Dice patch pam

docs.it4i/dice.md

@@ -27,12 +27,57 @@ We have to be sure about your identity, this will be done throught this steps:
 ![](img/aai2.jpg)
 ![](img/aai3-passwd.jpg)
 
-### You Need a Client to Connect to iRods Server
+### ***IT4I User (You Have IT4I Account With Access to Cluster Already)***
+
+- iRods clients are provided as a module
+- config file (for client) will be loaded with module too
+
+***How to mount your collection***
+
+```console
+ssh some_user@login.karolina.it4i.cz
+ml iRODS
+```
+
+now you can choose between Fuse client or iCommands
+
+***iCommands***
+
+```console
+iinit
+Enter your current PAM password:
+```
+```console
+ils
+/IT4I/home/some_user:
+  test.1
+  test.2
+  test.3
+  test.4
+```
+
+- upload `iput` , download `iget`
+- for more help, type `ihelp`
+
+***Fuse***
+
+```console
+./irodsfs -config ~/config.yml ~/IRODS
+cd ~/IRODS
+```
+
+you can work with fuse as an ordinary directory
+
+### ***Users Without IT4I Account (No Access to Cluster)***
+
+- we suppose, you will upload your data from your local pc/vm
+
+#### You Need a Client to Connect to iRods Server
 
 - there are many iRods clients, but we recommend theese:
 - Cyberduck - for windows / mac, GUI . Password from aai.it4i.cz (keycloak) works
+- Fuse (irodsfs lite) - for linux, cli
 - iCommands - for linux, cli . Password from aai.it4i.cz (keycloak) works
-- Fuse (irodsfs lite) - for linux, cli . Only local password created by support@it4i.cz works for now, we working on it.
 
 #### Cyberduck
 
@@ -42,6 +87,80 @@ We have to be sure about your identity, this will be done throught this steps:
 
 ![](img/irods-cyberduck.jpg)
 
+#### Irodsfs Lite
+
+- work with your irods collection like ordinary directory
+- this is linux client only, basic knowledge of commandline is neccessary
+
+```console
+cd ~
+wget https://docs.it4i.cz/irods1.it4i.cz.crt [k]
+wget https://github.com/cyverse/irodsfs/releases/download/v0.7.6/irodsfs_amd64_linux_v0.7.6.tar
+tar -xvf ~/irodsfs_amd64_linux_v0.7.6.tar
+mkdir ~/IRODS
+```
+
+settings:
+
+```console
+vim ~/config.yml
+```
+
+```console
+host: irods1.it4i.cz
+port: 1247
+proxy_user: some_user
+client_user: some_user
+zone: IT4I
+
+authscheme: "pam"
+ssl_ca_cert_file: "~/irods1.it4i.cz.crt"
+ssl_encryption_key_size: 32
+ssl_encryption_algorithm: "AES-256-CBC"
+ssl_encryption_salt_size: 8
+ssl_encryption_hash_rounds: 16
+
+path_mappings:
+  - irods_path: /IT4I/home/some_user
+    mapping_path: /
+    resource_type: dir
+```
+
+***How to start - mount your collection:***
+
+```console
+./irodsfs -config ~/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:
+
+time="2022-07-29 09:51:17.691988" level=info msg="Found FUSE Device. Starting iRODS FUSE Lite." function=parentMain package=main
+time="2022-07-29 09:51:17.692683" level=info msg="Running the process in the background mode" function=parentRun package=main
+time="2022-07-29 09:51:17.693381" level=info msg="Process id = 74772" function=parentRun package=main
+time="2022-07-29 09:51:17.693421" level=info msg="Sending configuration data" function=parentRun package=main
+time="2022-07-29 09:51:17.693772" level=info msg="Successfully sent configuration data to background process" function=parentRun package=main
+time="2022-07-29 09:51:18.008166" level=info msg="Successfully started background process" function=parentRun package=main
+```
+
+***How to put your data to iRODS***
+
+```console
+cp test1G.txt ~/IRODS
+```
+
+It works as ordinary filesystem
+
+```console
+ls -la ~/IRODS
+total 0
+-rwx------ 1 some_user some_user 1073741824 Nov  4  2021 test1G.txt
+```
+
+***How to stop - unmout your collection:***
+
+```console
+fusermount -u ~/IRODS
+```
+
 #### iCommands
 
