABLE audit.roles (
2   -audit_op CHAR(1) NOT NULL CHECK (audit_op IN ('D','I','U')),
3   -audit_user TEXT NOT NULL,
4   -audit_stamp TIMESTAMP NOT NULL,
5   -audit_txid INTEGER NOT NULL,
6   -id integer,
7   -name text
8   -);
9   -GRANT SELECT ON audit.roles TO "[% ro_role %]";
10   -GRANT SELECT,INSERT ON audit.roles TO "[% rw_role %]";
11   -CREATE OR REPLACE FUNCTION public.process_roles_audit()
12   -RETURNS TRIGGER AS $roles_audit$
13   - BEGIN
14   - IF (TG_OP = 'DELETE') THEN
15   - INSERT INTO audit.roles SELECT 'D', user, now(), txid_current(), OLD.*;
16   - ELSIF (TG_OP = 'UPDATE') THEN
17   - INSERT INTO audit.roles SELECT 'U', user, now(), txid_current(), NEW.*;
18   - ELSIF (TG_OP = 'INSERT') THEN
19   - INSERT INTO audit.roles SELECT 'I', user, now(), txid_current(), NEW.*;
20   - END IF;
21   - RETURN NULL;
22   - END;
23   -$roles_audit$ LANGUAGE plpgsql;
24   -CREATE TRIGGER roles_audit
25   -AFTER INSERT OR UPDATE OR DELETE ON public.roles
26   - FOR EACH ROW EXECUTE PROCEDURE public.process_roles_audit();
27   -CREATE TABLE audit.qc_seq_project_wells (
28   -audit_op CHAR(1) NOT NULL CHECK (audit_op IN ('D','I','U')),
29   -audit_user TEXT NOT NULL,
30   -audit_stamp TIMESTAMP NOT NULL,
31   -audit_txid INTEGER NOT NULL,
32   -id integer,
33   -qc_seq_project_id text,
34   -plate_name text,
35   -well_name text
36   -);
37   -GRANT SELECT ON audit.qc_seq_project_wells TO "[% ro_role %]";
38   -GRANT SELECT,INSERT ON audit.qc_seq_project_wells TO "[% rw_role %]";
39   -CREATE OR REPLACE FUNCTION public.process_qc_seq_project_wells_audit()
40   -RETURNS TRIGGER AS $qc_seq_project_wells_audit$
41   - BEGIN
42   - IF (TG_OP = 'DELETE') THEN
43   - INSERT INTO audit.qc_seq_project_wells SELECT 'D', user, now(), txid_current(), OLD.*;
44   - ELSIF (TG_OP = 'UPDATE') THEN
45   - INSERT INTO audit.qc_seq_project_wells SELECT 'U', user, now(), txid_current(), NEW.*;
46   - ELSIF (TG_OP = 'INSERT') THEN
47   - INSERT INTO audit.qc_seq_project_wells SELECT 'I', user, now(), txid_current(), NEW.*;
48   - END IF;
49   - RETURN NULL;
50   - END;
51   -$qc_seq_project_wells_audit$ LANGUAGE plpgsql;
52   -CREATE TRIGGER qc_seq_project_wells_audit
53   -AFTER INSERT OR UPDATE OR DELETE ON public.qc_seq_project_wells
54   - FOR EACH ROW EXECUTE PROCEDURE public.process_qc_seq_project_wells_audit();
55   -CREATE TABLE audit.schema_versions (
56   -audit_op CHAR(1) NOT NULL CHECK (audit_op IN ('D','I','U')),
57   -audit_user TEXT NOT NULL,
58   -audit_stamp TIMESTAMP NOT NULL,
59   -audit_txid INTEGER NOT NULL,
60   -version integer,
61   -deployed_at timestamp without time zone
62   -);
63   -GRANT SELECT ON audit.schema_versions TO "[% ro_role %]";
64   -GRANT SELECT,INSERT ON audit.schema_versions TO "[% rw_role %]";
65   -CREATE OR REPLACE FUNCTION public.process_schema_versions_audit()
66   -RETURNS TRIGGER AS $schema_versions_audit$
67   - BEGIN
68   - IF (TG_OP = 'DELETE') THEN
69   - INSERT INTO audit.schema_versions SELECT 'D', user, now(), txid_current(), OLD.*;
70   - ELSIF (TG_OP = 'UPDATE') THEN
71   - INSERT INTO audit.schema_versions SELECT 'U', user, now(), txid_current(), NEW.*;
