[med-svn] [tab2mage] 11/12: Update upstream source from tag 'upstream/20080626'
Andreas Tille
tille at debian.org
Sat Dec 30 16:40:43 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository tab2mage.
commit 2b7b1f157ad99a4a4db63186acc1d0cb3534b949
Merge: 415c43c 5fd54b7
Author: Andreas Tille <tille at debian.org>
Date: Sat Dec 30 17:39:06 2017 +0100
Update upstream source from tag 'upstream/20080626'
Update to upstream version '20080626'
with Debian dir c147ddfe302542ae697d1389507d0690bdbcf18b
COPYING | 44 +
Changes | 364 +
MAGETAB.txt | 135 +
MANIFEST | 706 +
META.yml | 25 +
Makefile.PL | 163 +
README | 187 +
README-windows.txt | 62 +
adv_inst/InstallConfig.yml-example | 51 +
adv_inst/README | 6 +
adv_inst/T2MInstaller.pm | 321 +
adv_inst/deploy.pl | 66 +
arraymage/arraymage.pl | 499 +
arraymage/cdf2mage.pl | 728 +
automation/admin/CHANGELOG | 604 +
automation/admin/INSTALL | 68 +
automation/admin/README | 153 +
automation/admin/README_LOGIN | 96 +
automation/admin/Rakefile | 10 +
.../admin/app/controllers/account_controller.rb | 52 +
automation/admin/app/controllers/application.rb | 7 +
.../app/controllers/array_designs_controller.rb | 124 +
.../admin/app/controllers/category_controller.rb | 70 +
.../admin/app/controllers/design_controller.rb | 66 +
.../admin/app/controllers/event_controller.rb | 21 +
.../app/controllers/experiments_controller.rb | 148 +
.../admin/app/controllers/factor_controller.rb | 6 +
.../admin/app/controllers/material_controller.rb | 66 +
.../admin/app/controllers/miamexps_controller.rb | 35 +
.../admin/app/controllers/organism_controller.rb | 90 +
.../admin/app/controllers/protocols_controller.rb | 90 +
.../controllers/quantitation_type_controller.rb | 6 +
.../admin/app/controllers/tab2mages_controller.rb | 43 +
.../admin/app/controllers/taxon_controller.rb | 71 +
.../admin/app/controllers/users_controller.rb | 89 +
automation/admin/app/helpers/account_helper.rb | 2 +
automation/admin/app/helpers/application_helper.rb | 3 +
.../admin/app/helpers/array_designs_helper.rb | 2 +
automation/admin/app/helpers/category_helper.rb | 2 +
automation/admin/app/helpers/design_helper.rb | 2 +
automation/admin/app/helpers/event_helper.rb | 2 +
automation/admin/app/helpers/experiments_helper.rb | 2 +
automation/admin/app/helpers/factor_helper.rb | 2 +
automation/admin/app/helpers/material_helper.rb | 2 +
automation/admin/app/helpers/miamexps_helper.rb | 2 +
automation/admin/app/helpers/organism_helper.rb | 2 +
automation/admin/app/helpers/protocols_helper.rb | 2 +
.../admin/app/helpers/quantitation_type_helper.rb | 2 +
automation/admin/app/helpers/tab2mages_helper.rb | 2 +
automation/admin/app/helpers/taxon_helper.rb | 2 +
automation/admin/app/helpers/users_helper.rb | 2 +
automation/admin/app/models/array_design.rb | 12 +
automation/admin/app/models/category.rb | 7 +
automation/admin/app/models/data_file.rb | 3 +
automation/admin/app/models/design.rb | 7 +
automation/admin/app/models/design_instance.rb | 4 +
automation/admin/app/models/event.rb | 8 +
automation/admin/app/models/experiment.rb | 43 +
automation/admin/app/models/factor.rb | 7 +
automation/admin/app/models/material.rb | 7 +
automation/admin/app/models/material_instance.rb | 4 +
automation/admin/app/models/organism.rb | 10 +
