| author | weiher |
| Mon, 05 Feb 2018 16:51:33 +0100 | |
| changeset 11 | ccfe3c7fa0d2 |
| parent 3 | b71be85a294c |
| child 13 | a21f3604f1db |
| permissions | -rw-r--r-- |
| 3 | 1 |
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\title{Labfolder at FHI Documentation}
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\date{Feb 05, 2018}
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\release{1.0}
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\author{Stefan Weiher}
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\newcommand{\sphinxlogo}{\vbox{}}
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\renewcommand{\releasename}{Release}
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\makeindex |
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\begin{document}
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\maketitle |
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\sphinxtableofcontents |
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\phantomsection\label{\detokenize{index::doc}}
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\chapter{Installation of labfolder}
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\label{\detokenize{installation:welcome-to-elog2labfolder-s-documentation}}\label{\detokenize{installation::doc}}\label{\detokenize{installation:installation-of-labfolder}}
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Labfolder is easy to install. Follow the instructions given in the \sphinxstyleemphasis{labfolder Installation Manual}. The broad steps are: \sphinxstylestrong{install MySQL, docker and labolder; configure labfolder via the server.cnf file}. This labfolder config file could look like this:
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\fvset{hllines={, ,}}%
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\begin{sphinxVerbatim}[commandchars=\\\{\}]
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\PYGZsh{} Network settings
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DEFAULT\PYGZus{}HTTP\PYGZus{}PROTOCOL=https://
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DEFAULT\PYGZus{}DOMAIN=labfolder.rz\PYGZhy{}berlin.mpg.de
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\PYGZsh{} JDBC Properties
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JDBC\PYGZus{}SERVER\PYGZus{}TIMEZONE=Europe/Berlin
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JDBC\PYGZus{}DATABASE\PYGZus{}URL=jdbc:mysql://localhost:3306/labfolder?useUnicode=true\PYGZam{}characterEncoding=UTF\PYGZhy{}8
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JDBC\PYGZus{}USERNAME=labfolder
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JDBC\PYGZus{}PASSWORD=fhilab
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JDBC\PYGZus{}SCHEMA\PYGZus{}NAME=labfolder
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\PYGZsh{}REMOVE\PYGZus{}ABANDONED\PYGZus{}TIMEOUT=60
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\PYGZsh{} Mail client properties
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MAIL\PYGZus{}STARTTLS=false
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MAIL\PYGZus{}AUTHENTICATION\PYGZus{}ENABLE=false
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MAIL\PYGZus{}HOST=mail.fhi\PYGZhy{}berlin.mpg.de
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MAIL\PYGZus{}PORT=25
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\PYGZsh{}MAIL\PYGZus{}USERNAME=
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\PYGZsh{}MAIL\PYGZus{}PASSWORD=
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MAIL\PYGZus{}EMAIL=ppb@fhi\PYGZhy{}berlin.mpg.de
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\PYGZsh{} Server Event logging
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LOG\PYGZus{}TO\PYGZus{}FILE=true
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\PYGZsh{}Maximum upload file size
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FILEUPLOAD\PYGZus{}MAXUPLOADSIZE=25000000
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\PYGZsh{} User and group control
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DEFAULT\PYGZus{}GROUP\PYGZus{}SIZE=50
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DEFAULT\PYGZus{}GROUP\PYGZus{}TYPE\PYGZus{}MAXI=true
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DEFAULT\PYGZus{}USER\PYGZus{}STORAGE=3221225472
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FEATURE\PYGZus{}GLOBAL\PYGZus{}PREVENT\PYGZus{}DELETE\PYGZus{}CONTENT=false
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\PYGZsh{} Terms and Privacy links