72   - ELSIF (TG_OP = 'INSERT') THEN
73   - INSERT INTO audit.schema_versions SELECT 'I', user, now(), txid_current(), NEW.*;
74   - END IF;
75   - RETURN NULL;
76   - END;
77   -$schema_versions_audit$ LANGUAGE plpgsql;
78   -CREATE TRIGGER schema_versions_audit
79   -AFTER INSERT OR UPDATE OR DELETE ON public.schema_versions
80   - FOR EACH ROW EXECUTE PROCEDURE public.process_schema_versions_audit();
81   -CREATE TABLE audit.qc_alignments (
82   -audit_op CHAR(1) NOT NULL CHECK (audit_op IN ('D','I','U')),
83   -audit_user TEXT NOT NULL,
84   -audit_stamp TIMESTAMP NOT NULL,
85   -audit_txid INTEGER NOT NULL,
86   -id integer,
87   -qc_seq_read_id text,
88   -qc_eng_seq_id integer,
89   -primer_name text,
90   -query_start integer,
91   -query_end integer,
92   -query_strand integer,
93   -target_start integer,
94   -target_end integer,
95   -target_strand integer,
96   -score integer,
97   -pass boolean,
98   -features text,
99   -cigar text,
100   -op_str text
101   -);
102   -GRANT SELECT ON audit.qc_alignments TO "[% ro_role %]";
103   -GRANT SELECT,INSERT ON audit.qc_alignments TO "[% rw_role %]";
104   -CREATE OR REPLACE FUNCTION public.process_qc_alignments_audit()
105   -RETURNS TRIGGER AS $qc_alignments_audit$
106   - BEGIN
107   - IF (TG_OP = 'DELETE') THEN
108   - INSERT INTO audit.qc_alignments SELECT 'D', user, now(), txid_current(), OLD.*;
109   - ELSIF (TG_OP = 'UPDATE') THEN
110   - INSERT INTO audit.qc_alignments SELECT 'U', user, now(), txid_current(), NEW.*;
111   - ELSIF (TG_OP = 'INSERT') THEN
112   - INSERT INTO audit.qc_alignments SELECT 'I', user, now(), txid_current(), NEW.*;
113   - END IF;
114   - RETURN NULL;
115   - END;
116   -$qc_alignments_audit$ LANGUAGE plpgsql;
117   -CREATE TRIGGER qc_alignments_audit
118   -AFTER INSERT OR UPDATE OR DELETE ON public.qc_alignments
119   - FOR EACH ROW EXECUTE PROCEDURE public.process_qc_alignments_audit();
120   -CREATE TABLE audit.user_role (
121   -audit_op CHAR(1) NOT NULL CHECK (audit_op IN ('D','I','U')),
122   -audit_user TEXT NOT NULL,
123   -audit_stamp TIMESTAMP NOT NULL,
124   -audit_txid INTEGER NOT NULL,
125   -user_id integer,
126   -role_id integer
127   -);
128   -GRANT SELECT ON audit.user_role TO "[% ro_role %]";
129   -GRANT SELECT,INSERT ON audit.user_role TO "[% rw_role %]";
130   -CREATE OR REPLACE FUNCTION public.process_user_role_audit()
131   -RETURNS TRIGGER AS $user_role_audit$
132   - BEGIN
133   - IF (TG_OP = 'DELETE') THEN
134   - INSERT INTO audit.user_role SELECT 'D', user, now(), txid_current(), OLD.*;
135   - ELSIF (TG_OP = 'UPDATE') THEN
136   - INSERT INTO audit.user_role SELECT 'U', user, now(), txid_current(), NEW.*;
137   - ELSIF (TG_OP = 'INSERT') THEN
138   - INSERT INTO audit.user_role SELECT 'I', user, now(), txid_current(), NEW.*;
139   - END IF;
140   - RETURN NULL;
141   - END;
142   -$user_role_audit$ LANGUAGE plpgsql;
143   -CREATE TRIGGER user_role_audit
144   -AFTER INSERT OR UPDATE OR DELETE ON public.user_role
145   - FOR EACH ROW EXECUTE PROCEDURE public.process_user_role_audit();