automation/admin/app/models/organism_instance.rb | 4 +
automation/admin/app/models/permission.rb | 6 +
automation/admin/app/models/protocol.rb | 4 +
automation/admin/app/models/quantitation_type.rb | 7 +
automation/admin/app/models/role.rb | 7 +
automation/admin/app/models/spreadsheet.rb | 3 +
automation/admin/app/models/taxon.rb | 8 +
automation/admin/app/models/user.rb | 59 +
automation/admin/app/views/account/login.rhtml | 22 +
automation/admin/app/views/account/logout.rhtml | 10 +
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automation/admin/app/views/account/welcome.rhtml | 12 +
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automation/admin/app/views/array_designs/new.rhtml | 8 +
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automation/admin/app/views/category/_form.rhtml | 34 +
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automation/admin/app/views/design/_form.rhtml | 43 +
automation/admin/app/views/design/_title.rhtml | 3 +
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automation/admin/app/views/design/list.rhtml | 40 +
automation/admin/app/views/design/new.rhtml | 8 +
automation/admin/app/views/event/_form.rhtml | 62 +
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automation/admin/app/views/event/edit.rhtml | 2 +
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automation/admin/app/views/experiments/_form.rhtml | 26 +
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automation/admin/app/views/experiments/list.rhtml | 71 +
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automation/admin/app/views/experiments/show.rhtml | 124 +
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automation/admin/app/views/layouts/admin.rhtml | 156 +
automation/admin/app/views/material/_form.rhtml | 33 +
automation/admin/app/views/material/_title.rhtml | 3 +
automation/admin/app/views/material/edit.rhtml | 8 +
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automation/admin/app/views/material/new.rhtml | 8 +
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automation/admin/app/views/protocols/_form.rhtml | 28 +
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automation/admin/app/views/tab2mages/_form.rhtml | 91 +
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automation/admin/app/views/tab2mages/_title.rhtml | 3 +
automation/admin/app/views/tab2mages/edit.rhtml | 35 +
automation/admin/app/views/tab2mages/list.rhtml | 97 +
automation/admin/app/views/tab2mages/new.rhtml | 13 +
automation/admin/app/views/taxon/_form.rhtml | 34 +
automation/admin/app/views/taxon/_title.rhtml | 3 +
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automation/admin/app/views/taxon/edit.rhtml | 8 +
automation/admin/app/views/taxon/list.rhtml | 43 +
automation/admin/app/views/taxon/new.rhtml | 8 +
automation/admin/app/views/users/_form.rhtml | 31 +
automation/admin/app/views/users/_title.rhtml | 3 +
automation/admin/app/views/users/edit.rhtml | 10 +
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automation/admin/app/views/users/new.rhtml | 8 +
automation/admin/app/views/users/show.rhtml | 8 +
automation/admin/config/README | 45 +
automation/admin/config/boot.rb | 19 +
automation/admin/config/database.yml-mysql | 20 +
automation/admin/config/database.yml-sqlite | 29 +
