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ida
 
 
 
 

IDA Command Line Tools

This repository provides a bash script ida for interacting with v2 of the IDA service from the command line. Examples are provided at the end of this guide.

Usage: ida [-h]
       ida upload    [-v] [-c config] [-i ignore] [-t host] [-p project]      target_pathname local_pathname
       ida download  [-v] [-c config]             [-t host] [-p project] [-f] target_pathname local_pathname
       ida copy      [-v] [-c config]             [-t host] [-p project] [-f] target_pathname new_target_pathname
       ida move      [-v] [-c config]             [-t host] [-p project]      target_pathname new_target_pathname
       ida delete    [-v] [-c config]             [-t host] [-p project]      target_pathname
       ida info      [-v] [-c config]             [-t host] [-p project] [-f] target_pathname
       ida inventory [-v] [-c config]             [-t host] [-p project]

       -h : show this guide
       -v : provide verbose output
       -c : configuration file
       -i : ignore file
       -t : target host (default: "https://ida.fairdata.fi")
       -p : project name
       -f : target_pathname is relative to frozen area, new_target_pathname is relative to staging area

Pathnames may correspond to either files or folders. If a folder is specified, then the action is performed for all files within that folder and all subfolders. Folders are downloaded as zip files. Actions can be performed on only one file or folder at a time.

Unless the -f parameter is specified, target_pathname and new_target_pathname are relative to the staging area of the specified project. If the -f parameter is specified, then the target_pathname is relative to the frozen area; and if the copy action is specified, the new_target_pathname is relative to the staging area of the specified project. The -f parameter is only allowed for download, copy, and info actions.

local_pathname is the pathname of a folder or file on the local system which is to be uploaded, or the pathname on the local system to which a file will be downloaded (either a single data file or the zip file for a data folder). Existing files will not be overwritten.

move can also be used to rename a file or folder without changing its location.

Installation

Download the ida script, ideally placing it in a location somewhere in your $PATH, and ensure that the script is executable:

chmod +x ida

The ida script requires that bash is installed on your system as /bin/bash and that curl is installed on your system somewhere in your $PATH.

Configuration

The ida script requires that certain parameters are defined, either via environment variables or provided as arguments.

Configuration file

The ida script will look for and load a file .ida-config if it exists in your home directory.

You can copy the provided example ida-config file from the templates subdirectory to your home directory as .ida-config and edit it accordingly.

It is also possible to explicitly specify a configuration file using the -c command line option.

Configuration settings will be taken from existing environment variables, followed by $HOME/.ida-config, followed by a configuration file specified with the -c command line option, followed by any other specified command line options; thus, it is possible to partially or completely override configuration settings defined at each subsequent level of specification.

Project

You may define the name of your project using the IDA_PROJECT environment variable.

IDA_PROJECT="myproject"

You may also specify the project using the -p command line option.

If you belong to more than one project, you can define whichever project is most frequently used and use the -p commmand line option to explicitly specify another project when different from the default.

All target pathnames are considered to be relative to the staging or frozen area of the specified project.

IDA Host

The IDA_HOST environment variable may be defined as something other than the main production service, when appropriate. If undefined, the script will default to the main production service.

IDA_HOST="https://ida.fairdata.fi"

Authentication

The ida script will need to be provided your IDA account credentials in order to access the project space.

The username and password credentials are the same as you use to log in to the IDA web UI, and are managed in the CSC Customer Portal MyCSC.

Account credentials should ideally be defined using netrc.

You can copy the provided example netrc file from the templates subdirectory to your home directory as .ida-config and edit it accordingly. Be sure to set the permissions of your netrc file securely:

chmod go-rwx $HOME/.netrc

If a .netrc file exists in your home directory, the script will retrieve your credentials from there. If no .netrc file exists in your home directory, you will be prompted to enter your credentials on each invocation.

App passwords

If you prefer not to use or store your personal account password, it is possible to create an application specific password which can be used and stored in place of your official account password.

To create an app password, log in to the IDA web UI, and open the settings view by selecting "Personal" from the pull down settings menu at the top right of the view, and then either select the "Security" section in the left hand navigation pane or scroll down to the security section.

In the field provided, enter a name for your new app password and click "Create new app password". The new app password will be displayed, and must be copied and saved immediately. It will not be possible to view the app password again, though it will be listed by the provided name and you will be able to delete it and remove it from use.

Enter or store the app password in your .netrc file, the same as you would your official personal account password.

