Merge branch 'release/1.3.2' into develop

BU-ISCIII · May 14, 2019 · 61d1416 · 61d1416
2 parents f353828 + dffba2e
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diff --git a/README.md b/README.md
@@ -12,8 +12,8 @@ For installation and usage instructions please refer to the [wiki](https://githu
 For any problems or bug reporting please post us an [issue](https://github.com/BU-ISCIII/iSkyLIMS/issues)
 
 ## iSkyLIMS Demo
-iSkyLIMS demo is available for your convenience, in a virtual machine image, running on VirtualBox.  
-Download the VM image using with your favorite ftp client with the following information:
+iSkyLIMS demo is available for your convenience, in a virtual machine image, running on VirtualBox and as a Singularity container.  
+Download the VM image and/or the container using with your favorite ftp client with the following information:
 
 ```
 Server: sftpbioinfo.isciii.es
@@ -43,3 +43,42 @@ Log into iSkyLIMS with different roles using the following credentials:
 - As wetlab manager role the user is **John_manager** and password **iSkyLIMS**
 - If you need to login as django administrator type the url http://localhost/admin using user : **admin** and password : **iSkyLIMS**
 
+### Run singularity container. (BETA - this method will be improved shorty, but it works for now)
+
+1. First you need to have installed singularity. Please follow [vendor instructions](https://www.sylabs.io/guides/3.0/user-guide/installation.html#install-the-centos-rhel-package-using-yum). We recommend using epel package installation as 2.6 version of singularity is enough for our purposes.
+
+2. Shell into the container (you need to use sudo).
+
+```Bash
+sudo singularity shell iskylims.simg
+```
+3. Start needed services
+
+```Bash
+service smbd start
+service mysql start
+apachectl -D FOREGROUND
+# If you want to play with the image you can execute this last command in foreground.
+apachectl -D FOREGROUND &
+```
+4. Open your preferred browser (Firefox or Chome) and type:
+
+```
+localhost
+```
+iSkyLIMS website will be shown!! You can explore the website using this two users:
+- bioinfoadm: user inside WetlabManager and Admin_iSkyLIMS groups with manager permissions. (**passwd:**"iskylims")
+- regular_user01 and regular_user02: regular users with regular permissions.
+
+With bioinfoadm user you can access Admin panel:
+```
+localhost/admin
+```
+There you can access User table and change regular_user01 and regular_user02 passwords.
+
+5. Don't forguet to stop the services before exiting the container, it will prevent possible conflicts with your local installation.
+```Bash
+service smbd stop
+service mysql stop
+apachectl stop
+```
diff --git a/conf/dump_errors.json b/conf/dump_errors.json
@@ -0,0 +1 @@
+[{"model": "iSkyLIMS_wetlab.runerrors", "pk": 1, "fields": {"errorCode": "0", "errorText": "No Error"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 2, "fields": {"errorCode": "1", "errorText": "Invalid Sample Sheet"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 3, "fields": {"errorCode": "2", "errorText": "Application Unknown"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 4, "fields": {"errorCode": "4", "errorText": "Experiment name already exists"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 5, "fields": {"errorCode": "5", "errorText": "Project name already exists"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 6, "fields": {"errorCode": "6", "errorText": "User not defined"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 7, "fields": {"errorCode": "7", "errorText": "Empty Experiment name in Sample Sheet"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 8, "fields": {"errorCode": "8", "errorText": "Time expiration for including Sample Sheet in the run"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 9, "fields": {"errorCode": "9", "errorText": "Time expiration for completion of the run"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 10, "fields": {"errorCode": "10", "errorText": "Project not defined in database"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 11, "fields": {"errorCode": "11", "errorText": "Unable to store data in  \"RawDemuxStats\" database"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 12, "fields": {"errorCode": "12", "errorText": "Unable to fetch Demultiplexing Stats files"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 13, "fields": {"errorCode": "13", "errorText": "Unable