help pages updated

CSCfi · May 28, 2024 · c4f139b · c4f139b
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diff --git a/help/a-flip.md b/help/a-flip.md
@@ -1,7 +1,7 @@
 # a-flip
 
 ```text
-a-flip is a tool to make individual files temporarily available in the internet.
+a-flip is a tool to make individual files temporary available in the internet.
 
 a-flip copies a file to Allas into a bucket that can be publicly accessed. Thus, anyone with the address (URL) of the
 uploaded data object can read and download the data with a web browser or tools like *wget* and *curl*.
@@ -13,7 +13,7 @@ The basic syntax of the command is:
 
   a-flip file_name
 
-The file is uploaded to a bucket _username-projectNumber_-flip.
+The file is uploaded to a bucket _username-projectNumber_-flip. You can define other bucket names can't be used.
 The URL to the uploaded object is:
 
 https://a3s.fi/username-projectNumber-flip/object_name

diff --git a/help/a-get.md b/help/a-get.md
@@ -26,7 +26,20 @@ Options:
 
 --sk <secret key>             Secret key to open crypt4gh encryption.
 
---s3cmd                       Use S3 protocol and s3cmd command for data retrieval instead of Swift protocol and rclone.
+-T, --tmpdir                  Define a directory that will be used to store 
+                              temporary files of the download process.
+
+
+--allas                       Get data from Allas with swift protocol in stead of currently set storage server. 
+                              Normally this (Allas with swft) is the default and this option is not needed,
+                              but if you have set e.g. Lumi-O as the default storage server, this option can be
+                              used to get data from Allas without changing the default storage server.
+                              
+--s3cmd                       Use Allas with S3 protocol.
+
+--lumi                        Get data from Lumi-O with S3 protocol in stead of the default storage server. 
+                              If Lumi-O is defined to be the default storage server and this option is not needed.
+                           
 
 Related commands: a-put, a-find, a-info, a-delete
 

diff --git a/help/a-list.md b/help/a-list.md
@@ -1,7 +1,10 @@
 # a-list
 
 ```text
-This tool is used to list buckets and objects in Allas. If bucket name is not defined, all buckets are listed. If bucket name is defined, then objects inside the bucket are listed.
+This tool is used to list buckets and objects in Allas or Lumi-o. If bucket name is not defined, all buckets are listed. 
+If bucket name is defined, then objects inside the bucket are listed.
+
+
 
    a-list <bucket_name>
 
@@ -14,6 +17,20 @@ Options:
 
 -p, --prefix            List only objects starting with the given prefix.
 
+
+Working with shared buckets:
+
+                        When you list a contents of a bucket with a-list, the command checks if the bucket used 
+                        belongs to the current project. If it does not belong to the project, the name of the shared 
+                        bucket is stored to Allas or Lumi-o ( into object project-number-a-tools/buckets_shared_to).
+                        When you check the available buckets with command a-list, the command shows also the names of
+                        the shared buckets stored to Allas or Lumi-o. NOTE that this option shows information about only about 
+                        shared buckets that have previously been used by a-list. Thus you can't use a-list check if some
+                        new buckets has been shared to you.
+
+
+                    
+
 Related commands: a-put, a-get, a-delete, a-find
 
 ```
diff --git a/help/a-put.md b/help/a-put.md
@@ -2,7 +2,7 @@
 
 ```text
 This tool is used to upload data from the disk environment 
-of CSC's supercomputers to Allas storage environment. 
+of CSC's supercomputers to Allas and Lumi-o storage environments. 
 a-put can be used in other environments too.
 
 The basic syntax of the command is:
@@ -11,29 +11,30 @@ The basic syntax of the command is:
 
 By default this tool performs following operations:
 
-1. Ensures that you have working connection to Allas storage 
+1. Ensures that you have working connection to the storage 
    service.
 
 2. In case of directory, the content of the directory is 
    collected into a single file (using tar command).
 
 3. By default the data is uploaded to Allas using rclone command 
-   and swift protocol. S3 protocol is available too.
+   and swift protocol. Lumi-o and Allas with S3 protocol is available too.
 
 NOTE! Data was compression with zstdmt command is no longer done by 
 default before the upload.
 
 
-The location were data is stored in Allas can be defined with 
+The location were data is stored in the storage server (Allas or Lumi-o) can be defined with 
 options --bucket (-b) and --object (-o).
 