automation/admin/config/environment.rb | 66 +
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automation/admin/config/environments/production.rb | 19 +
automation/admin/config/environments/test.rb | 19 +
automation/admin/config/lighttpd.conf | 53 +
automation/admin/config/routes.rb | 19 +
automation/admin/db/database-mysql.dump | 932 +
automation/admin/db/database-mysql.schema | 829 +
.../admin/db/migration/migrate_2.0_to_2.1.sql | 183 +
.../admin/db/migration/migrate_2.1_to_2.2.sql | 125 +
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automation/admin/db/schema.pdf | Bin 0 -> 374471 bytes
automation/admin/db/schema.rb | 347 +
automation/admin/doc/README_FOR_APP | 2 +
automation/admin/lib/acl_system.rb | 31 +
automation/admin/lib/annotation.rb | 96 +
automation/admin/lib/login_system.rb | 87 +
automation/admin/log/server.log | 0
automation/admin/public/.htaccess | 40 +
automation/admin/public/404.html | 8 +
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automation/admin/public/javascripts/controls.js | 750 +
automation/admin/public/javascripts/dragdrop.js | 584 +
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automation/admin/public/javascripts/prototype.js | 1785 ++
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automation/admin/script/console | 3 +
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automation/admin/script/performance/profiler | 3 +
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automation/admin/script/process/spinner | 3 +
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automation/admin/test/fixtures/array_designs.yml | 9 +
automation/admin/test/fixtures/categories.yml | 9 +
automation/admin/test/fixtures/data_files.yml | 5 +
automation/admin/test/fixtures/designs.yml | 13 +
automation/admin/test/fixtures/events.yml | 9 +
automation/admin/test/fixtures/experiments.yml | 18 +
automation/admin/test/fixtures/factors.yml | 7 +
automation/admin/test/fixtures/materials.yml | 11 +
automation/admin/test/fixtures/organisms.yml | 13 +
automation/admin/test/fixtures/permissions.yml | 17 +
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automation/admin/test/fixtures/protocols.yml | 11 +
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automation/admin/test/fixtures/roles.yml | 11 +
automation/admin/test/fixtures/roles_users.yml | 5 +
automation/admin/test/fixtures/spreadsheets.yml | 5 +
automation/admin/test/fixtures/taxons.yml | 11 +
automation/admin/test/fixtures/users.yml | 16 +
.../test/functional/account_controller_test.rb | 81 +
.../functional/array_designs_controller_test.rb | 88 +
.../test/functional/category_controller_test.rb | 21 +
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.../admin/test/functional/event_controller_test.rb | 21 +
.../test/functional/experiments_controller_test.rb | 94 +
.../test/functional/factor_controller_test.rb | 21 +
.../test/functional/material_controller_test.rb | 21 +
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.../test/functional/protocols_controller_test.rb | 88 +
.../quantitation_type_controller_test.rb | 21 +
.../test/functional/tab2mages_controller_test.rb | 18 +
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automation/admin/test/test_helper.rb | 28 +