 - this is linux client only, basic knowledge of commandline is neccessary
@@ -54,12 +173,13 @@ wget -qO - https://packages.irods.org/renci-irods.yum.repo | sudo tee /etc/yum.r
 sudo yum install epel-release -y
 sudo yum install irods-icommands
 mkdir ~/.irods/
+wget https://docs.it4i.cz/irods1.it4i.cz.crt [k]
 ```
 
 Copy&paste + edit irods_user_name
 
 ```console
-$ cat .irods/irods_environment.json
+$ vim ~/.irods/irods_environment.json
 {
     "irods_host": "irods1.it4i.cz",
     "irods_port": 1247,
@@ -67,7 +187,7 @@ $ cat .irods/irods_environment.json
     "irods_zone_name": "IT4I",
     "irods_authentication_scheme": "PAM",
     "irods_ssl_verify_server": "cert",
-    "irods_ssl_ca_certificate_file": "/etc/ssl/certs/irods1.it4i.cz.crt",
+    "irods_ssl_ca_certificate_file": "~/irods1.it4i.cz.crt",
     "irods_encryption_algorithm": "AES-256-CBC",
     "irods_encryption_key_size": 32,
     "irods_encryption_num_hash_rounds": 16,
@@ -77,13 +197,13 @@ $ cat .irods/irods_environment.json
 
 ```console
 $ pwd
-/root/.irods
+/some_user/.irods
 
 $ ls -la
 total 16
-drwx------. 2 root root 136 Sep 29 08:53 .
-dr-xr-x---. 6 root root 206 Sep 29 08:53 ..
--rw-r--r--. 1 root root 253 Sep 29 08:14 irods_environment.json
+drwx------. 2 some_user some_user 136 Sep 29 08:53 .
+dr-xr-x---. 6 some_user some_user 206 Sep 29 08:53 ..
+-rw-r--r--. 1 some_user some_user 253 Sep 29 08:14 irods_environment.json
 ```
 
  **How to Start:**
@@ -97,56 +217,26 @@ Enter your current PAM password:
 $ ils
 /IT4I/home/some_user:
   file.jpg
-  file2.png
-  file3.test
-  file4.txt
-  file5.xlsx
 ```
 
-#### Irodsfs Lite
-
-- work with your irods collection like ordinary directory
+***how to put your data to IRODS***
 
 ```console
-wget https://github.com/cyverse/irodsfs/releases/download/v0.7.3/irodsfs_amd64_linux_v0.7.3.tar
-tar -xvf irodsfs_amd64_linux_v0.7.3.tar
-mkdir /mount/irods
+$ iput cesnet.crt
 ```
 
-settings:
-
 ```console
-vim config.yml
-
-host: irods1.it4i.cz
-port: 1247
-proxy_user: some_user
-client_user: some_user
-zone: IT4I
-
-path_mappings:
-  - irods_path: /IT4I/home/some_user
-    mapping_path: /
-    resource_type: dir
-```
-
-How to start - mount your collection:
-
-```console
-./irodsfs -config ~/config.yml ~/mount/irods
-
-time="2022-07-13 14:42:18.088338" level=info msg="Logging to /tmp/irodsfs_cb7brah44s3cedmmstp0.log" function=processArguments package=main
-Password: ##type your password here
-
-ls -la /mount/irods/
-total 0
--rwx------ 1 some_user some_user 1073741824 Nov  4  2021 test1G.txt
+$ ils
+/IT4I/home/some_user:
+  cesnet.crt
 ```
 
-How to stop - unmout your collection:
+***How to download data***
 
 ```console
-fusermount -u /mount/irods
+$ iget cesnet.crt
+ls -la ~
+-rw-r--r--. 1 some_user some_user 1464 Jul 20 13:44 cesnet.crt
 ```
 
 For more commands, use the `ihelp` command.
@@ -161,3 +251,4 @@ For more commands, use the `ihelp` command.
 [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
+[k]: https://docs.it4i.cz/irods1.it4i.cz.crt