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siskin

Various tasks for heterogeneous metadata handling for project finc at Leipzig University Library. Based on luigi from Spotify.

We use a couple of scripts in the repository to harvest about twenty data sources of various flavors (FTPs, OAIs, HTTPs), mix and match CSV, XML and JSON, run conversions and deduplication to create a single file that is indexable and conforms to a customized VuFind SOLR schema, running on an unified index host serving part of the data in the online catalogs of partners. Apart from this workflow, we use many one-step conversion scripts to generate a custom MARC format.

DOI Project Status: Active – The project has reached a stable, usable state and is being actively developed.

Luigi (and other frameworks) allow to divide complex workflows into a set of tasks, which form a DAG. The task logic is implemented in Python, but it is easy to use external tools, e.g. via ExternalProgram or shellout. Luigi is workflow glue and scales up (HDFS) and down (local scheduler).

More on Luigi:

More about the project:

Contents.


Install

$ pip install -U siskin

The siskin project includes a bunch of scripts, that allow to create, inspect or remove tasks or task artifacts.

Starting 02/2020, only Python 3 is supported.

Run taskchecksetup to see, what additional tools might need to be installed (this is a manually curated list, not everything is required for every task).

$ taskchecksetup
ok      7z
ok      csvcut
ok      curl
ok      filterline
ok      flux.sh
ok      groupcover
ok      iconv
ok      iconv-chunks
ok      jq
ok      metha-sync
ok      pigz
ok      solrbulk
ok      span-import
ok      unzip
ok      wget
ok      xmllint
ok      yaz-marcdump

Update

For siskin updates a

$ pip install -U siskin

should suffices. If newer versions of external program are required, than please update those manually (e.g. via your OS' package manager).

Run

List tasks:

$ tasknames

A task is an encapsulation of a processing step and can be in theory, anything; Typical tasks are: fetching data from FTP, OAI endpoint or an HTTP API, format conversions, filters or reports. Many tasks are parameterized by date (with the default often being today), which allows siskin to keep track, whether an artifact is update-to-date or not.

Run simple task:

$ taskdo DOAJHarvest

Documentation:

$ taskdocs | less -R

Remove artefacts of a task:

$ taskrm DOAJHarvest

Inspect the source code of a task:

$ taskinspect AILocalData
class AILocalData(AITask):
    """
    Extract a CSV about source, id, doi and institutions for deduplication.
    """
    date = ClosestDateParameter(default=datetime.date.today())
    batchsize = luigi.IntParameter(default=25000, significant=False)

    def requires(self):
        return AILicensing(date=self.date)
    ...

Create an aggregated file for finc

There are a couple of prerequisites:

  • siskin is installed
  • most additional tools are installed (or: output of the taskchecksetup is mostly green)
  • credentials are configured in /etc/siskin/siskin.ini or ~/.config/siskin/siskin.ini
  • some static data (that cannot be accessed over the net) is put into place (and configured in siskin.ini)
  • sufficient disk space is available

The update process itself consists of various updates:

  • all data sources (crossref, doaj, ...) are updated, as needed (e.g. FTP is synced, OAI is harvested, API, ...)
  • the licensing data is fetched from AMSL

This dependency graph of these operations can become complex:

However, if everything is put into place, a single command will suffice:

$ taskdo AIUpdate --workers 4

This can be a long running (hours, days) command, depending on the state of the already cached data.

Note: Currently a jour fixe (the 15th of a month) is used as default for the licensing information (another task, called AMSLFilterConfigFreeze should be run daily for this to work). The jour fixe can be overriden with the current information, by passing a parameter to the AILicensing task:

$ taskdo AIUpdate --workers 4 --AILicensing-override

Once the task is completed, the output of the two tasks:

  • AIExport (solr)
  • AIRedact (blob, currently microblob)

can be put into their respective data stores (e.g. via solrbulk).

Configuration

The siskin package harvests all kinds of data sources, some of which might be protected. All credentials and a few other configuration options go into a siskin.ini, either in /etc/siskin/ or ~/.config/siskin/. If both files are present, the local options take precedence.

Luigi uses a bit of configuration as well, put it under /etc/luigi/.

Completions on task names will save you typing and time, so put siskin_compeletion.sh under /etc/bash_completion.d or somewhere else.