automation/admin/test/unit/array_design_test.rb | 14 +
automation/admin/test/unit/category_test.rb | 14 +
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bin/convert_to_mcmr.pl | 116 +
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docs/ArrayExpress/ArrayMAGE.html | 476 +
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docs/ArrayExpress/Curator/Config.html | 462 +
docs/ArrayExpress/Curator/Database.html | 137 +
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docs/ArrayExpress/Curator/Logger.html | 204 +
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docs/ArrayExpress/Curator/Standalone.html | 87 +
docs/ArrayExpress/Curator/Validate.html | 184 +
docs/ArrayExpress/Curator/Visualize.html | 86 +
docs/ArrayExpress/Datafile.html | 478 +
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examples/magetab/real/E-TABM-66_sdrf.txt | 154 +
examples/magetab/real/E-TABM-70.idf | 28 +
examples/magetab/real/E-TABM-70_sdrf.txt | 65 +
examples/magetab/real/solexa_example.idf | 36 +
examples/magetab/real/solexa_example.sdrf.txt | 11 +
examples/magetab/two_color/Data1.txt | 37 +
examples/magetab/two_color/Data2.txt | 40 +
examples/magetab/two_color/Data3.txt | 37 +
examples/magetab/two_color/Data4.txt | 40 +
examples/magetab/two_color/NormData1.txt | 11 +
examples/magetab/two_color/NormData2.txt | 11 +
examples/magetab/two_color/NormData3.txt | 11 +
examples/magetab/two_color/NormData4.txt | 11 +
examples/magetab/two_color/test.idf | 49 +
examples/magetab/two_color/test_sdrf.txt | 6 +
examples/normalized_data/Data1.txt | 37 +
examples/normalized_data/Data2.txt | 40 +
examples/normalized_data/NormData1.txt | 11 +
examples/normalized_data/NormData2.txt | 11 +
examples/normalized_data/normalized_data.png | Bin 0 -> 10751 bytes
examples/normalized_data/normalized_data.txt | 40 +
examples/other_QTs.txt | 27 +
examples/parameters/Data1.txt | 37 +
examples/parameters/Data2.txt | 40 +
examples/parameters/parameters.png | Bin 0 -> 10138 bytes
examples/parameters/parameters.txt | 39 +
examples/real/E-MEXP-880.png | Bin 0 -> 210713 bytes
examples/real/E-MEXP-880.txt | 68 +
examples/real/E-TABM-102.png | Bin 0 -> 103372 bytes
examples/real/E-TABM-102.txt | 56 +
examples/real/E-TABM-134.png | Bin 0 -> 67443 bytes
examples/real/E-TABM-134.txt | 57 +
examples/real/E-TABM-136.png | Bin 0 -> 83344 bytes
examples/real/E-TABM-136.txt | 106 +
examples/real/E-TABM-140.png | Bin 0 -> 138852 bytes
examples/real/E-TABM-140.txt | 108 +
examples/real/E-TABM-16.png | Bin 0 -> 213842 bytes
examples/real/E-TABM-16.txt | 166 +
examples/real/E-TABM-163.png | Bin 0 -> 73767 bytes
examples/real/E-TABM-163.txt | 55 +
examples/real/E-TABM-18.png | Bin 0 -> 85899 bytes
examples/real/E-TABM-18.txt | 82 +
examples/real/E-TABM-22.png | Bin 0 -> 420693 bytes
examples/real/E-TABM-22.txt | 274 +
examples/real/E-TABM-33.png | Bin 0 -> 86924 bytes
examples/real/E-TABM-33.txt | 55 +
examples/real/E-TABM-35.png | Bin 0 -> 118759 bytes
examples/real/E-TABM-35.txt | 94 +
examples/real/E-TABM-54.png | Bin 0 -> 263753 bytes
examples/real/E-TABM-54.txt | 287 +
examples/real/E-TABM-66.png | Bin 0 -> 171814 bytes
examples/real/E-TABM-66.txt | 184 +
examples/real/E-TABM-70.png | Bin 0 -> 63144 bytes
examples/real/E-TABM-70.txt | 101 +
examples/reference/Data1.txt | 37 +