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TERMS\PYGZus{}OF\PYGZus{}USE\PYGZus{}LINK=https://www.labfolder.com/terms\PYGZhy{}external\PYGZhy{}servers/
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PRIVACY\PYGZus{}LINK=https://www.labfolder.com/privacy\PYGZhy{}external\PYGZhy{}servers/
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\PYGZsh{} LDAP Authentication
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FEATURE\PYGZus{}LDAP\PYGZus{}AUTHENTICATION=true
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LDAP\PYGZus{}URL=ldap://ldap.rz\PYGZhy{}berlin.mpg.de:389
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LDAP\PYGZus{}BASE=ou=people,dc=ppb,dc=rz\PYGZhy{}berlin,dc=mpg,dc=de
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\PYGZsh{}LDAP\PYGZus{}SERVER\PYGZus{}TYPE=
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LDAP\PYGZus{}USER\PYGZus{}DN=cn=pwCheck,dc=rz\PYGZhy{}berlin,dc=mpg,dc=de
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LDAP\PYGZus{}PASSWORD=ProstetnikVogonJeltz
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\PYGZsh{}LDAP\PYGZus{}ANONYMOUS\PYGZus{}READ\PYGZus{}ONLY=
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LDAP\PYGZus{}USER\PYGZus{}DN\PYGZus{}PATTERNS=uid=\PYGZob{}0\PYGZcb{}
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\PYGZsh{}LDAP\PYGZus{}IS\PYGZus{}TLS\PYGZus{}ENABLED=
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\PYGZsh{}LDAP\PYGZus{}IS\PYGZus{}ATTRIBUTE\PYGZus{}SEARCH\PYGZus{}ENABLED=
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\PYGZsh{}LDAP\PYGZus{}ATTRIBUTE\PYGZus{}SEARCH\PYGZus{}NAME=
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\PYGZsh{} Usage monitoring
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ACTIVE\PYGZus{}USER\PYGZus{}REPORT\PYGZus{}USE\PYGZus{}DEFAULT\PYGZus{}MAIL\PYGZus{}CLIENT=true
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CUSTOMER\PYGZus{}IDENTIFIER=\PYGZsq{}Fritz\PYGZhy{}Haber\PYGZhy{}Institut\PYGZsq{}
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\PYGZsh{} Mendeley
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FEATURE\PYGZus{}MENDELEY=false
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\PYGZsh{}MENDELEY\PYGZus{}CLIENT\PYGZus{}ID=
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\PYGZsh{}MENDELEY\PYGZus{}CLIENT\PYGZus{}SECRET=
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\PYGZsh{}MENDELEY\PYGZus{}CLIENT\PYGZus{}CALLBACKURL=http://localhost:9091/eln/mendeley/oauthCallback
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\PYGZsh{} Dropbox
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FEATURE\PYGZus{}DROPBOX=false
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\PYGZsh{}DROPBOX\PYGZus{}CONSUMER\PYGZus{}KEY=
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\PYGZsh{}DROPBOX\PYGZus{}CONSUMER\PYGZus{}SECRET=
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\PYGZsh{} Figshare
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FEATURE\PYGZus{}FIGSHARE=false
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\PYGZsh{} XHTML Export
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FEATURE\PYGZus{}XHTML\PYGZus{}EXPORT=true
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EXPORT\PYGZus{}DOCUMENT\PYGZus{}REPOSITORY\PYGZus{}TYPE=fileSystem
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\end{sphinxVerbatim}
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The configuration is explained in detail in the installation manual. Now, \sphinxstylestrong{create the labfolder database and run labfolder} (see the manual for details). Additionally, you could install Apache and set it up as a reverse proxy in order to make labfolder only available through https. The exact steps are:
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\fvset{hllines={, ,}}%
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\begin{sphinxVerbatim}[commandchars=\\\{\}]
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labfolder@lf:\PYGZti{}\PYGZdl{} sudo apt\PYGZhy{}get install build\PYGZhy{}essential
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labfolder@lf:\PYGZti{}\PYGZdl{} sudo apt install apache2
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labfolder@lf:\PYGZti{}\PYGZdl{} sudo a2enmod proxy proxy\PYGZus{}ajp proxy\PYGZus{}http rewrite deflate headers proxy\PYGZus{}balancer proxy\PYGZus{}connect proxy\PYGZus{}html xml2enc
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labfolder@lf:\PYGZti{}\PYGZdl{} sudo a2enmod ssl
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\PYGZsh{}\PYGZsh{}\PYGZsh{} Use certificates from e.g. let\PYGZsq{}s encrypt. Please see below for more information.