$ tree etc
etc
├── bash_completion.d
│   └── siskin_completion.sh
├── luigi
│   ├── luigi.cfg
│   └── logging.ini
└── siskin
    └── siskin.ini

All configuration values can be inspected quickly with:

$ taskconfig
[core]
home = /var/siskin

[imslp]
listings-url = https://example.org/abc

[jstor]

ftp-username = abc
ftp-password = d3f
...

Software versioning

Since siskin works mostly on data, software versioning differs a bit, but we try to adhere to the following rules:

  • major changes: You need to recreate all your data from scratch.
  • minor changes: We added, renamed or removed at least one task. You will have to recreate a subset of the tasks to see the changes. You might need to change pipelines depending on those tasks, because they might not exist any more or have been renamed.
  • revision changes: A modification within existing tasks (e.g. bugfixes). You will have to recreate a subset of the tasks to see this changes, but no new task is introduced. No pipeline is broken, that wasn't already.

These rules apply for version 0.2.0 and later. To see the current version, use:

$ taskversion
0.43.3

Schema changes

To remove all files of a certain format (due to schema changes or such) it helps, if naming is uniform:

$ tasknames | grep IntermediateSchema | xargs -I {} taskrm {}
...

Apart from that, all upstream tasks need to be removed manually (consult the map) as this is not automatic yet.

Task dependencies

Inspect task dependencies with:

$ taskdeps JstorIntermediateSchema
  └─ JstorIntermediateSchema(date=2018-05-25)
      └─ AMSLService(date=2018-05-25, name=outboundservices:discovery)
      └─ JstorCollectionMapping(date=2018-05-25)
      └─ JstorIntermediateSchemaGenericCollection(date=2018-05-25)

Or visually via graphviz.

$ taskdeps-dot JstorIntermediateSchema | dot -Tpng > deps.png

Evolving workflows

Development

To converge the project on a common format run:

$ make imports style

This will fix import order and code style in-place. Requires isort and yapf installed. Should be executed under Python 3 only (as Python 2 isort seems to have differing opinions).

Other tools:

Naming conventions

Some conventions are enforced by tools (e.g. imports, yapf), but the following may be considered as well.

Task names and filenames

  • task class names that produce MARC21 should have suffix MARC, e.g. ArchiveMARC
  • task class names that produce intermediate schema files should have suffix IntermediateSchema, e.g. ArchiveIntermediateSchema
  • task for a single source should share a prefix, e.g. ArchiveMARC, ArchiveISSNList
  • source prefix names should follow the source names (e.g. site of publisher), in German: vorlagegetreu, e.g. DOAJHarvest, GallicaMARC
  • potentially long source names can be shortened, e.g. Umweltbibliothek can become UmBi... in umbi.py
  • it is recommended that the source file name follows the source name, e.g. DOAJ tasks live in doaj.py

Module docstrings for tasks (and scripts)

Rough examples:

# coding: utf-8
# pylint: ...
#
# Copyright 2019 ... GPL-3.0+ snippet
# ...
# @license GPL-3.0+ <http://spdx.org/licenses/GPL-3.0+>

"""

Source: Gallica
SID: 20
Ticket: #14793
Origin: OAI
Updates: monthly

Config:

[vkfilm]
input = /path/to/file
password = helloadmin

"""

Quoting style

  • use double quotes, if possible

Executable

  • if a module can be used as standalone script, then it should include the following line as first line:
#!/usr/bin/env python

Python 2/3 considerations

  • use six, if necessary
  • use __future__ imports if necessary
  • prefer io.open to raw open, e.g. Python 2 builtin has no keyword encoding
  • string literals should be written with the u prefix (obsolete in Python 3, but required in Python 2)

Debugging

  • prefer logging over print statements

Open for discussion

  • one suffix for data acquisition tasks, e.g. Harvest, Get, Fetch, Download, ...

Deployment

A distribution can be created via Makefile.

$ make dist
$ tree dist/
dist/
└── siskin-0.62.0.tar.gz

The tarball can be installed via pip:

$ pip install siskin-0.62.0.tar.gz

If access to PyPI is possible, one can upload the tarball there with:

$ make upload

Which in turn allows to install siskin via:

$ pip install -U siskin

on the target machine.

TODO

  • The naming of the scripts is a bit unfortunate, taskdo, taskcat, .... Maybe better siskin run, siskin cat, siskin rm and so on.
  • Investigate pytest for testing tasks, given inputs.

Misc

A short video using luigi's on_success and on_failure handlers to make the processing audible.

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