to store data in \"SamplesInProject\" database"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 14, "fields": {"errorCode": "14", "errorText": "Unable to store data in  \"StatsFlSummary\" database"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 15, "fields": {"errorCode": "15", "errorText": "Unable to store data in  \"StatsLaneSummary\" database"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 16, "fields": {"errorCode": "16", "errorText": "Unable to store data in  \"RawTopUnknowBarcodes\" database"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 17, "fields": {"errorCode": "17", "errorText": "Unable to fetch folder to get run disk usage"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 18, "fields": {"errorCode": "18", "errorText": "Unable to fetch log files"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 19, "fields": {"errorCode": "19", "errorText": "Unable to fetch Sample Sheet"}}]
diff --git a/conf/dump_runstates.json b/conf/dump_runstates.json
@@ -0,0 +1 @@
+[{"model": "iSkyLIMS_wetlab.runstates", "pk": 1, "fields": {"runStateName": "Pre-Recorded"}}, {"model": "iSkyLIMS_wetlab.runstates", "pk": 2, "fields": {"runStateName": "Recorded"}}, {"model": "iSkyLIMS_wetlab.runstates", "pk": 3, "fields": {"runStateName": "Sample Sent"}}, {"model": "iSkyLIMS_wetlab.runstates", "pk": 4, "fields": {"runStateName": "Processing Run"}}, {"model": "iSkyLIMS_wetlab.runstates", "pk": 5, "fields": {"runStateName": "Processed Run"}}, {"model": "iSkyLIMS_wetlab.runstates", "pk": 6, "fields": {"runStateName": "Processing Bcl2fastq"}}, {"model": "iSkyLIMS_wetlab.runstates", "pk": 7, "fields": {"runStateName": "Processed Bcl2fastq"}}, {"model": "iSkyLIMS_wetlab.runstates", "pk": 8, "fields": {"runStateName": "Completed"}}, {"model": "iSkyLIMS_wetlab.runstates", "pk": 9, "fields": {"runStateName": "Cancelled"}}, {"model": "iSkyLIMS_wetlab.runstates", "pk": 10, "fields": {"runStateName": "Error"}}, {"model": "iSkyLIMS_wetlab.runstates", "pk": 11, "fields": {"runStateName": "Processing Metrics"}}, {"model": "iSkyLIMS_wetlab.runstates", "pk": 12, "fields": {"runStateName": "Processing Demultiplexing"}}]
diff --git a/conf/pythonPackagesRequired.txt b/conf/pythonPackagesRequired.txt
@@ -17,5 +17,6 @@ interop
 mysqlclient
 paramiko
 pysmb
+weasyPrint
 zinnia-wysiwyg-wymeditor
 
diff --git a/...bIntroduction/WetlabFormNewLibraryKit.png → ...customization/WetlabFormNewLibraryKit.png b/...bIntroduction/WetlabFormNewLibraryKit.png → ...customization/WetlabFormNewLibraryKit.png
diff --git a/img/customization/admin_add_groups.png b/img/customization/admin_add_groups.png
diff --git a/img/customization/usersTable.png → img/customization/admin_add_users.png b/img/customization/usersTable.png → img/customization/admin_add_users.png
diff --git a/img/customization/admin_assign_groups.png b/img/customization/admin_assign_groups.png
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diff --git a/img/customization/admin_user_creation.png b/img/customization/admin_user_creation.png
diff --git a/img/customization/user_registration_form.png b/img/customization/user_registration_form.png
diff --git a/...etlab/wetlabIntroduction/wetlabHeader.png → img/customization/wetlabHeader.png b/...etlab/wetlabIntroduction/wetlabHeader.png → img/customization/wetlabHeader.png
diff --git a/img/userGuideDrylab/admin_menu_create_services.png b/img/userGuideDrylab/admin_menu_create_services.png
diff --git a/img/userGuideDrylab/create_bioinformatics_consulting_service.png b/img/userGuideDrylab/create_bioinformatics_consulting_service.png
diff --git a/img/userGuideDrylab/create_file_extensions.png b/img/userGuideDrylab/create_file_extensions.png
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diff --git a/img/userGuideDrylab/create_platforms.png b/img/userGuideDrylab/create_platforms.png
diff --git a/img/userGuideDrylab/create_user_support_service.png b/img/userGuideDrylab/create_user_support_service.png
diff --git a/img/userGuideDrylab/drylabCounselingRequest/drylabMenuCounselingRequest.png b/img/userGuideDrylab/drylabCounselingRequest/drylabMenuCounselingRequest.png
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diff --git a/...deDrylab/drylabServicesStatistics/drylab_services_statistics_number_request.png b/...deDrylab/drylabServicesStatistics/drylab_services_statistics_number_request.png