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\PYGZsh{}\PYGZsh{}\PYGZsh{} create /etc/apache2/sites\PYGZhy{}available/labfolder.conf with virtual hosts for http and https:
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labfolder@lf:\PYGZti{}\PYGZdl{} sudo a2ensite labfolder.conf
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labfolder@lf:\PYGZti{}\PYGZdl{} sudo a2dissite 000\PYGZhy{}default.conf
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labfolder@lf:\PYGZti{}\PYGZdl{} sudo service apache2 restart
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\end{sphinxVerbatim}
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To get SSL certificates from letsencrypt is quite straight forward. For example this guide shows how to set up SSL certificates: |
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\sphinxurl{https://www.digitalocean.com/community/tutorials/how-to-secure-apache-with-let-s-encrypt-on-ubuntu-16-04}
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The Apache labfolder config file could look like this: |
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\fvset{hllines={, ,}}%
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\begin{sphinxVerbatim}[commandchars=\\\{\}]
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\PYG{o}{\PYGZlt{}}\PYG{n}{VirtualHost} \PYG{o}{*}\PYG{p}{:}\PYG{l+m+mi}{80}\PYG{o}{\PYGZgt{}}
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\PYG{n}{ErrorLog} \PYG{o}{/}\PYG{n}{var}\PYG{o}{/}\PYG{n}{log}\PYG{o}{/}\PYG{n}{apache2}\PYG{o}{/}\PYG{n}{error}\PYG{o}{.}\PYG{n}{log}
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\PYG{n}{LogLevel} \PYG{n}{warn}
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\PYG{n}{ServerName} \PYG{n}{labfolder}\PYG{o}{.}\PYG{n}{rz}\PYG{o}{\PYGZhy{}}\PYG{n}{berlin}\PYG{o}{.}\PYG{n}{mpg}\PYG{o}{.}\PYG{n}{de}
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\PYG{n}{Redirect} \PYG{o}{/} \PYG{n}{https}\PYG{p}{:}\PYG{o}{/}\PYG{o}{/}\PYG{n}{labfolder}\PYG{o}{.}\PYG{n}{rz}\PYG{o}{\PYGZhy{}}\PYG{n}{berlin}\PYG{o}{.}\PYG{n}{mpg}\PYG{o}{.}\PYG{n}{de}\PYG{o}{/}
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\PYG{o}{\PYGZlt{}}\PYG{o}{/}\PYG{n}{VirtualHost}\PYG{o}{\PYGZgt{}}
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\PYG{o}{\PYGZlt{}}\PYG{n}{VirtualHost} \PYG{o}{*}\PYG{p}{:}\PYG{l+m+mi}{443}\PYG{o}{\PYGZgt{}}
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\PYG{n}{ErrorLog} \PYG{o}{/}\PYG{n}{var}\PYG{o}{/}\PYG{n}{log}\PYG{o}{/}\PYG{n}{apache2}\PYG{o}{/}\PYG{n}{error}\PYG{o}{.}\PYG{n}{log}
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\PYG{n}{LogLevel} \PYG{n}{warn}
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\PYG{n}{ServerName} \PYG{n}{labfolder}\PYG{o}{.}\PYG{n}{rz}\PYG{o}{\PYGZhy{}}\PYG{n}{berlin}\PYG{o}{.}\PYG{n}{mpg}\PYG{o}{.}\PYG{n}{de}
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\PYG{n}{SSLEngine} \PYG{n}{On}
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\PYG{n}{SSLCertificateFile} \PYG{o}{/}\PYG{n}{etc}\PYG{o}{/}\PYG{n}{letsencrypt}\PYG{o}{/}\PYG{n}{live}\PYG{o}{/}\PYG{n}{labfolder}\PYG{o}{.}\PYG{n}{rz}\PYG{o}{\PYGZhy{}}\PYG{n}{berlin}\PYG{o}{.}\PYG{n}{mpg}\PYG{o}{.}\PYG{n}{de}\PYG{o}{/}\PYG{n}{fullchain}\PYG{o}{.}\PYG{n}{pem}
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\PYG{n}{SSLCertificateKeyFile} \PYG{o}{/}\PYG{n}{etc}\PYG{o}{/}\PYG{n}{letsencrypt}\PYG{o}{/}\PYG{n}{live}\PYG{o}{/}\PYG{n}{labfolder}\PYG{o}{.}\PYG{n}{rz}\PYG{o}{\PYGZhy{}}\PYG{n}{berlin}\PYG{o}{.}\PYG{n}{mpg}\PYG{o}{.}\PYG{n}{de}\PYG{o}{/}\PYG{n}{privkey}\PYG{o}{.}\PYG{n}{pem}
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\PYG{n}{ProxyPass} \PYG{o}{/} \PYG{n}{http}\PYG{p}{:}\PYG{o}{/}\PYG{o}{/}\PYG{l+m+mf}{141.14}\PYG{o}{.}\PYG{l+m+mf}{138.230}\PYG{p}{:}\PYG{l+m+mi}{9091}\PYG{o}{/}
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\PYG{n}{ProxyPassReverse} \PYG{o}{/} \PYG{n}{http}\PYG{p}{:}\PYG{o}{/}\PYG{o}{/}\PYG{l+m+mf}{141.14}\PYG{o}{.}\PYG{l+m+mf}{138.230}\PYG{p}{:}\PYG{l+m+mi}{9091}\PYG{o}{/}
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\PYG{o}{\PYGZlt{}}\PYG{o}{/}\PYG{n}{VirtualHost}\PYG{o}{\PYGZgt{}}
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\end{sphinxVerbatim}
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\chapter{Groups, ownership and sharing in labfolder}
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\label{\detokenize{groups:groups-ownership-and-sharing-in-labfolder}}\label{\detokenize{groups::doc}}
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As labfolder user you can create groups (ultimately: group projects) and private projects. In \sphinxstyleemphasis{Manage \textgreater{} Projects} you see all projects that you own and that you are a member of.