Ignore file

The ida script will look for and use a file .ida-ignore if it exists in your home directory, to exclude files matching certain patterns from upload.

This is useful when uploading entire folders, to exclude special system files such as .DS_Store on OS-X or various temporary or log files which might exist within the local filesystem but are not part of the data to be stored in IDA.

You can copy the provided example ida-ignore file from the templates subdirectory to your home directory as .ida-ignore and edit it accordingly.

It is also possible to explicitly specify an ignore file using the -i command line option.

The ignore file should contain one pattern per line, and will be applied only to filenames, not to pathnames or portions of pathnames. Patterns should be compatible with those understood by the -name option of the POSIX find command.

Collision Avoidance for File Operations

All users belonging to a given project have the same rights, and may interact with, add, and remove project data concurrently. To help avoid one user unintentionally interfering with another user's activity, the IDA service employs a number of checks and restrictions to ensure that multiple concurrent users' activities do not collide in undesirable ways.

Operations on files in the staging area, including uploading, deleting, renaming, and moving (but not downloading), will not be allowed if they intersect with the scope of an action that is being initiated.

If an action is initiated in the web UI of the service, it takes precidence over any batch operations utilizing the command line tools, such that the batch operations may be blocked by the initiated action. In such cases, the command line tools will exit with an error message.

More details can be found in the online user guide.

Info and Listing Output

The output of the info action is both human friendly as well as easily parsable by script.

File Info

File info consists of a sequence of field::value pairs, one per line, with the field name followed by a colon ":" and padded by one or more spaces. E.g.

project:    12345
pathname:   /2017-08/Experiment_1/test01.dat
area:       frozen
type:       file
pid:        5c41b5d90561a361661419f75150
size:       446
checksum:   sha256:56293a80e0394d252e995f2debccea8223e4b5b2b150bee212729b3b39ac4d46
encoding:   application/octet-stream
modified:   2017-01-03T19:27:42Z
frozen:     2017-01-18T11:17:15Z

Fields included for all files, in either the staging or frozen areas:

  • project
  • pathname
  • area
  • type
  • size
  • encoding
  • modified

Additional fields provided for all files in the frozen area, if values exist:

  • pid
  • checksum
  • frozen

Note: If the info for a file in the frozen area does not include a "checksum" field, it means that postprocessing is still ongoing for the freeze action with which the file is associated. Check the pending actions section of the IDA service web UI to monitor the status of pending actions.

Folder Info

Folder info consists of a sequence of field::value pairs, one per line, with the field name followed by a colon ":" and padded by one or more spaces. Field::value pair lines are followed by a heading "contents:" on its own line, followed by zero or more pathnames, one per line, corresponding to the files or folders contained within the specified folder. E.g.

project:    12345
pathname:   /2017-08/Experiment_2
area:       staging
type:       folder
size:       23040
contents:
  /2017-08/Experiment_1/test01.dat
  /2017-08/Experiment_1/test02.dat
  /2017-08/Experiment_1/test03.dat
  /2017-08/Experiment_1/test04.dat
  /2017-08/Experiment_1/test05.dat

Each pathname is indented with whitespace, and thereby easily distinguished from lines with field::value pairs, where the field name begins at the start of each line.

Folder pathnames end in a forward slash "/", and thereby easily distinguished from file pathnames, which never end in a forward slash.

Empty folders will have no output lines following the "contents:" heading.

To retrieve a listing of the root contents of either the staging or frozen area for a project, the target pathname "/" can be specified.

Fields included for all folders, in either the staging or frozen areas:

  • project
  • pathname
  • area
  • type
  • size
  • contents

File Inventory

The output of the inventory action is encoded as a JSON object with the following example structure:

{
    "project": "some_project",
    "created": "2020-03-13T12:58:36Z",
    "totalFiles": 83,
    "totalStagedFiles": 45,
    "totalFrozenFiles": 38,
    "staging": {
        "\/relative\/pathname\/of\/staged\/file.dat": {
            "size": 1234,
            "modified": "2020-02-11T14:04:26Z"
        },
        ...
    },
    "frozen": {
        "\/relative\/pathname\/of\/frozen\/file.dat": {
            "size": 4567,
            "modified": "2020-02-11T14:04:26Z",
            "pid": "5e4ea9a829bfe465487185f441180",
            "checksum": "sha256:b5bb9d8014a0f9b1d61e21e796d78dccdf1352f23cd32812f4850b878ae4944c",
            "frozen": "2020-02-20T15:07:32Z"
        },
        ...
    }
}

Local File Checksum Generation

The included utility ida-checksum can be used to generate a checksum for a local file, of the same format (SHA-256, lowercase) used by the IDA service.