diff --git a/...serGuideDrylab/drylabServicesStatistics/drylab_services_statistics_per_area.png b/...serGuideDrylab/drylabServicesStatistics/drylab_services_statistics_per_area.png
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diff --git a/...ylab/drylabServicesStatistics/drylab_services_statistics_requested_services.png b/...ylab/drylabServicesStatistics/drylab_services_statistics_requested_services.png
diff --git a/img/userGuideDrylab/drylabServicesStatistics/drylab_services_statistics_status.png b/img/userGuideDrylab/drylabServicesStatistics/drylab_services_statistics_status.png
diff --git a/...ab/drylabServicesStatistics/drylab_services_statistics_user_number_services.png b/...ab/drylabServicesStatistics/drylab_services_statistics_user_number_services.png
diff --git a/...eDrylab/drylabServicesStatistics/drylab_services_statistics_user_percentage.png b/...eDrylab/drylabServicesStatistics/drylab_services_statistics_user_percentage.png
diff --git a/...ideDrylab/drylabServicesStatistics/drylab_services_statistics_user_services.png b/...ideDrylab/drylabServicesStatistics/drylab_services_statistics_user_services.png
diff --git a/...drylabServicesStatistics/drylab_services_statistics_user_services_per_month.png b/...drylabServicesStatistics/drylab_services_statistics_user_services_per_month.png
diff --git a/...erGuideDrylab/drylabUserActivity/drylabCurrent OpenUserSessionsInfoProvided.png b/...erGuideDrylab/drylabUserActivity/drylabCurrent OpenUserSessionsInfoProvided.png
diff --git a/img/userGuideDrylab/drylabUserActivity/drylabMenuUserActivity.png b/img/userGuideDrylab/drylabUserActivity/drylabMenuUserActivity.png
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diff --git a/img/userGuideDrylab/drylab_ongoing_services.png b/img/userGuideDrylab/drylab_ongoing_services.png
diff --git a/img/userGuideIntroduction/iSkyLIMS_homepage.png b/img/userGuideIntroduction/iSkyLIMS_homepage.png
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diff --git a/...Wetlab/wetlabProducingReports/WetlabProducingReportsQuarterlyProvidedInfo_1.png b/...Wetlab/wetlabProducingReports/WetlabProducingReportsQuarterlyProvidedInfo_1.png
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diff --git a/img/userGuideWetlab/wetlabReports/reports_graphic_q30.png b/img/userGuideWetlab/wetlabReports/reports_graphic_q30.png
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diff --git a/img/userGuideWetlab/wetlabStatistics/menu_statistics_experiment.png b/img/userGuideWetlab/wetlabStatistics/menu_statistics_experiment.png
diff --git a/img/userGuideWetlab/wetlabStatistics/menu_statistics_investigator.png b/img/userGuideWetlab/wetlabStatistics/menu_statistics_investigator.png
diff --git a/img/userGuideWetlab/wetlabStatistics/menu_statistics_library.png b/img/userGuideWetlab/wetlabStatistics/menu_statistics_library.png
diff --git a/img/userGuideWetlab/wetlabStatistics/menu_statistics_time.png b/img/userGuideWetlab/wetlabStatistics/menu_statistics_time.png
diff --git a/img/userGuideWetlab/wetlabStatistics/statistics_investigator_basic_info.png b/img/userGuideWetlab/wetlabStatistics/statistics_investigator_basic_info.png
diff --git a/img/userGuideWetlab/wetlabStatistics/statistics_investigator_comparison.png b/img/userGuideWetlab/wetlabStatistics/statistics_investigator_comparison.png
diff --git a/img/userGuideWetlab/wetlabStatistics/statistics_investigator_graphic.png b/img/userGuideWetlab/wetlabStatistics/statistics_investigator_graphic.png
diff --git a/...rGuideWetlab/wetlabStatistics/statistics_investigator_sequencer_utilization.png b/...rGuideWetlab/wetlabStatistics/statistics_investigator_sequencer_utilization.png
diff --git a/img/userGuideWetlab/wetlabStatistics/statistics_library_comparison.png b/img/userGuideWetlab/wetlabStatistics/statistics_library_comparison.png
diff --git a/img/userGuideWetlab/wetlabStatistics/statistics_library_graphic_match.png b/img/userGuideWetlab/wetlabStatistics/statistics_library_graphic_match.png
diff --git a/img/userGuideWetlab/wetlabStatistics/statistics_library_matches.png b/img/userGuideWetlab/wetlabStatistics/statistics_library_matches.png
diff --git a/img/userGuideWetlab/wetlabStatistics/statistics_library_used_project.png b/img/userGuideWetlab/wetlabStatistics/statistics_library_used_project.png
diff --git a/img/userGuideWetlab/wetlabStatistics/statistics_time_disk_space_used.png b/img/userGuideWetlab/wetlabStatistics/statistics_time_disk_space_used.png