146   -CREATE TABLE audit.qc_templates (
147   -audit_op CHAR(1) NOT NULL CHECK (audit_op IN ('D','I','U')),
148   -audit_user TEXT NOT NULL,
149   -audit_stamp TIMESTAMP NOT NULL,
150   -audit_txid INTEGER NOT NULL,
151   -id integer,
152   -name text,
153   -created_at timestamp without time zone
154   -);
155   -GRANT SELECT ON audit.qc_templates TO "[% ro_role %]";
156   -GRANT SELECT,INSERT ON audit.qc_templates TO "[% rw_role %]";
157   -CREATE OR REPLACE FUNCTION public.process_qc_templates_audit()
158   -RETURNS TRIGGER AS $qc_templates_audit$
159   - BEGIN
160   - IF (TG_OP = 'DELETE') THEN
161   - INSERT INTO audit.qc_templates SELECT 'D', user, now(), txid_current(), OLD.*;
162   - ELSIF (TG_OP = 'UPDATE') THEN
163   - INSERT INTO audit.qc_templates SELECT 'U', user, now(), txid_current(), NEW.*;
164   - ELSIF (TG_OP = 'INSERT') THEN
165   - INSERT INTO audit.qc_templates SELECT 'I', user, now(), txid_current(), NEW.*;
166   - END IF;
167   - RETURN NULL;
168   - END;
169   -$qc_templates_audit$ LANGUAGE plpgsql;
170   -CREATE TRIGGER qc_templates_audit
171   -AFTER INSERT OR UPDATE OR DELETE ON public.qc_templates
172   - FOR EACH ROW EXECUTE PROCEDURE public.process_qc_templates_audit();
173   -CREATE TABLE audit.qc_eng_seqs (
174   -audit_op CHAR(1) NOT NULL CHECK (audit_op IN ('D','I','U')),
175   -audit_user TEXT NOT NULL,
176   -audit_stamp TIMESTAMP NOT NULL,
177   -audit_txid INTEGER NOT NULL,
178   -id integer,
179   -method text,
180   -params text
181   -);
182   -GRANT SELECT ON audit.qc_eng_seqs TO "[% ro_role %]";
183   -GRANT SELECT,INSERT ON audit.qc_eng_seqs TO "[% rw_role %]";
184   -CREATE OR REPLACE FUNCTION public.process_qc_eng_seqs_audit()
185   -RETURNS TRIGGER AS $qc_eng_seqs_audit$
186   - BEGIN
187   - IF (TG_OP = 'DELETE') THEN
188   - INSERT INTO audit.qc_eng_seqs SELECT 'D', user, now(), txid_current(), OLD.*;
189   - ELSIF (TG_OP = 'UPDATE') THEN
190   - INSERT INTO audit.qc_eng_seqs SELECT 'U', user, now(), txid_current(), NEW.*;
191   - ELSIF (TG_OP = 'INSERT') THEN
192   - INSERT INTO audit.qc_eng_seqs SELECT 'I', user, now(), txid_current(), NEW.*;
193   - END IF;
194   - RETURN NULL;
195   - END;
196   -$qc_eng_seqs_audit$ LANGUAGE plpgsql;
197   -CREATE TRIGGER qc_eng_seqs_audit
198   -AFTER INSERT OR UPDATE OR DELETE ON public.qc_eng_seqs
199   - FOR EACH ROW EXECUTE PROCEDURE public.process_qc_eng_seqs_audit();
200   -CREATE TABLE audit.qc_alignment_regions (
201   -audit_op CHAR(1) NOT NULL CHECK (audit_op IN ('D','I','U')),
202   -audit_user TEXT NOT NULL,
203   -audit_stamp TIMESTAMP NOT NULL,
204   -audit_txid INTEGER NOT NULL,
205   -qc_alignment_id integer,
206   -name text,
207   -length integer,
208   -match_count integer,
209   -query_str text,
210   -target_str text,
211   -match_str text,
212   -pass boolean
213   -);
214   -GRANT SELECT ON audit.qc_alignment_regions TO "[% ro_role %]";
215   -GRANT SELECT,INSERT ON audit.qc_alignment_regions TO "[% rw_role %]";
216   -CREATE OR REPLACE FUNCTION public.process_qc_alignment_regions_audit()
217   -RETURNS TRIGGER AS $qc_alignment_regions_audit$
218   - BEGIN