 The default option is that data that locates in: 
   - scratch in Puhti is uploaded to bucket:  project_number-puhti-SCRATCH
   - scratch in Mahti is uploaded to bucket:  project_number-mahti-SCRATCH
   - projappl in Puhti is uploaded to bucket:  project_number-puhti-PROJAPPL
-  - projappl in Mahti is uploaded to bucket:  project_number-Mahti-PROJAPPL
+  - projappl in Mahti is uploaded to bucket:  project_number-mahti-PROJAPPL
   - LOCAL_SCRATCH in Puhti is uploaded to bucket: project_number-puhti-LOCAL_SCRATCH
-
+  - project in Lumi is uploaded to bucket:  project_number-lumi-o-project
+  - flash in Lumi is uploaded to bucket:  project_number-lumi-o-flash
 In other cases the data uploaded to by default : username-project_number-MISC
 
 For example for user kkaytaj belonging in project_201234, data 
@@ -135,8 +136,18 @@ a-put command line options:
                             to Allas. 
                             With --public-key you can do the encryption with both
                             CSC and your own public key. By default data is stored to bucket with name:
-                            your-project-number_SD-CONNECT,
+                            your-project-number_SD-CONNECT.
+
+
+-A, --allas                     Upload data to Allas with swift protocol in stead of currently set storage server. 
+                            Normally this (Allas with swift) is the default and this option is not needed,
+                            but if you have set e.g. Lumi-O as the default storage server, this option can be
+                            used to upload data to Allas without changing the default storage server.
+                              
+--s3cmd                     Use Allas with S3 protocol.
 
+-L, --lumi                      Upload data to Lumi-O with S3 protocol in stead of the default storage server. 
+                            If Lumi-O is defined to be the default storage server and this option is not needed.
 
 Related commands: a-find, a-get, a-delete, a-info
 ```
diff --git a/help/allas-backup.md b/help/allas-backup.md
@@ -21,10 +21,10 @@ allas-backup can be used for following five operations:
 
   allas-backup <file_name>  or
   allas-backup add <file_name>       Add a new backup version (snapshot) of the given file 
-                                 or directory to the back up repository.
+                                     or directory to the back up repository.
 
   allas-backup list                  Lists the snapshots saved to the repository. 
-                                 Option: -last lists only the latest versions of different snapshots.
+                                     Option: -last lists only the latest versions of different snapshots.
  
   allas-backup files <snapshot_id>   List the files that the snapshot includes.
 
@@ -36,6 +36,10 @@ allas-backup can be used for following five operations:
 
   allas-backup delete <snapshot_id>  Deletes a snapshot from the backup repository.
 
+  allas-backup dump <snapshot_id> -f <file>   Retrieve contents of a file in the snapshot.
+
+  allas-backup unlock                Remove Restic lock files.
+
   Extra options:
  
   -b, -bucket                        Use specific bucket for your repository. Note that this makes

diff --git a/help/allas-dir-to-bucket.md b/help/allas-dir-to-bucket.md
@@ -64,9 +64,10 @@ allas-dir-to-bucket command line options:
                             (default: current username).
 
 -h, --help                  Print this help.
-
+ 
+OS_PASSWORD not defined!
 allas-dir-to-bucket needs to have your Allas password stored in an environment variable.
-To do this, you need to setup you Allas connection with a command that sets this variable.
+Please setup you Allas connection with a command that sets this variable.
 
  In Puhti and Mahti use:
       allas-conf -k

diff --git a/help/allas-swift-md5-diff.py.md b/help/allas-swift-md5-diff.py.md
@@ -0,0 +1,19 @@
+# allas-swift-md5-diff.py
+
+```text
+usage: allas-swift-md5-diff.py [-h] [-v {1,2}]
+                               file_name bucket_name object_name
+
+Compare checksums of a local file and an Allas object, outputs the local file
+name if they differ. Requires swift connection
+
+positional arguments:
+  file_name             name of the local file
+  bucket_name           name of the Allas bucket
+  object_name           name of the object in the Allas bucket
+
+options:
+  -h, --help            show this help message and exit
+  -v {1,2}, --verbosity {1,2}
+                        increase output verbosity
+```
diff --git a/help/index.md b/help/index.md
@@ -22,8 +22,6 @@
 
 [a-put](./a-put.md)
 
-[a-put-batch](./a-put-batch.md)
-
 [a-stream](./a-stream.md)
 
 [allas-add-S3-permissions](./allas-add-S3-permissions.md)
@@ -40,3 +38,5 @@
 
 [allas-share-bucket](./allas-share-bucket.md)
 
+[allas-swift-md5-diff.py](./allas-swift-md5-diff.py.md)
+