examples/reference/Data2.txt | 40 +
examples/reference/Data3.txt | 11 +
examples/reference/reference.png | Bin 0 -> 13757 bytes
examples/reference/reference.txt | 42 +
examples/two_color/Data1.txt | 37 +
examples/two_color/Data2.txt | 40 +
examples/two_color/two_color.png | Bin 0 -> 11098 bytes
examples/two_color/two_color.txt | 45 +
index.html | 356 +
lib/ArrayExpress/ArrayMAGE.pm | 658 +
lib/ArrayExpress/ArrayMAGE/ArrayDesign.pm | 42 +
lib/ArrayExpress/ArrayMAGE/BioSequence.pm | 96 +
lib/ArrayExpress/ArrayMAGE/CompositeGroup.pm | 84 +
lib/ArrayExpress/ArrayMAGE/CompositeSequence.pm | 119 +
lib/ArrayExpress/ArrayMAGE/Database.pm | 53 +
lib/ArrayExpress/ArrayMAGE/Feature.pm | 80 +
lib/ArrayExpress/ArrayMAGE/FeatureReporterMap.pm | 88 +
lib/ArrayExpress/ArrayMAGE/NullObject.pm | 25 +
lib/ArrayExpress/ArrayMAGE/ProgressBar.pm | 40 +
lib/ArrayExpress/ArrayMAGE/Reporter.pm | 131 +
lib/ArrayExpress/ArrayMAGE/ReporterCompositeMap.pm | 75 +
lib/ArrayExpress/ArrayMAGE/ReporterGroup.pm | 84 +
lib/ArrayExpress/ArrayMAGE/Zone.pm | 62 +
lib/ArrayExpress/AutoSubmission/Creator.pm | 514 +
lib/ArrayExpress/AutoSubmission/DB.pm | 3539 ++++
.../AutoSubmission/DB/Accessionable.pm | 56 +
lib/ArrayExpress/AutoSubmission/DB/ArrayDesign.pm | 59 +
.../AutoSubmission/DB/ArrayDesignExperiment.pm | 23 +
.../AutoSubmission/DB/ArrayDesignOrganism.pm | 23 +
lib/ArrayExpress/AutoSubmission/DB/Category.pm | 33 +
.../AutoSubmission/DB/CategoryDesign.pm | 21 +
.../AutoSubmission/DB/CategoryMaterial.pm | 22 +
.../AutoSubmission/DB/CategoryTaxon.pm | 21 +
lib/ArrayExpress/AutoSubmission/DB/DataFile.pm | 23 +
lib/ArrayExpress/AutoSubmission/DB/DataFormat.pm | 23 +
lib/ArrayExpress/AutoSubmission/DB/Design.pm | 32 +
.../AutoSubmission/DB/DesignInstance.pm | 22 +
lib/ArrayExpress/AutoSubmission/DB/Event.pm | 49 +
lib/ArrayExpress/AutoSubmission/DB/Experiment.pm | 324 +
.../AutoSubmission/DB/ExperimentFactor.pm | 23 +
.../AutoSubmission/DB/ExperimentLoadedData.pm | 20 +
lib/ArrayExpress/AutoSubmission/DB/ExperimentQT.pm | 23 +
lib/ArrayExpress/AutoSubmission/DB/Factor.pm | 24 +
lib/ArrayExpress/AutoSubmission/DB/File.pm | 35 +
lib/ArrayExpress/AutoSubmission/DB/LoadedData.pm | 44 +
lib/ArrayExpress/AutoSubmission/DB/Material.pm | 32 +
.../AutoSubmission/DB/MaterialInstance.pm | 23 +
lib/ArrayExpress/AutoSubmission/DB/Organism.pm | 34 +
.../AutoSubmission/DB/OrganismInstance.pm | 23 +
lib/ArrayExpress/AutoSubmission/DB/Permission.pm | 22 +
.../AutoSubmission/DB/PermissionRole.pm | 21 +
lib/ArrayExpress/AutoSubmission/DB/Platform.pm | 23 +
lib/ArrayExpress/AutoSubmission/DB/Protocol.pm | 115 +
.../AutoSubmission/DB/QualityMetric.pm | 29 +
.../AutoSubmission/DB/QualityMetricInstance.pm | 23 +
.../AutoSubmission/DB/QuantitationType.pm | 24 +
lib/ArrayExpress/AutoSubmission/DB/Role.pm | 27 +
lib/ArrayExpress/AutoSubmission/DB/RoleUser.pm | 20 +
lib/ArrayExpress/AutoSubmission/DB/Spreadsheet.pm | 22 +
lib/ArrayExpress/AutoSubmission/DB/Taxon.pm | 28 +
lib/ArrayExpress/AutoSubmission/DB/User.pm | 29 +
lib/ArrayExpress/AutoSubmission/Daemon.pm | 435 +
lib/ArrayExpress/AutoSubmission/Daemon/Checker.pm | 295 +
lib/ArrayExpress/AutoSubmission/Daemon/Exporter.pm | 219 +
.../AutoSubmission/Daemon/MAGETABChecker.pm | 57 +
.../AutoSubmission/Daemon/MAGETABExporter.pm | 64 +