diff --git a/img/userGuideWetlab/wetlabStatistics/statistics_time_projects.png b/img/userGuideWetlab/wetlabStatistics/statistics_time_projects.png
diff --git a/img/userGuideWetlab/wetlabStatistics/statistics_time_runs.png b/img/userGuideWetlab/wetlabStatistics/statistics_time_runs.png
diff --git a/img/userGuideWetlab/wetlabStatistics/statistics_time_undetermined.png b/img/userGuideWetlab/wetlabStatistics/statistics_time_undetermined.png
diff --git a/img/userGuideWetlab/wetlabStatistics/statistics_time_unknow_bar_pie.png b/img/userGuideWetlab/wetlabStatistics/statistics_time_unknow_bar_pie.png
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		[{"model": "iSkyLIMS_wetlab.runerrors", "pk": 1, "fields": {"errorCode": "0", "errorText": "No Error"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 2, "fields": {"errorCode": "1", "errorText": "Invalid Sample Sheet"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 3, "fields": {"errorCode": "2", "errorText": "Application Unknown"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 4, "fields": {"errorCode": "4", "errorText": "Experiment name already exists"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 5, "fields": {"errorCode": "5", "errorText": "Project name already exists"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 6, "fields": {"errorCode": "6", "errorText": "User not defined"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 7, "fields": {"errorCode": "7", "errorText": "Empty Experiment name in Sample Sheet"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 8, "fields": {"errorCode": "8", "errorText": "Time expiration for including Sample Sheet in the run"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 9, "fields": {"errorCode": "9", "errorText": "Time expiration for completion of the run"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 10, "fields": {"errorCode": "10", "errorText": "Project not defined in database"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 11, "fields": {"errorCode": "11", "errorText": "Unable to store data in \"RawDemuxStats\" database"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 12, "fields": {"errorCode": "12", "errorText": "Unable to fetch Demultiplexing Stats files"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 13, "fields": {"errorCode": "13", "errorText": "Unable to store data in \"SamplesInProject\" database"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 14, "fields": {"errorCode": "14", "errorText": "Unable to store data in \"StatsFlSummary\" database"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 15, "fields": {"errorCode": "15", "errorText": "Unable to store data in \"StatsLaneSummary\" database"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 16, "fields": {"errorCode": "16", "errorText": "Unable to store data in \"RawTopUnknowBarcodes\" database"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 17, "fields": {"errorCode": "17", "errorText": "Unable to fetch folder to get run disk usage"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 18, "fields": {"errorCode": "18", "errorText": "Unable to fetch log files"}}, {"model": "iSkyLIMS_wetlab.runerrors", "pk": 19, "fields": {"errorCode": "19", "errorText": "Unable to fetch Sample Sheet"}}]
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		@@ -0,0 +1 @@
		[{"model": "iSkyLIMS_wetlab.runstates", "pk": 1, "fields": {"runStateName": "Pre-Recorded"}}, {"model": "iSkyLIMS_wetlab.runstates", "pk": 2, "fields": {"runStateName": "Recorded"}}, {"model": "iSkyLIMS_wetlab.runstates", "pk": 3, "fields": {"runStateName": "Sample Sent"}}, {"model": "iSkyLIMS_wetlab.runstates", "pk": 4, "fields": {"runStateName": "Processing Run"}}, {"model": "iSkyLIMS_wetlab.runstates", "pk": 5, "fields": {"runStateName": "Processed Run"}}, {"model": "iSkyLIMS_wetlab.runstates", "pk": 6, "fields": {"runStateName": "Processing Bcl2fastq"}}, {"model": "iSkyLIMS_wetlab.runstates", "pk": 7, "fields": {"runStateName": "Processed Bcl2fastq"}}, {"model": "iSkyLIMS_wetlab.runstates", "pk": 8, "fields": {"runStateName": "Completed"}}, {"model": "iSkyLIMS_wetlab.runstates", "pk": 9, "fields": {"runStateName": "Cancelled"}}, {"model": "iSkyLIMS_wetlab.runstates", "pk": 10, "fields": {"runStateName": "Error"}}, {"model": "iSkyLIMS_wetlab.runstates", "pk": 11, "fields": {"runStateName": "Processing Metrics"}}, {"model": "iSkyLIMS_wetlab.runstates", "pk": 12, "fields": {"runStateName": "Processing Demultiplexing"}}]