219   - IF (TG_OP = 'DELETE') THEN
220   - INSERT INTO audit.qc_alignment_regions SELECT 'D', user, now(), txid_current(), OLD.*;
221   - ELSIF (TG_OP = 'UPDATE') THEN
222   - INSERT INTO audit.qc_alignment_regions SELECT 'U', user, now(), txid_current(), NEW.*;
223   - ELSIF (TG_OP = 'INSERT') THEN
224   - INSERT INTO audit.qc_alignment_regions SELECT 'I', user, now(), txid_current(), NEW.*;
225   - END IF;
226   - RETURN NULL;
227   - END;
228   -$qc_alignment_regions_audit$ LANGUAGE plpgsql;
229   -CREATE TRIGGER qc_alignment_regions_audit
230   -AFTER INSERT OR UPDATE OR DELETE ON public.qc_alignment_regions
231   - FOR EACH ROW EXECUTE PROCEDURE public.process_qc_alignment_regions_audit();
232   -CREATE TABLE audit.users (
233   -audit_op CHAR(1) NOT NULL CHECK (audit_op IN ('D','I','U')),
234   -audit_user TEXT NOT NULL,
235   -audit_stamp TIMESTAMP NOT NULL,
236   -audit_txid INTEGER NOT NULL,
237   -id integer,
238   -name text,
239   -password text
240   -);
241   -GRANT SELECT ON audit.users TO "[% ro_role %]";
242   -GRANT SELECT,INSERT ON audit.users TO "[% rw_role %]";
243   -CREATE OR REPLACE FUNCTION public.process_users_audit()
244   -RETURNS TRIGGER AS $users_audit$
245   - BEGIN
246   - IF (TG_OP = 'DELETE') THEN
247   - INSERT INTO audit.users SELECT 'D', user, now(), txid_current(), OLD.*;
248   - ELSIF (TG_OP = 'UPDATE') THEN
249   - INSERT INTO audit.users SELECT 'U', user, now(), txid_current(), NEW.*;
250   - ELSIF (TG_OP = 'INSERT') THEN
251   - INSERT INTO audit.users SELECT 'I', user, now(), txid_current(), NEW.*;
252   - END IF;
253   - RETURN NULL;
254   - END;
255   -$users_audit$ LANGUAGE plpgsql;
256   -CREATE TRIGGER users_audit
257   -AFTER INSERT OR UPDATE OR DELETE ON public.users
258   - FOR EACH ROW EXECUTE PROCEDURE public.process_users_audit();
259   -CREATE TABLE audit.qc_test_results (
260   -audit_op CHAR(1) NOT NULL CHECK (audit_op IN ('D','I','U')),
261   -audit_user TEXT NOT NULL,
262   -audit_stamp TIMESTAMP NOT NULL,
263   -audit_txid INTEGER NOT NULL,
264   -id integer,
265   -qc_run_id character(36),
266   -qc_eng_seq_id integer,
267   -qc_seq_project_well_id integer,
268   -score integer,
269   -pass boolean
270   -);
271   -GRANT SELECT ON audit.qc_test_results TO "[% ro_role %]";
272   -GRANT SELECT,INSERT ON audit.qc_test_results TO "[% rw_role %]";
273   -CREATE OR REPLACE FUNCTION public.process_qc_test_results_audit()
274   -RETURNS TRIGGER AS $qc_test_results_audit$
275   - BEGIN
276   - IF (TG_OP = 'DELETE') THEN
277   - INSERT INTO audit.qc_test_results SELECT 'D', user, now(), txid_current(), OLD.*;
278   - ELSIF (TG_OP = 'UPDATE') THEN
279   - INSERT INTO audit.qc_test_results SELECT 'U', user, now(), txid_current(), NEW.*;
280   - ELSIF (TG_OP = 'INSERT') THEN
281   - INSERT INTO audit.qc_test_results SELECT 'I', user, now(), txid_current(), NEW.*;
282   - END IF;
283   - RETURN NULL;
284   - END;
285   -$qc_test_results_audit$ LANGUAGE plpgsql;
286   -CREATE TRIGGER qc_test_results_audit
287   -AFTER INSERT OR UPDATE OR DELETE ON public.qc_test_results
288   - FOR EACH ROW EXECUTE PROCEDURE public.process_qc_test_results_audit();