.../AutoSubmission/Daemon/MXChecker.pm | 271 +
.../AutoSubmission/Daemon/MXExporter.pm | 247 +
.../AutoSubmission/Daemon/T2MChecker.pm | 32 +
.../AutoSubmission/Daemon/T2MExporter.pm | 47 +
lib/ArrayExpress/AutoSubmission/Spreadsheet.pm | 1079 ++
lib/ArrayExpress/AutoSubmission/WebForm.pm | 1601 ++
.../AutoSubmission/templates/_annotate.html | 183 +
.../AutoSubmission/templates/_display.html | 48 +
.../templates/_display_annotation.html | 28 +
.../AutoSubmission/templates/_foot.html | 3 +
.../AutoSubmission/templates/_head.html | 62 +
.../AutoSubmission/templates/choose.html | 49 +
.../AutoSubmission/templates/create.html | 16 +
.../AutoSubmission/templates/create_user.html | 29 +
.../AutoSubmission/templates/delete.html | 14 +
.../AutoSubmission/templates/edit.html | 15 +
.../templates/email_signup_confirmation.txt | 16 +
.../templates/email_subs_confirmation.txt | 14 +
.../AutoSubmission/templates/error.html | 22 +
.../AutoSubmission/templates/file_upload.html | 63 +
.../AutoSubmission/templates/insert.html | 8 +
.../AutoSubmission/templates/intro.html | 65 +
.../AutoSubmission/templates/login.html | 65 +
.../AutoSubmission/templates/logout.html | 13 +
.../AutoSubmission/templates/magetab_intro.html | 42 +
.../AutoSubmission/templates/magetab_template.html | 37 +
.../AutoSubmission/templates/magetab_upload.html | 152 +
.../AutoSubmission/templates/signup.html | 82 +
.../AutoSubmission/templates/submitted.html | 32 +
.../templates/subs_notify_curator.txt | 15 +
.../AutoSubmission/templates/template.html | 37 +
.../AutoSubmission/templates/update.html | 8 +
.../AutoSubmission/templates/upload.html | 148 +
lib/ArrayExpress/Curator/Common.pm | 620 +
lib/ArrayExpress/Curator/Config.pm | 589 +
lib/ArrayExpress/Curator/Config.yml | 89 +
lib/ArrayExpress/Curator/Database.pm | 672 +
lib/ArrayExpress/Curator/Entrez_list.pm | 121 +
lib/ArrayExpress/Curator/Entrez_list.txt | 19188 +++++++++++++++++++
lib/ArrayExpress/Curator/ExperimentChecker.pm | 2428 +++
lib/ArrayExpress/Curator/Logger.pm | 409 +
lib/ArrayExpress/Curator/MAGE.pm | 2504 +++
lib/ArrayExpress/Curator/MAGE/Definitions.pm | 1181 ++
lib/ArrayExpress/Curator/MIAMExpress.pm | 2509 +++
lib/ArrayExpress/Curator/Report.pm | 438 +
lib/ArrayExpress/Curator/Standalone.pm | 167 +
lib/ArrayExpress/Curator/Tab2MAGE.pm | 2602 +++
lib/ArrayExpress/Curator/Validate.pm | 1084 ++
lib/ArrayExpress/Curator/Visualize.pm | 356 +
lib/ArrayExpress/Datafile.pm | 3685 ++++
lib/ArrayExpress/Datafile/Affymetrix.pm | 166 +
lib/ArrayExpress/Datafile/Affymetrix/CDF.pm | 136 +
.../Datafile/Affymetrix/CDF/GDAC_CDF.pm | 201 +
.../Datafile/Affymetrix/CDF/XDA_CDF.pm | 226 +
lib/ArrayExpress/Datafile/Affymetrix/CDFFactory.pm | 130 +
lib/ArrayExpress/Datafile/Affymetrix/CEL.pm | 294 +
lib/ArrayExpress/Datafile/Affymetrix/CEL/CELv3.pm | 281 +
lib/ArrayExpress/Datafile/Affymetrix/CEL/CELv4.pm | 298 +
lib/ArrayExpress/Datafile/Affymetrix/CELFactory.pm | 131 +
lib/ArrayExpress/Datafile/Affymetrix/CHP.pm | 375 +
lib/ArrayExpress/Datafile/Affymetrix/CHP/CHPv12.pm | 229 +
lib/ArrayExpress/Datafile/Affymetrix/CHP/CHPv13.pm | 208 +
lib/ArrayExpress/Datafile/Affymetrix/CHP/CHPv8.pm | 115 +
.../Datafile/Affymetrix/CHP/GDAC_CHP.pm | 379 +
.../Datafile/Affymetrix/CHP/XDA_CHP.pm | 335 +
