bagit-create 0.1.1

Create BagIt packages harvesting data from upstream sources

bagit-create

Python module and CLI tool to prepare SIPs (according to the CERN SIP specification), harvesting metadata and files from various souces, such as digital repositories powered by Invenio software, Invenio, CERN Open Data,..

Install

If you just need to run BagIt Create from the command line:

# Install from PyPi
pip install bagit-create

# Check installed version
bic --version

For development, you can clone this repository and then install it with the -e flag:

# Clone the repository
git clone https://gitlab.cern.ch/digitalmemory/bagit-create
cd bagit-create

# Create a virtual environment and activate it
python -m venv env
source env/bin/activate

# Install the project in editable mode
pip install -e .

# Check installed version
bic --version

# Run tests
python -m pytest

Usage

Supported sources

Four pipelines (Invenio 1.x, Invenio 3.x, CERN Open Data, Indico) are currently implemented, supporting the following digital repositories:

Name	Source ID	URL	Pipeline
CERN Document Server	cds	https://cds.cern.ch/	Invenio v1.x
ILC Document Server	ilcdoc	http://ilcdoc.linearcollider.org	Invenio v1.x
CERN Open Data	cod	https://opendata.cern.ch/	CERN Open Data
Zenodo	zenodo	https://zenodo.org/	Invenio v3.x
CERN Indico	indico	https://indico.cern.ch/	Indico v3.0.x*
ILC Agenda	ilcagenda	https://agenda.linearcollider.org/	Indico v3.0.x*

* requires additional configuration

Indico

To use any Indico pipeline you need an API Token. From your browser, login to the Indico instance, go to "Preferences" and then "API Token". Create new token, name can be anything. Select (at least) Everything (all methods) and Classic API (read only) as scopes. Note down the token and set the INDICO_KEY environement variable to it.

export INDICO_KEY=<INDICO_API_TOKEN>

CLI

Some examples:

CDS:

# (Expect error) Removed resource
bic --recid 1 --source cds

# (Expect error) Public resource but metadata requires authorisation
bic --recid 1000 --source cds

# Resource with a lot of large videos, light bag
bic --recid 1000571 --source cds --dry-run

# Resource with just a PDF
bic --recid 2728246 --source cds

ilcdoc:

# ilcdoc #
bic --source ilcdoc --recid 62959 --verbose
bic --source ilcdoc --recid 34794 --verbose

Zenodo

bic --recid 3911261 --source zenodo --verbose
bic --recid 3974864 --source zenodo --verbose

Indico

bic --recid 1024767 --source indico 

CERN Open Data

bic --recid 1 --source cod --dry-run --verbose
bic --recid 8884 --source cod --dry-run --verbose --alternate-uri
bic --recid 8884 --source cod --dry-run --verbose
bic --recid 5200 --source cod --dry-run --verbose
bic --recid 8888 --source cod --dry-run --verbose

bic --recid 10101 --source cod --dry-run --verbose
bic --recid 10102 --source cod --dry-run --verbose
bic --recid 10103 --source cod --dry-run --verbose
bic --recid 10104 --source cod --dry-run --verbose
bic --recid 10105 --source cod --dry-run --verbose

bic --recid 10101 --source cod --verbose
bic --recid 10102 --source cod --verbose
bic --recid 10103 --source cod --verbose
bic --recid 10104 --source cod --verbose
bic --recid 10105 --source cod --verbose

CLI options:

  --version                       Show the version and exit.
  --recid TEXT                    Record ID of the resource the upstream
                                  digital repository. Required by every
                                  pipeline but local.

  -s, --source [cds|ilcdoc|cod|zenodo|inveniordm|indico|local|ilcagenda]
                                  Select source pipeline from the supported
                                  ones.  [required]

  -d, --dry-run                   Skip downloads and create a `light` bag,
                                  without any payload.

  -a, --alternate-uri             Use alternative uri instead of https for
                                  fetch.txt (e.g. root endpoints  for CERN
                                  Open Data instead of http).

