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#!/bin/bash

echo Cloning repository...
git clone git@github.com:organization/project.git
cd project

echo
echo Removing origin
git remote rm origin

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/var/log/tomcat6/catalina.out {
    copytruncate
    weekly
    rotate 52
    compress
    missingok
    create 0644 tomcat tomcat
}

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{{velocity}}
#foreach ($p in $services.query.xwql("from doc.object(PhenoTips.PatientClass) as patient where :matEtn member of patient.maternal_ethnicity").bindValue('matEtn', 'irish').execute())
  * [[$p]]
#end
{{/velocity}}

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{{velocity}}
##set ($format = $services.jodatime.getISODateFormatter())
#set ($format = $services.jodatime.getDateTimeFormatterForPattern('yyyy-MM'))
#set($q = $services.query.hql("select doc.creationDate from XWikiDocument doc, BaseObject as obj, DBStringListProperty phenotype, LongProperty iid where obj.name=doc.fullName and obj.className = ? and doc.fullName not in (?, ?) and obj.id=phenotype.id.id and phenotype.id.name = ? and (? in elements(phenotype.list)) and iid.id.id = obj.id and iid.id.name = 'identifier' and iid.value >= 0 order by doc.creationDate asc").bindValues(["PhenoTips.PatientClass", "PhenoTips.PatientClassTemplate", "PhenoTips.PatientTemplate", "extended_phenotype", "HP:0000118"]))
|=Month|=Patient records created
#foreach ($i in $q.execute())
  #set ($date = $format.print($i))
  #if ($prevDate != $date)
    #if($prevDate)
      |$prevDate|$count

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To set or update the visibility for all patient records, including the template used for future patients, open /bin/edit/Sandbox/UpdateVisibility in a browser while logged in with an administrative account, paste the following snippet, and press Preview.

WARNING: Pressing Preview doesn't preview the changes, it will actually modify the permissions!

Things you can adjust:

• the target visibility, at line 2 replace private with the desired value (hidden, private, matchable, public, open)
• skip the patient template by replacing the query at line 3 with 'from doc.object(PhenoTips.PatientClass) as p where doc.name <> ''PatientTemplate'''
• only include records of a certain user by replacing the query at line 3 with 'from doc.object(PhenoTips.PatientClass) as p, doc.object(PhenoTips.OwnerClass) as o where o.owner = ''xwiki:XWiki.username'''
• only include records of a certain workgroup by replacing the query at line 3 with `'from doc.object(PhenoTips.PatientClass) as p, doc.object(Phen

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To add a new collaborator for all patient records, including the template used for future patients, open /bin/edit/Sandbox/AddCollaborator in a browser while logged in with an administrative account, paste the following snippet, and press Preview.

WARNING: Pressing Preview doesn't preview the changes, it will actually modify the permissions!

Things you can adjust:

• the target access level, at line 2 replace edit with the desired value (view, edit, manage)
• the target collaborator, at line 3 replace groupname with the desired group name, or uncomment line 5 and replace username with the desired username
• skip the patient template by replacing the query at line 6 with 'from doc.object(PhenoTips.PatientClass) as p where doc.name <> ''PatientTemplate'''
• only include records of a certain user by replacing the query at line 6 with 'from doc.object(PhenoTips.PatientClass) as p, doc.object(PhenoTips.OwnerClass) as o where o.owner = ''xwiki:XWiki.username'''

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This script renumbers all patient records in a PhenoTips instance, adding a specified offset, for example for merging two PhenoTips instances.

Open /bin/edit/Sandbox/Renumber in a browser while logged in with an administrative account, paste the following snippet, and press Preview. Don't forget to adjust the $offset variable with the correct value.

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# Creating a user:

curl -u Admin:admin -X PUT -d "parent=XWiki.XWikiUsers" -H "Content-Type: application/x-www-form-urlencoded"  http://localhost:8080/rest/wikis/xwiki/spaces/XWiki/pages/jdoe
curl -u Admin:admin -X POST -d 'className=XWiki.XWikiUsers&property#first_name=John&property#last_name=Doe&property#email=jdoe@company.com&property#password=pass1234' -H "Content-Type: application/x-www-form-urlencoded"  http://localhost:8080/rest/wikis/xwiki/spaces/XWiki/pages/jdoe/objects

# Deleting a user:
curl -u Admin:admin -X DELETE http://localhost:8080/rest/wikis/xwiki/spaces/XWiki/pages/jdoe


# Creating a workgroup:

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find -name *.xed -exec sed -e 's/<installed.installed type="boolean">true<\/installed.installed>/<installed.installed type="boolean">false<\/installed.installed>/' -i \{\} \;

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# Change the following three variables to what you need:
XAUTH='Admin:admin'
USER='Admin'
MAPPING='PhenoTips.Detailed physical phenotype configuration'

XOBJNR=`curl -s -u ${XAUTH} http://localhost:8080/rest/wikis/xwiki/spaces/XWiki/pages/${USER}/objects | sed -r -e ': start' -e 's/(<\/[^>]+?>)([^\n])/\1\n\2/g' -e 't start' | grep -E '<headline>phenotips_mapping</headline>' -B 5 | grep -E '<number>' | sed -r -e 's/.*>(.*)<.*/\1/'`

if [[ -n $XOBJNR ]]
  then curl -s -o /dev/null -u ${XAUTH} -X PUT -H 'Content-Type: text/plain' -d "${MAPPING}" http://localhost:8080/rest/wikis/xwiki/spaces/XWiki/pages/${USER}/objects/XWiki.ConfigurationClass/${XOBJNR}/properties/value
  else curl -s -o /dev/null -u ${XAUTH} -X POST -H 'Content-Type: application/x-www-form-urlencoded' -d "className=XWiki.ConfigurationClass&property#property=phenotips_mapping&property#value=${MAPPING}" http://localhost:8080/rest/wikis/xwiki/spaces/XWiki/pages/${USER}/objects