diff --git a/docs.it4i/dice.md b/docs.it4i/dice.md index b3811cd6ade0701a5a998d2a6c0d659f7d218993..e287042c95a04248449b7cf228f6ed79c1a8f9cb 100644 --- a/docs.it4i/dice.md +++ b/docs.it4i/dice.md @@ -18,10 +18,18 @@ The integrated Rule-Oriented Data System (iRODS) is an open source data manageme We have to be sure about your identity, this will be done throught this steps: -- at the first, fill this request for eudat [https://www.eudat.eu/contact-support-request?Service=B2SAFE][h] -- sign to MyAccessId [https://ds.myaccessid.org/][g] , after that, please create account at B2Access [https://b2access.eudat.eu/][d] -- after successfull login to B2Access, please sign in to our AAI at : [https://aai.it4i.cz/realms/IT4i_AAI/account/#/][f] throught your B2Access account. You can set new password. this new password will work for cyberduck and icommands. -- finally, contact our support@it4i.cz by crypted mail, we will create account at our iRods server and send you crypted mail. +- at the first, fill this request for [EUDAT][h] + + + +- sign to [MyAccessID][g] , after that, please create account at [B2ACCESS][d] , pages requests valid personal certificate (e.g from GEANT) + + + + + +- after successfull login to B2Access, please sign in to our [AAI][f] throught your B2Access account. You can set new password. this new password will work for cyberduck and icommands. +- finally, contact our support@it4i.cz by mail, we will create your account at our iRODS server.   @@ -39,49 +47,66 @@ We have to be sure about your identity, this will be done throught this steps: ssh some_user@karolina.it4i.cz ml irodsfs ``` -- config files for irodsfs and icommands will be loaded + +- config files for irodsfs and icommands will be loaded - now you can choose between Fuse client or iCommands ***Fuse*** ```console -$ ml irodsfs +ssh some_user@karolina.it4i.cz +[some_use@login4.karolina ~]$ ml irodsfs -The following have been reloaded with a version change: - 1) iRODS/0.7.3 => iRODS/0.7.6 +irodsfs configuration file has been created at /home/dvo0012/.irods/config.yml +iRODS environment file has been created at /home/dvo0012/.irods/irods_environment.json -iRODS configuration file has been created at /home/some_user/.config/iRODS/config.yml. +to start irodsfs, run: irodsfs -config ~/.irods/config.yml ~/IRODS +to start iCommands, run: iinit -To mount your iRODS repository at ~/IRODS, run - irodsfs -config ~/.config/iRODS/config.yml ~/IRODS +For more information, see https://docs.it4i.cz/dice/ +``` -To unmount it, run - fusermount -u ~/IRODS +To mount your iRODS collection to ~/IRODS, run -$ irodsfs -config ~/.config/iRODS/config.yml ~/IRODS -time="2022-08-01 12:44:22.980139" level=info msg="Logging to /tmp/irodsfs_cbjqt1ib1ls3g1gtnnog.log" function=processArguments package=main +```console +[some_user@login4.karolina ~]$ irodsfs -config ~/.irods/config.yml ~/IRODS +time="2022-08-04 08:54:13.222836" level=info msg="Logging to /tmp/irodsfs_cblmq5ab1lsaj31vrv20.log" function=processArguments package=main Password: -time="2022-08-01 12:44:27.319063" level=info msg="Found FUSE Device. Starting iRODS FUSE Lite." function=parentMain package=main -time="2022-08-01 12:44:27.319319" level=info msg="Running the process in the background mode" function=parentRun package=main -time="2022-08-01 12:44:27.319721" level=info msg="Process id = 64406" function=parentRun package=main -time="2022-08-01 12:44:27.319752" level=info msg="Sending configuration data" function=parentRun package=main -time="2022-08-01 12:44:27.319909" level=info msg="Successfully sent configuration data to background process" function=parentRun package=main -time="2022-08-01 12:44:27.555090" level=info msg="Successfully started background process" function=parentRun package=main +time="2022-08-04 08:54:18.698811" level=info msg="Found FUSE Device. Starting iRODS FUSE Lite." function=parentMain package=main +time="2022-08-04 08:54:18.699080" level=info msg="Running the process in the background mode" function=parentRun package=main +time="2022-08-04 08:54:18.699544" level=info msg="Process id = 27145" function=parentRun package=main +time="2022-08-04 08:54:18.699572" level=info msg="Sending configuration data" function=parentRun package=main +time="2022-08-04 08:54:18.699730" level=info msg="Successfully sent configuration data to background process" function=parentRun package=main +time="2022-08-04 08:54:18.922490" level=info msg="Successfully started background process" function=parentRun package=main +``` + +To unmount it, run + +```console +fusermount -u ~/IRODS ``` you can work with fuse as an ordinary directory ( ls, cd, cp, mv etc ) -***iCommands*** +***iCommands*** ```console -ml irodsfs -iinit +ssh some_user@karolina.it4i.cz +[some_use@login4.karolina ~]$ ml irodsfs +irodsfs configuration file has been created at /home/dvo0012/.irods/config.yml. + to start irods fs run: irodsfs -config ~/.irods/config.yml ~/IRODS + +iCommands environment file has been created at /home/$USER/.irods/irods_environment.json. + to start iCommands run: iinit + +[some_use@login4.karolina ~]$ iinit Enter your current PAM password: ``` + - put you password you set in keycloak ```console -ils +[some_use@login4.karolina ~]$ ils /IT4I/home/some_user: test.1 test.2 @@ -128,7 +153,7 @@ mkdir ~/IRODS settings: ```console -vim ~/config.yml +[some_user@local_pc ~]$ vim ~/.rods/config.yml ``` ```console @@ -154,7 +179,7 @@ path_mappings: ***How to start - mount your collection:*** ```console -./irodsfs -config ~/config.yml ~/IRODS +[some_user@local_pc ~]$ ./irodsfs -config ~/.irods/config.yml ~/IRODS time="2022-07-29 09:51:11.720831" level=info msg="Logging to /tmp/irodsfs_cbhp2rucso0ef0s7dtl0.log" function=processArguments package=main Password: @@ -169,13 +194,13 @@ time="2022-07-29 09:51:18.008166" level=info msg="Successfully started backgroun ***How to put your data to iRODS*** ```console -cp test1G.txt ~/IRODS +[some_use@local_pc ~]$ cp test1G.txt ~/IRODS ``` It works as ordinary filesystem ```console -ls -la ~/IRODS +[some_user@local_pc ~]$ ls -la ~/IRODS total 0 -rwx------ 1 some_user some_user 1073741824 Nov 4 2021 test1G.txt ``` @@ -183,7 +208,7 @@ total 0 ***How to stop - unmout your collection:*** ```console -fusermount -u ~/IRODS +[some_user@local_pc ~]$ fusermount -u ~/IRODS ``` #### iCommands @@ -198,15 +223,15 @@ sudo rpm --import https://packages.irods.org/irods-signing-key.asc sudo wget -qO - https://packages.irods.org/renci-irods.yum.repo | sudo tee /etc/yum.repos.d/renci-irods.yum.repo sudo yum install epel-release -y sudo yum install python-psutil python-jsonschema -sudo yum install irods-icommands-4.2.7-1.x86_64 +sudo yum install irods-icommands-4.2.7-1.x86_64 mkdir ~/.irods/ cd ~ && wget https://docs.it4i.cz/irods1.it4i.cz.crt [k] ``` -Copy&paste + edit irods_user_name +Copy&paste + edit ***irods_user_name*** ```console -$ vim ~/.irods/irods_environment.json +[some_user@local_pc ~]$ vim ~/.irods/irods_environment.json { "irods_host": "irods1.it4i.cz", "irods_port": 1247, @@ -223,10 +248,10 @@ $ vim ~/.irods/irods_environment.json ``` ```console -$ pwd +[some_user@local_pc ~]$ pwd /some_user/.irods -$ ls -la +[some_user@local_pc ~]$ ls -la total 16 drwx------. 2 some_user some_user 136 Sep 29 08:53 . dr-xr-x---. 6 some_user some_user 206 Sep 29 08:53 .. @@ -238,10 +263,10 @@ dr-xr-x---. 6 some_user some_user 206 Sep 29 08:53 .. **step 1:** ```console -$ iinit +[some_user@local_pc ~]$ iinit Enter your current PAM password: -$ ils +[some_user@local_pc ~]$ ils /IT4I/home/some_user: file.jpg ``` @@ -249,11 +274,11 @@ $ ils ***how to put your data to IRODS*** ```console -$ iput cesnet.crt +[some_user@local_pc ~]$ iput cesnet.crt ``` ```console -$ ils +[some_user@local_pc ~]$ ils /IT4I/home/some_user: cesnet.crt ``` @@ -261,7 +286,7 @@ $ ils ***How to download data*** ```console -$ iget cesnet.crt +[some_user@local_pc ~]$ iget cesnet.crt ls -la ~ -rw-r--r--. 1 some_user some_user 1464 Jul 20 13:44 cesnet.crt ``` @@ -274,7 +299,7 @@ For more commands, use the `ihelp` command. [c]: https://irods.org/ [d]: https://b2access.eudat.eu/ [f]: https://aai.it4i.cz/realms/IT4i_AAI/account/#/ -[g]: https://ds.myaccessid.org/ +[g]: https://mms.myaccessid.org/profile/ [h]: https://www.eudat.eu/contact-support-request?Service=B2SAFE [i]: https://cyberduck.io/download/ [j]: http://docs.snic.se/wiki/IRODS_iCommands_installation_on_Ubuntu_20.04#Authenticate_and_test_iRODS_iCommands_client diff --git a/docs.it4i/img/B2ACCESS.jpg b/docs.it4i/img/B2ACCESS.jpg new file mode 100644 index 0000000000000000000000000000000000000000..2454fea88eb2711b8e62ef7b6fa42db3ce344a71 Binary files /dev/null and b/docs.it4i/img/B2ACCESS.jpg differ diff --git a/docs.it4i/img/crypto.jpg b/docs.it4i/img/crypto.jpg new file mode 100644 index 0000000000000000000000000000000000000000..47aeb9a631c7a4248dcedb0bf7f86e9934b97d3f Binary files /dev/null and b/docs.it4i/img/crypto.jpg differ diff --git a/docs.it4i/img/eudat.jpg b/docs.it4i/img/eudat.jpg new file mode 100644 index 0000000000000000000000000000000000000000..326269ec240602c493af44878be5597fa182359b Binary files /dev/null and b/docs.it4i/img/eudat.jpg differ diff --git a/docs.it4i/img/eudat_request.jpg b/docs.it4i/img/eudat_request.jpg new file mode 100644 index 0000000000000000000000000000000000000000..96bf947af458db4ada330e542f0c2977d1ab158a Binary files /dev/null and b/docs.it4i/img/eudat_request.jpg differ