  -v, --verbose                   Enable basic logging (verbose, 'info'
                                  level).

  -vv, --very-verbose             Enable verbose logging (very verbose,
                                  'debug' level).

  -b, --bibdoc                    [ONLY for Supported Invenio v1 pipelines]
                                  Get metadata for a CDS record from the
                                  bibdocfile utility
                                  (`/opt/cdsweb/bin/bibdocfile` must be
                                  available in the system).

  --bd-ssh-host TEXT              [ONLY for Supported Invenio v1 pipelines]
                                  Specify SSH host to run bibdocfile. Access
                                  must be promptless. (See documentation for
                                  usage and configuration). By default uses
                                  the local machine.

  -t, --target TEXT               Output folder for the generated SIP. By
                                  default uses the same folder  the tool is
                                  being executed from.

  -sp, --source_path TEXT         [Local source ONLY, required] Set path of
                                  the local folder to use as a source.

  -u, --author TEXT               [Local source ONLY] Specify the Author of
                                  data.

  -tb, --source_base_path TEXT    [Local source ONLY] Specify a part of the
                                  path as  relevant for extracting an
                                  hierachy.

  --help                          Show this message and exit.

Module

BIC can easily be run inside other Python scripts. Just import it and use the process method with the same parameters you can pass to the CLI.

E.g., this snippet creates SIP packages for CDS resources from ID 2728246 to 27282700.

import bagit_create

for i in range(2728246, 27282700):
    result = bagit_create.main.process(
        source="cds", recid=i, loglevel=3
    )
    if result["status"] == 0:
        print("Success")
    else:
        print("Error")

Accessing CERN firewalled websites

If the upstream source you're trying to access is firewalled, you can set up a SOCKS5 proxy via a SSH tunnel through LXPLUS and then run bic through it with tools like proxychains or tsocks. E.g.:

Bring up the SSH tunnel:

ssh -D 1337 -q -N -f -C lxplus.cern.ch

The proxy will be up at socks5://localhost:1337. After having installed tsocks, edit the its configuration file (/etc/tsocks.conf) as follows:

[...]
server = localhost
server_type = 5
server_port = 1337
[...]

Now, just run bic as documented here but prepend tsocks to the command:

tsocks bic --recid 1024767 --source indico -vv

Module

The BagIt-Create tool can be used from other python scripts easily:

from bagit_create.main import process

process(recid=2272168, source="cds")

bibdocfile

The bibdocfile command line utility can be used to get metadata for CDS, exposing internal file paths and hashes normally not available through the CDS API.

If the executable is available in the path (i.e. you can run /opt/cdsweb/bin/bibdocfile) just append --bibdoc:

bic --recid 2751237 --source cds --bibdoc -v

If this is not the case, you can pass a --bd-ssh-host parameter specifying the name of an SSH configured connection pointing to a machine able to run the command for you. Be aware that your machine must be able to establish such connection without any user interaction (the script will run ssh <THE_PROVIDED_SSH_HOST> bibdocfile ..args).

Since in a normal CERN scenario this can't be possible due to required ProxyJumps/OTP authentication steps, you can use the ControlMaster feature of any recent version of OpenSSH, allowing to reuse sockets for connecting:

Add an entry in ~/.ssh/config to set up the SSH connection to the remote machine able to run bibdocfile for you in the following way:

Host <SSH_NAME>
  User <YOUR_USER>
  Hostname <HOSTNAME.cern.ch>
  ProxyJump <LXPLUS_or_AIADM>
  ControlMaster auto
  ControlPath ~/.ssh/control:%h:%p:%r

Then, run ssh <SSH_NAME> in a shell, authenticate and keep it open. OpenSSH will now reuse this socket everytime you run <SSH_NAME>, allowing BagItCreate tool to run bibdocfile over this ssh connection for you, if you pass the bd-ssh-host parameter:

bic --recid 2751237 --source cds --bibdoc --bd-ssh-host=<SSH_NAME> -v