lib/ArrayExpress/Datafile/Affymetrix/CHPFactory.pm | 159 +
.../Datafile/Affymetrix/Calvin/Binary.pm | 145 +
lib/ArrayExpress/Datafile/Affymetrix/Calvin/CEL.pm | 125 +
lib/ArrayExpress/Datafile/Affymetrix/Calvin/CHP.pm | 83 +
.../Datafile/Affymetrix/Calvin/Component.pm | 105 +
.../Datafile/Affymetrix/Calvin/DataColumn.pm | 68 +
.../Datafile/Affymetrix/Calvin/DataGroup.pm | 105 +
.../Datafile/Affymetrix/Calvin/DataHeader.pm | 80 +
.../Datafile/Affymetrix/Calvin/DataSet.pm | 143 +
.../Datafile/Affymetrix/Calvin/Facade.pm | 127 +
.../Datafile/Affymetrix/Calvin/Generic.pm | 128 +
.../Datafile/Affymetrix/Calvin/Parameter.pm | 19 +
lib/ArrayExpress/Datafile/Affymetrix/EXP.pm | 396 +
lib/ArrayExpress/Datafile/Affymetrix/EXPFactory.pm | 108 +
lib/ArrayExpress/Datafile/Affymetrix/Parser.pm | 355 +
lib/ArrayExpress/Datafile/ArrayDesign.pm | 215 +
lib/ArrayExpress/Datafile/Binary.pm | 189 +
lib/ArrayExpress/Datafile/DataMatrix.pm | 762 +
lib/ArrayExpress/Datafile/Metrics.pm | 195 +
lib/ArrayExpress/Datafile/Parser.pm | 2016 ++
lib/ArrayExpress/Datafile/QT_list.pm | 342 +
lib/ArrayExpress/Datafile/QT_list.txt | 1087 ++
lib/ArrayExpress/MAGETAB.pm | 911 +
lib/ArrayExpress/MAGETAB/Checker.pm | 2034 ++
lib/ArrayExpress/MAGETAB/Checker/IDF.pm | 76 +
lib/ArrayExpress/MAGETAB/DataMatrix.pm | 548 +
lib/ArrayExpress/MAGETAB/IDF.pm | 881 +
lib/ArrayExpress/MAGETAB/SDRF.pm | 3486 ++++
lib/ArrayExpress/MAGETAB/TabFile.pm | 926 +
lib/ArrayExpress/Tracking/CelQC.pm | 171 +
lib/ArrayExpress/Tracking/Event.pm | 27 +
lib/ArrayExpress/Tracking/QCJobManager.pm | 180 +
lib/ArrayExpress/Tracking/QueryHandler.pm | 769 +
t/affy_calvin.t | 205 +
t/affy_cdf.t | 51 +
t/affy_cel.t | 108 +
t/affy_chp.t | 118 +
t/affy_exp.t | 103 +
t/affy_xda_cdf.t | 26 +
t/affy_xda_cel.t | 103 +
t/affy_xda_chp.t | 127 +
t/array_design.t | 28 +
t/arraymage.t | 11 +
t/binary.t | 23 +
t/common.t | 123 +
t/config.t | 11 +
t/creator.t | 20 +
t/daemon.t | 26 +
t/daemon_checker.t | 24 +
t/daemon_exporter.t | 24 +
t/daemon_mxchecker.t | 23 +
t/daemon_mxexporter.t | 23 +
t/data/dummy.CDF | 192 +
t/data/test.CEL | 49 +
t/data/test.CHP | Bin 0 -> 11922 bytes
t/data/test.EXP | 49 +
t/data/test.gpr | 37 +
t/data/test.txt | 8 +
t/data/test_calvin.CHP | Bin 0 -> 19567 bytes
t/data/test_fgem.txt | 11 +
t/data/test_xda.CEL | Bin 0 -> 670 bytes
t/data/test_xda.CHP | Bin 0 -> 1013 bytes
t/data_metrics.t | 11 +
t/database.t | 11 +
t/datafile.t | 467 +
t/datafile_parser.t | 11 +
t/db.t | 58 +
t/entrez_list.t | 11 +
t/experiment_checker.t | 11 +
t/fgem.t | 107 +
t/logger.t | 11 +
t/mage.t | 19 +
t/mage_defs.t | 11 +
t/magetab.t | 10 +
t/magetab_checker.t | 11 +
t/magetab_datamatrix.t | 10 +
t/magetab_idf.t | 10 +
t/magetab_sdrf.t | 10 +
t/magetab_tabfile.t | 10 +
t/miamexpress.t | 22 +
t/qt_list.t | 11 +
t/report.t | 11 +
t/spreadsheet.t | 21 +
t/standalone.t | 10 +
t/tab2mage.t | 40 +
t/tracking.t | 36 +
t/validate.t | 19 +
t/visualize.t | 11 +
t/web_form.t | 25 +
util/AE_insert_celfiles.pl | 202 +
util/fillin_null_rows.pl | 124 +
util/join_by_first_column.pl | 122 +
util/mx_legacy_check.pl | 155 +
util/mx_qt_update.pl | 94 +
util/t2m_legacy_check.pl | 138 +
util/t2m_update_docs.pl | 93 +
706 files changed, 118226 insertions(+)
--
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