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\section{Private projects}
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\label{\detokenize{groups:private-projects}}
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You alone are the owner of these projects in \sphinxstyleemphasis{My Private Projects}. Their ownership cannot be transfered from you to anyone else via the webinterface. Only via accepting the invitation to a group with the policy that private projects are not allowed the content of the former private project would be visible (and administrable) also to the group’s admin(s). By directly manipulating the database the ownership could be changed to an active user as well.
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\noindent{\hspace*{\fill}\sphinxincludegraphics[width=0.700\linewidth]{{private_projects}.png}\hspace*{\fill}}
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\sphinxstylestrong{Private projects are possible through a back door} if a user creates their own group which doesn’t necessarily mean that they invite other users to this group. In their own group they could create as many (private) projects as they like.
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\section{Group projects}
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\label{\detokenize{groups:group-projects}}
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Any labfolder user can create groups and subgroups in \sphinxstyleemphasis{Manage \textgreater{} Groups \textgreater{} Button “+Add”}. But within an already existing group a member can only create subgroups if they are set as an administrator of this group. In the role of the admin you can do the following:
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\begin{itemize}
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\item {}
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Create (sub)groups |
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\item {}
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Invite users to your (sub)group via e-mail |
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\item {}
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Move users between subgroups |
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\item {}
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Set and remove (sub)group members as admins |
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\item {}
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Remove users from a (sub)group e.g. when they are leaving the institute (\sphinxstylestrong{In this case the ownership of this user’s projects within the (sub)group needs to be transfered first!})
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\item {}
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Delete (sub)groups (before deleting it you need to remove all group members) |
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\end{itemize}
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\section{Group settings}
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\label{\detokenize{groups:group-settings}}
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Administrators of groups (but not the ones of the subgroups) can edit the general settings of groups. |
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\noindent{\hspace*{\fill}\sphinxincludegraphics[width=0.700\linewidth]{{group_settings}.png}\hspace*{\fill}}
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\begin{itemize}
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\item {}
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Through the option \sphinxstyleemphasis{Prevent group members from deleting content} all users (including the admin) are prevented from deleting projects or any other data from the labfolder database. Projects will merely be hidden if a user decides to \sphinxstyleemphasis{Remove} it from their list of projects.
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\item {}
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By checking the option \sphinxstyleemphasis{Prevent group members from having private projects}, group members will not be allowed to have private projects. All private projects of group members will be moved into the group projects, but will not be shared with any other group members.
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\item {}
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By switching on \sphinxstyleemphasis{Users can be members of several subgroups}, users which are already members of a group can be invited again to another subgroup within the group. If switched to off members cannot be invited to subgroups of their current group.