289   -CREATE TABLE audit.qc_seq_reads (
290   -audit_op CHAR(1) NOT NULL CHECK (audit_op IN ('D','I','U')),
291   -audit_user TEXT NOT NULL,
292   -audit_stamp TIMESTAMP NOT NULL,
293   -audit_txid INTEGER NOT NULL,
294   -id text,
295   -description text,
296   -qc_seq_project_well_id integer,
297   -primer_name text,
298   -seq text,
299   -length integer
300   -);
301   -GRANT SELECT ON audit.qc_seq_reads TO "[% ro_role %]";
302   -GRANT SELECT,INSERT ON audit.qc_seq_reads TO "[% rw_role %]";
303   -CREATE OR REPLACE FUNCTION public.process_qc_seq_reads_audit()
304   -RETURNS TRIGGER AS $qc_seq_reads_audit$
305   - BEGIN
306   - IF (TG_OP = 'DELETE') THEN
307   - INSERT INTO audit.qc_seq_reads SELECT 'D', user, now(), txid_current(), OLD.*;
308   - ELSIF (TG_OP = 'UPDATE') THEN
309   - INSERT INTO audit.qc_seq_reads SELECT 'U', user, now(), txid_current(), NEW.*;
310   - ELSIF (TG_OP = 'INSERT') THEN
311   - INSERT INTO audit.qc_seq_reads SELECT 'I', user, now(), txid_current(), NEW.*;
312   - END IF;
313   - RETURN NULL;
314   - END;
315   -$qc_seq_reads_audit$ LANGUAGE plpgsql;
316   -CREATE TRIGGER qc_seq_reads_audit
317   -AFTER INSERT OR UPDATE OR DELETE ON public.qc_seq_reads
318   - FOR EACH ROW EXECUTE PROCEDURE public.process_qc_seq_reads_audit();
319   -CREATE TABLE audit.qc_runs (
320   -audit_op CHAR(1) NOT NULL CHECK (audit_op IN ('D','I','U')),
321   -audit_user TEXT NOT NULL,
322   -audit_stamp TIMESTAMP NOT NULL,
323   -audit_txid INTEGER NOT NULL,
324   -id character(36),
325   -created_at timestamp without time zone,
326   -created_by_id integer,
327   -profile text,
328   -qc_template_id integer,
329   -software_version text,
330   -upload_complete boolean
331   -);
332   -GRANT SELECT ON audit.qc_runs TO "[% ro_role %]";
333   -GRANT SELECT,INSERT ON audit.qc_runs TO "[% rw_role %]";
334   -CREATE OR REPLACE FUNCTION public.process_qc_runs_audit()
335   -RETURNS TRIGGER AS $qc_runs_audit$
336   - BEGIN
337   - IF (TG_OP = 'DELETE') THEN
338   - INSERT INTO audit.qc_runs SELECT 'D', user, now(), txid_current(), OLD.*;
339   - ELSIF (TG_OP = 'UPDATE') THEN
340   - INSERT INTO audit.qc_runs SELECT 'U', user, now(), txid_current(), NEW.*;
341   - ELSIF (TG_OP = 'INSERT') THEN
342   - INSERT INTO audit.qc_runs SELECT 'I', user, now(), txid_current(), NEW.*;
343   - END IF;
344   - RETURN NULL;
345   - END;
346   -$qc_runs_audit$ LANGUAGE plpgsql;
347   -CREATE TRIGGER qc_runs_audit
348   -AFTER INSERT OR UPDATE OR DELETE ON public.qc_runs
349   - FOR EACH ROW EXECUTE PROCEDURE public.process_qc_runs_audit();
350   -CREATE TABLE audit.qc_template_wells (
351   -audit_op CHAR(1) NOT NULL CHECK (audit_op IN ('D','I','U')),
352   -audit_user TEXT NOT NULL,
353   -audit_stamp TIMESTAMP NOT NULL,
354   -audit_txid INTEGER NOT NULL,
355   -id integer,
356   -qc_template_id integer,
357   -name text,
358   -qc_eng_seq_id integer
359   -);
360   -GRANT SELECT ON audit.qc_template_wells TO "[% ro_role %]";
361   -GRANT SELECT,INSERT ON audit.qc_template_wells TO "[% rw_role %]";
362   -CREATE OR REPLACE FUNCTION public.process_qc_template_wells_audit()