Usage: ida-checksum -h
       ida-checksum local_pathname

Special Notes

Files named .htaccess and files with a suffix of either .part or .filepart may not be uploaded. The filenames will need to be changed in some manner, such as zipping the file or adding some other suffix or name change. These restrictions are due to security and other internal management contraints of the underlying Nextcloud platform employed by the IDA service.

Note that files are not officially stored persistently in the IDA service until they are frozen, which can only be done using the web UI of the service.

Examples

For the following examples, it is assumed that the user has defined their primary project in their .ida-config file and their account credentials in their .netrc file.

Note that when uploading, copying or moving files or folders, complete target pathnames in the project staging area must always be specified, not merely the pathname of the folder into which data will be uploaded or moved.

Upload a local folder named "run42" to the staging area with the relative pathname "/2017-04/Experiment_42":

ida upload /2017-04/Experiment_42 run42

Upload a local file named "run42/test66.dat" to the staging area with the relative pathname "/2017-04/Experiment_42/test66.dat":

ida upload /2017-04/Experiment_42/test66.dat run42/test66.dat

Download a folder from the staging area with the relative pathname "/2017-04/Experiment_42" to the local file "run42.zip":

ida download /2017-04/Experiment_42 run42.zip

Download a folder from the frozen area with the relative pathname "/2017-04/Experiment_42" to the local file "run42.zip":

ida download -f /2017-04/Experiment_42 run42.zip

Download a file from the staging area with the relative pathname "/2017-04/Experiment_42/test66.dat" to the local pathname "run42/test66.dat":

ida download /2017-04/Experiment_42/test66.dat run42/test66.dat

Download a file from the frozen area with the relative pathname "/2017-04/Experiment_42/test66.dat" to the local pathname "run42/test66.dat":

ida download -f /2017-04/Experiment_42/test66.dat run42/test66.dat

Rename (move) a folder in the staging area from "/2017-04/Experiment_42" to "/2017-04/Experiment_42a":

ida move /2017-04/Experiment_42 /2017-04/Experiment_42a

Copy a file in the staging area from "/2017-04/Experiment_42/test66.dat" to "/2017-04/Experiment_42/verified/test66.dat":

ida copy /2017-04/Experiment_42/test66.dat /2017-04/Experiment_42/verified/test66.dat

    The folder path "/2017-04/Experiment_42/verified" will be created if it does not already exist.

Copy a file from the frozen area from "/2017-04/Experiment_42/baseline.dat" to the staging area as "/2019-10/Experiment_56/baseline.dat":

ida copy -f /2017-04/Experiment_42/baseline.dat /2019-10/Experiment_56/baseline.dat

    The folder path "/2019-10/Experiment_56" will be created in the staging area if it does not already exist.

Move a file in the staging area from "/2017-04/Experiment_42/test66.dat" to "/2017-04/Experiment_42/verified/test66.dat":

ida move /2017-04/Experiment_42/test66.dat /2017-04/Experiment_42/verified/test66.dat

    The folder path "/2017-04/Experiment_42/verified" will be created if it does not already exist.

Delete a folder from the staging area with the relative pathname "/2017-04/Experiment_42":

ida delete /2017-04/Experiment_42

Delete a file from the staging area with the relative pathname "/2017-04/Experiment_42/test66.dat":

ida delete /2017-04/Experiment_42/test66.dat

Retrieve info about a folder in the staging area with the relative pathname "/2017-04/Experiment_42":

ida info /2017-04/Experiment_42

Retrieve info about a folder in the frozen area with the relative pathname "/2017-04/Experiment_42":

ida info -f /2017-04/Experiment_42

Retrieve info about a file in the staging area with the relative pathname "/2017-04/Experiment_42/test66.dat":

ida info /2017-04/Experiment_42/test66.dat

Retrieve info about a file in the frozen area with the relative pathname "/2017-04/Experiment_42/test66.dat":

ida info -f /2017-04/Experiment_42/test66.dat

Retrieve info about the root of the staging area of the project:

ida info /

Retrieve info about the root of the frozen area of the project:

ida info -f /

Retrieve an inventory of all project files stored in the service:

ida inventory