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\end{itemize}
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\chapter{Import and export of projects and entries}
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\label{\detokenize{import_export::doc}}\label{\detokenize{import_export:import-and-export-of-projects-and-entries}}
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\section{Import}
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\label{\detokenize{import_export:import}}
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The import of projects (from another labfolder instance or from another logbook software) is only possible via the labfolder API. An import of labfolder-own projects via webinterface is not possible to date. You can find the API documentation here: |
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\begin{DUlineblock}{0em}
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\item[] Version 1: \sphinxurl{http://labfolder.rz-berlin.mpg.de:9091/api/v1}
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\item[] Version 2: \sphinxurl{https://labfolder.rz-berlin.mpg.de/api/v2/docs/development.html}
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\end{DUlineblock}
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Version 2 is still in the development phase. |
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\section{Export}
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\label{\detokenize{import_export:export}}
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Exporting projects (or just single entries) is possible in three different formats: PDF, XHTML and JSON. The export as PDF can be done from within a project … |
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\noindent{\hspace*{\fill}\sphinxincludegraphics[width=0.700\linewidth]{{export_of_projects}.png}\hspace*{\fill}}
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… or from the project overview (\sphinxstyleemphasis{Manage \textgreater{} Projects}):
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\noindent{\hspace*{\fill}\sphinxincludegraphics[width=0.700\linewidth]{{export_of_projects2}.png}\hspace*{\fill}}
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The XHTML export can be done via the settings: |
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\noindent{\hspace*{\fill}\sphinxincludegraphics[width=0.700\linewidth]{{export_xhtml}.png}\hspace*{\fill}}
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However, to use this type of export it has to be installed first in the \sphinxstyleemphasis{Manage \textgreater{} Apps} section. By means of the XHTML export all projects that one owns will be exported. A detailled selection of projects or entries to be exported is not possible. As soon as the export process is finished a download link appears in the settings in \sphinxstyleemphasis{Data exports}. The downloadable ZIP file contains all images and files along with an index.html file that contains information about all entries. You could open and view the index.html file in a browser similar to the view in labfolder.
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The JSON export is only useable via the API endpoint \sphinxcode{GET /entries}. However, at the moment the response only contains useful information such as dates and tags. The author name is hidden behind the author ID and the entry text content is completely missing.
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\chapter{Importing projects from e.g. the ELOGbook to Labfolder at the FHI}
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\label{\detokenize{importing_from_elog:importing-projects-from-e-g-the-elogbook-to-labfolder-at-the-fhi}}\label{\detokenize{importing_from_elog::doc}}
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The ELOG entries of a certain project need to be exported as \sphinxstyleemphasis{Raw} which looks like this:
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\fvset{hllines={, ,}}%
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\begin{sphinxVerbatim}[commandchars=\\\{\}]
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\PYGZdl{}@MID@\PYGZdl{}: 12
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Date: Tue, 03 Dec 2013 12:15:14 +0100 |
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Author: Wieland SchÃ\P{}llkopf
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Author Email: mailto:wschoell@fhi\PYGZhy{}berlin.mpg.de
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Category: Shift summary |
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Subject: 1st solid\PYGZhy{}state experiment with FHI FEL
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Severity: DOCU |
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Keywords: |
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Record date: 1386069171 |
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Attachment: |
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Encoding: HTML |
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======================================== |
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\PYGZlt{}p\PYGZgt{}Today Alex Paarmann and Marc Herzog are measuring in the wavelength range from 10 to 20 micron with a 0.5 mm thick GGG (Gadolinium Gallium Garnet, \PYGZlt{}a title=\PYGZdq{}Gadolinium\PYGZdq{} href=\PYGZdq{}http://en.wikipedia.org/wiki/Gadolinium\PYGZdq{}\PYGZgt{}Gd\PYGZlt{}/a\PYGZgt{}\PYGZlt{}sub\PYGZgt{}3\PYGZlt{}/sub\PYGZgt{}\PYGZlt{}a title=\PYGZdq{}Gallium\PYGZdq{} href=\PYGZdq{}http://en.wikipedia.org/wiki/Gallium\PYGZdq{}\PYGZgt{}Ga\PYGZlt{}/a\PYGZgt{}\PYGZlt{}sub\PYGZgt{}5\PYGZlt{}/sub\PYGZgt{}\PYGZlt{}a title=\PYGZdq{}Oxygen\PYGZdq{} href=\PYGZdq{}http://en.wikipedia.org/wiki/Oxygen\PYGZdq{}\PYGZgt{}O\PYGZlt{}/a\PYGZgt{}\PYGZlt{}sub\PYGZgt{}12\PYGZlt{}/sub\PYGZgt{}). Electron energy is set to 26 MeV.\PYGZlt{}/p\PYGZgt{}
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\end{sphinxVerbatim}
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The entry shown above looks like this in the ELOG webinterface: |
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\noindent{\hspace*{\fill}\sphinxincludegraphics[width=1.000\linewidth]{{elog_entry}.png}\hspace*{\fill}}
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What is noticeable is that the ELOG export comes with an “Ã\P{}” instead of an “ö”. Interestingly, if only entries done by Wieland are exported the export file has UTF-8 encoding which can actually print German “Umlaute” (ö, ä, ü). If, however, all entries are exported the encoding changes to an encoding that cannot handle e.g. “ö”.