363   -RETURNS TRIGGER AS $qc_template_wells_audit$
364   - BEGIN
365   - IF (TG_OP = 'DELETE') THEN
366   - INSERT INTO audit.qc_template_wells SELECT 'D', user, now(), txid_current(), OLD.*;
367   - ELSIF (TG_OP = 'UPDATE') THEN
368   - INSERT INTO audit.qc_template_wells SELECT 'U', user, now(), txid_current(), NEW.*;
369   - ELSIF (TG_OP = 'INSERT') THEN
370   - INSERT INTO audit.qc_template_wells SELECT 'I', user, now(), txid_current(), NEW.*;
371   - END IF;
372   - RETURN NULL;
373   - END;
374   -$qc_template_wells_audit$ LANGUAGE plpgsql;
375   -CREATE TRIGGER qc_template_wells_audit
376   -AFTER INSERT OR UPDATE OR DELETE ON public.qc_template_wells
377   - FOR EACH ROW EXECUTE PROCEDURE public.process_qc_template_wells_audit();
378   -CREATE TABLE audit.qc_run_seq_project (
379   -audit_op CHAR(1) NOT NULL CHECK (audit_op IN ('D','I','U')),
380   -audit_user TEXT NOT NULL,
381   -audit_stamp TIMESTAMP NOT NULL,
382   -audit_txid INTEGER NOT NULL,
383   -qc_run_id character(36),
384   -qc_seq_project_id text
385   -);
386   -GRANT SELECT ON audit.qc_run_seq_project TO "[% ro_role %]";
387   -GRANT SELECT,INSERT ON audit.qc_run_seq_project TO "[% rw_role %]";
388   -CREATE OR REPLACE FUNCTION public.process_qc_run_seq_project_audit()
389   -RETURNS TRIGGER AS $qc_run_seq_project_audit$
390   - BEGIN
391   - IF (TG_OP = 'DELETE') THEN
392   - INSERT INTO audit.qc_run_seq_project SELECT 'D', user, now(), txid_current(), OLD.*;
393   - ELSIF (TG_OP = 'UPDATE') THEN
394   - INSERT INTO audit.qc_run_seq_project SELECT 'U', user, now(), txid_current(), NEW.*;
395   - ELSIF (TG_OP = 'INSERT') THEN
396   - INSERT INTO audit.qc_run_seq_project SELECT 'I', user, now(), txid_current(), NEW.*;
397   - END IF;
398   - RETURN NULL;
399   - END;
400   -$qc_run_seq_project_audit$ LANGUAGE plpgsql;
401   -CREATE TRIGGER qc_run_seq_project_audit
402   -AFTER INSERT OR UPDATE OR DELETE ON public.qc_run_seq_project
403   - FOR EACH ROW EXECUTE PROCEDURE public.process_qc_run_seq_project_audit();
404   -CREATE TABLE audit.qc_seq_projects (
405   -audit_op CHAR(1) NOT NULL CHECK (audit_op IN ('D','I','U')),
406   -audit_user TEXT NOT NULL,
407   -audit_stamp TIMESTAMP NOT NULL,
408   -audit_txid INTEGER NOT NULL,
409   -id text
410   -);
411   -GRANT SELECT ON audit.qc_seq_projects TO "[% ro_role %]";
412   -GRANT SELECT,INSERT ON audit.qc_seq_projects TO "[% rw_role %]";
413   -CREATE OR REPLACE FUNCTION public.process_qc_seq_projects_audit()
414   -RETURNS TRIGGER AS $qc_seq_projects_audit$
415   - BEGIN
416   - IF (TG_OP = 'DELETE') THEN
417   - INSERT INTO audit.qc_seq_projects SELECT 'D', user, now(), txid_current(), OLD.*;
418   - ELSIF (TG_OP = 'UPDATE') THEN
419   - INSERT INTO audit.qc_seq_projects SELECT 'U', user, now(), txid_current(), NEW.*;
420   - ELSIF (TG_OP = 'INSERT') THEN
421   - INSERT INTO audit.qc_seq_projects SELECT 'I', user, now(), txid_current(), NEW.*;
422   - END IF;
423   - RETURN NULL;
424   - END;
425   -$qc_seq_projects_audit$ LANGUAGE plpgsql;
426   -CREATE TRIGGER qc_seq_projects_audit
427   -AFTER INSERT OR UPDATE OR DELETE ON public.qc_seq_projects
428   - FOR EACH ROW EXECUTE PROCEDURE public.process_qc_seq_projects_audit();
6 ddl/templates/versions/1/fixtures.sql
... ... @@ -1,6 +0,0 @@
1   -
2   -INSERT INTO schema_versions (version) VALUES (1);
3   -
4   -INSERT INTO roles (name)
5   -VALUES ('admin'),('edit'),('read');
6   -
173 ddl/templates/versions/1/up.sql
... ... @@ -1,173 +0,0 @@
1   ---
2   --- Initial schema version. Contains tables to store users, roles and qc data
3   ---
4   -
5   ---
6   --- Schema metadata
7   ---
8   -CREATE TABLE schema_versions (
9   - version INTEGER NOT NULL,
10   - deployed_at TIMESTAMP NOT NULL DEFAULT CURRENT_TIMESTAMP,
11   - PRIMARY KEY (version, deployed_at)
12   -);
13   -GRANT SELECT ON schema_versions TO "[% ro_role %]", "[% rw_role %]";
14   -
15   ---
16   --- Users and roles
17   ---
18   -CREATE TABLE users (
19   - id SERIAL PRIMARY KEY,
20   - name TEXT NOT NULL UNIQUE CHECK (name <> ''),
21   - password TEXT
22   -);
23   -GRANT SELECT ON users TO "[% ro_role %]";
24   -GRANT SELECT, INSERT, UPDATE, DELETE ON users TO "[% rw_role %]";
25   -GRANT USAGE ON SEQUENCE users_id_seq TO "[% rw_role %]";
26   -
27   -CREATE TABLE roles (
28   - id SERIAL PRIMARY KEY,
29   - name TEXT NOT NULL UNIQUE CHECK (name <> '')
30   -);
31   -GRANT SELECT ON roles TO "[% ro_role %]";
32   -GRANT SELECT, INSERT, UPDATE, DELETE ON roles TO "[% rw_role %]";
33   -GRANT USAGE ON SEQUENCE roles_id_seq TO "[% rw_role %]";
34   -
35   -CREATE TABLE user_role (
36   - user_id INTEGER NOT NULL REFERENCES users(id),
37   - role_id INTEGER NOT NULL REFERENCES roles(id),
38   - PRIMARY KEY (user_id, role_id)
39   -);
40   -GRANT SELECT ON user_role TO "[% ro_role %]";
41   -GRANT SELECT, INSERT, UPDATE, DELETE ON user_role TO "[% rw_role %]";
42   -
43   ---
44   --- Data for sequencing QC
45   ---
46   -CREATE TABLE qc_eng_seqs (
47   - id SERIAL PRIMARY KEY,
48   - method TEXT NOT NULL,
49   - params TEXT NOT NULL,
50   - UNIQUE ( method, params )
51   -);
52   -GRANT SELECT ON qc_eng_seqs TO "[% ro_role %]";
53   -GRANT SELECT, INSERT, UPDATE, DELETE ON qc_eng_seqs TO "[% rw_role %]";
54   -GRANT USAGE ON SEQUENCE qc_eng_seqs_id_seq TO "[% rw_role %]";
55   -
56   -CREATE TABLE qc_templates (
57   - id SERIAL PRIMARY KEY,
58   - name TEXT NOT NULL,
59   - created_at TIMESTAMP NOT NULL DEFAULT CURRENT_TIMESTAMP,
60   - UNIQUE (name, created_at)
61   -);
62   -GRANT SELECT ON qc_templates TO "[% ro_role %]";
63   -GRANT SELECT, INSERT, UPDATE, DELETE ON qc_templates TO "[% rw_role %]";
64   -GRANT USAGE ON SEQUENCE qc_templates_id_seq TO "[% rw_role %]";
65   -
66   -CREATE TABLE qc_template_wells (
67   - id SERIAL PRIMARY KEY,
68   - qc_template_id INTEGER NOT NULL REFERENCES qc_templates(id),
69   - name TEXT NOT NULL CHECK (name ~ '^[A-O](0[1-9]|1[0-9]|2[0-4])$'),
70   - qc_eng_seq_id INTEGER NOT NULL REFERENCES qc_eng_seqs(id),
71   - UNIQUE (qc_template_id, name)
72   -);
73   -GRANT SELECT ON qc_template_wells TO "[% ro_role %]";
74   -GRANT SELECT, INSERT, UPDATE, DELETE ON qc_template_wells TO "[% rw_role %]";