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After importing the above ELOG entry into labfolder this entry appears like that: |
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\noindent{\hspace*{\fill}\sphinxincludegraphics[width=1.000\linewidth]{{entry_after_import}.png}\hspace*{\fill}}
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\section{Using python to import from ELOG to labfolder}
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\label{\detokenize{importing_from_elog:using-python-to-import-from-elog-to-labfolder}}
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There is a GitHub project containing a python program for importing a raw (see the export example above) ELOG project. Get the project files by typing: |
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\fvset{hllines={, ,}}%
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\begin{sphinxVerbatim}[commandchars=\\\{\}]
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\PYGZdl{} git clone https://github.molgen.mpg.de/weiher/elog2labfolder.git
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\end{sphinxVerbatim}
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The script \sphinxstyleemphasis{elog2labfolder.py} is meant to be executed from remote, that is, not on the machine on which labfolder is running. A prerequisit is the python MySQLDB package because for a few methods the labfolder API cannot be used, instead, direct manipulation of the labfolder MySQL database is needed. The actual labfolder API is applied in the methodes collected in \sphinxstyleemphasis{myPythonAPIv1.py} and \sphinxstyleemphasis{myPythonAPIv2.py}. Mostly, API version 2 is used but adding text at the end of an entry can only be accomplished by using the version 1 API call. \sphinxstyleemphasis{getListOfAuthors.py} gives you a list of all authors in a raw ELOG export file.
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\section{Alternatives to the manipulating the labfolder DB on MySQL level}
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\label{\detokenize{importing_from_elog:alternatives-to-the-manipulating-the-labfolder-db-on-mysql-level}}
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As mentioned previously: a few methods in the python API use a direct manipulation of the labfolder DB via MySQL queries. These methods are: |
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\begin{itemize}
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\item {}
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\sphinxstyleemphasis{createUserAccount(email, author, entryContent, verboseOutput, cursor, db)}: If an author of an ELOG logbook entry has not yet a labolder account this account is created on the fly by setting a default (encrypted) password. This password is irrelevant because labfolder checks the entered password with the one from the LDAP server. Note: when setting a password in the DB labfolder’s LDAP authentication needs to be disabled (FEATURE\_LDAP\_AUTHENTICATION=false) and enabled again after the setting process is finished.
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\item {}
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\sphinxstyleemphasis{updateAuthor(userID, blockID, cursor, db)}: Update the author of an entry. With the script \sphinxstyleemphasis{elog2labfolder.py} an entry is created with the author that is the person whose labfolder credentials are used to get the login token. Via this method the true author can be set to the passed in \sphinxstyleemphasis{userID}.
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\item {}
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\sphinxstyleemphasis{updateDateAndTime(date, blockID, cursor, db)}: Similar to \sphinxstyleemphasis{updateAuthor()} this method sets the creation and modification date to the creation time and date of the entry to be imported. This is necessary because otherwise creation and modification date are the time and date of the import of the entry.
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\end{itemize}
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The labfolder support suggested the following alternative involving using the labfolder API: |
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\begin{itemize}
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\item {}
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… siehe E-Mail (gesendet) vom 15.12. … |
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\end{itemize}
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\renewcommand{\indexname}{Index}
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\printindex |
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\end{document} |