75   -GRANT USAGE ON SEQUENCE qc_template_wells_id_seq TO "[% rw_role %]";
76   -
77   -CREATE TABLE qc_runs (
78   - id CHAR(36) PRIMARY KEY,
79   - created_at TIMESTAMP NOT NULL DEFAULT CURRENT_TIMESTAMP,
80   - created_by_id INTEGER NOT NULL REFERENCES users(id),
81   - profile TEXT NOT NULL,
82   - qc_template_id INTEGER NOT NULL REFERENCES qc_templates(id),
83   - software_version TEXT NOT NULL,
84   - upload_complete BOOLEAN NOT NULL DEFAULT FALSE
85   -);
86   -GRANT SELECT ON qc_runs TO "[% ro_role %]";
87   -GRANT SELECT, INSERT, UPDATE, DELETE ON qc_runs TO "[% rw_role %]";
88   -
89   -CREATE TABLE qc_seq_projects (
90   - id TEXT PRIMARY KEY
91   -);
92   -GRANT SELECT ON qc_seq_projects TO "[% ro_role %]";
93   -GRANT SELECT, INSERT, UPDATE, DELETE ON qc_seq_projects TO "[% rw_role %]";
94   -
95   -CREATE TABLE qc_seq_project_wells (
96   - id SERIAL PRIMARY KEY,
97   - qc_seq_project_id TEXT NOT NULL REFERENCES qc_seq_projects(id),
98   - plate_name TEXT NOT NULL,
99   - well_name TEXT NOT NULL,
100   - UNIQUE(qc_seq_project_id,plate_name,well_name)
101   -);
102   -GRANT SELECT ON qc_seq_project_wells TO "[% ro_role %]";
103   -GRANT SELECT, INSERT, UPDATE, DELETE ON qc_seq_project_wells TO "[% rw_role %]";
104   -GRANT USAGE ON qc_seq_project_wells_id_seq TO "[% rw_role %]";
105   -
106   -CREATE TABLE qc_seq_reads (
107   - id TEXT PRIMARY KEY,
108   - description TEXT NOT NULL DEFAULT '',
109   - qc_seq_project_well_id INTEGER NOT NULL REFERENCES qc_seq_project_wells(id),
110   - primer_name TEXT NOT NULL,
111   - seq TEXT NOT NULL,
112   - length INTEGER NOT NULL
113   -);
114   -GRANT SELECT ON qc_seq_reads TO "[% ro_role %]";
115   -GRANT SELECT, INSERT, UPDATE, DELETE ON qc_seq_reads TO "[% rw_role %]";
116   -
117   -CREATE INDEX ON qc_seq_reads(qc_seq_project_well_id);
118   -
119   -CREATE TABLE qc_run_seq_project (
120   - qc_run_id CHAR(36) NOT NULL REFERENCES qc_runs(id),
121   - qc_seq_project_id TEXT NOT NULL REFERENCES qc_seq_projects(id),
122   - PRIMARY KEY(qc_run_id, qc_seq_project_id)
123   -);
124   -GRANT SELECT ON qc_run_seq_project TO "[% ro_role %]";
125   -GRANT SELECT, INSERT, UPDATE, DELETE ON qc_run_seq_project TO "[% rw_role %]";
126   -
127   -CREATE TABLE qc_test_results (
128   - id SERIAL PRIMARY KEY,
129   - qc_run_id CHAR(36) NOT NULL REFERENCES qc_runs(id),
130   - qc_eng_seq_id INTEGER NOT NULL REFERENCES qc_eng_seqs(id),
131   - qc_seq_project_well_id INTEGER NOT NULL REFERENCES qc_seq_project_wells(id),
132   - score INTEGER NOT NULL DEFAULT 0,
133   - pass BOOLEAN NOT NULL DEFAULT FALSE,
134   - UNIQUE(qc_run_id, qc_eng_seq_id, qc_seq_project_well_id)
135   -);
136   -GRANT SELECT ON qc_test_results TO "[% ro_role %]";
137   -GRANT SELECT, INSERT, UPDATE, DELETE ON qc_test_results TO "[% rw_role %]";
138   -GRANT USAGE ON SEQUENCE qc_test_results_id_seq TO "[% rw_role %]";
139   -
140   -CREATE TABLE qc_alignments (
141   - id SERIAL PRIMARY KEY,
142   - qc_seq_read_id TEXT NOT NULL REFERENCES qc_seq_reads(id),
143   - qc_eng_seq_id INTEGER NOT NULL REFERENCES qc_eng_seqs(id),
144   - primer_name TEXT NOT NULL,