impresso_pycommons

Python module with bits of code (objects, functions) highly-reusable within the impresso project.

Please refer to the documentation for further information on this library.

Installation

With pip:

pip install impresso-commons

Notes

The library supports configuration of s3 credentials via project-specific local .env files.

License

The second project 'impresso - Media Monitoring of the Past II. Beyond Borders: Connecting Historical Newspapers and Radio' is funded by the Swiss National Science Foundation (SNSF) under grant number CRSII5_213585 and the Luxembourg National Research Fund under grant No. 17498891.

Aiming to develop and consolidate tools to process and explore large-scale collections of historical newspapers and radio archives, and to study the impact of this tooling on historical research practices, Impresso II builds upon the first project – 'impresso - Media Monitoring of the Past' (grant number CRSII5_173719, Sinergia program). More information at https://impresso-project.ch.

Copyright (C) 2024 The impresso team (contributors to this program: Matteo Romanello, Maud Ehrmann, Alex Flückinger, Edoardo Tarek Hölzl, Pauline Conti).

This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU Affero General Public License for more details.

Data Versioning

Motivation

The versioning package of impresso_commons contains several modules and scripts that allow to version Impresso's data at various stages of the processing pipeline. The main goal of this approach is to version the data and track information at every stage to:

1. Ensure data consisteny and ease of debugging: Data elements should be consistent across stages, and inconsistencies/differences should be justifiable through the identification of data leakage points.
2. Allow partial updates: It should be possible to (re)run all or part of the processes on subsets of the data, knowing which version of the data was used at each step. This can be necessary when new media collections arrive, or when an existing collection has been patched.
3. Ensure transparency: Citation of the various data stages and datasets should be straightforward; users should know when using the interface exactly what versions they are using, and should be able to consult the precise statistics related to them.

Data Stages

Impresso's data processing pipeline is organised in thre main data "meta-stages", mirroring the main processing steps. During each of those meta-stages, different formats of data are created as output of processes and in turn used as inputs to other downstream tasks.

1. [Data Preparation]: Conversion of the original media collections to unified base formats which will serve as input to the various data enrichment tasks and processes. Produces prepared data.
   • Includes the data stages: canonical, rebuilt, evenized-rebuilt and passim (rebuilt format adapted to the passim algorithm).
2. [Data Enrichment]: All processes and tasks performing text and media mining on the prepared data, through which media collections are enriched with various annotations at different levels, and turned into vector representations.
   • Includes the data stages: entities, langident, text-reuse, topics, ocrqa, embeddings, (and lingproc).
3. [Data Indexation]: All processes of data ingestion of the prepared and enriched data into the backend servers: Solr and MySQL.
   • Includes the data stages: solr-ingestion-text, solr-ingestion-entities, solr-ingestion-emb, mysql-ingestion.
4. [Data Releases]: Packages of Impresso released data, composed of the datasets of all previously mentioned data stages, along with their corresponding versioned manifests, to be cited on the interface.
   • They will be accessible on the impresso-data-release GitHub repository.

TODO: Update/finalize the exact list of stages once every stage has been included.

Data Manifests

The versioning aiming to document the data at each step through versions and statistics is implemented through manifest files, in JSON format which follow a specific schema. (TODO update JSON schema with yearly modif date.)

After each processing step, a manifest should be created documenting the changes made to the data resulting from that processing. It can also be created on the fly during a processing, and in-between processings to count and sanity-check the contents of a given S3 bucket. Once created, the manifest file will automatically be uploaded to the S3 bucket corresponding to the data it was computed on, and optionally pushed to the impresso-data-release repository to keep track of all changes made throughout the versions.

Computing a manifest - compute_manifest.py script

The script compute_manifest.py, allows one to compute a manifest on the data present within a specific S3 bucket. The CLI for this script is the following:

python compute_manifest.py --config-file=<cf> --log-file=<lf> [--scheduler=<sch> --nworkers=<nw> --verbose]

Where the config_file should be a simple json file, with specific arguments, all described here.

• The script uses dask to parallelize its task. By default, it will start a local cluster, with 8 as the default number of workers (the parameter nworkers can be used to specify any desired value).
• Optinally, a dask scheduler and workers can be started in separate terminal windows, and their IP provided to the script via the scheduler parameter.

Computing a manifest on the fly during a process

It's also possible to compute a manfest on the fly during a process. In particular when the output from the process is not stored on S3, this method is more adapted; eg. for data indexation. To do so, some simple modifications should be made to the process' code:

1. Instantiation of a DataManifest object: The DataManifest class holds all methods and attributes necessary to generate a manifest. It counts a relatively large number of input arguments (most of which are optional) which allow a precise specification and configuration, and ease all other interactions with the instantiated manifest object. All of them are also described in the manifest configuration:

   • Example instantiation:

   manifest = DataManifest(
       data_stage="passim", # DataStage.PASSIM also accepted
       s3_output_bucket="32-passim-rebuilt-final/passim", # includes partition within bucket
       s3_input_bucket="22-rebuilt-final", # includes partition within bucket
       git_repo="/local/path/to/impresso-pycommons",
       temp_dir="/local/path/to/git_temp_folder",
       staging=False, # If True, will be pushed to 'staging' branch of impresso-data-release, else 'master'
       is_patch=True,
       patched_fields=["series", "id"], # example of modified fields in the passim-rebuilt schema
       previous_mft_path=None, # a manifest already exists on S3 inside "32-passim-rebuilt-final/passim"
       only_counting=False,
       notes="Patching some information in the passim-rebuilt",
       push_to_git=True,
   )

2. Addition of data and counts: Once the manifest is instantiated the main interaction with the instantiated manifest object will be through the add_by_title_year or add_by_ci_id methods (two other with "replace" instead also exist, as well as add_count_list_by_title_year, all described in the documentation), which take as input:

   • The media title and year to which the provided counts correspond
   • The counts dict which maps string keys to integer values. Each data stage has its own set of keys to instantiate, which can be obtained through the get_count_keys method or the NewspaperStatistics class. The values corresponding to each key can be computed by the user "by hand" or by using/adapting functions like counts_for_canonical_issue (or counts_for_rebuilt) to the given situation. All such functions can be found in the versioning helpers.py.
     • Note that the count keys will always include at least "content_items_out" and "issues".
   • Example:

   # for all title-years pairs or content-items processed within the task
   
   counts = ... # compute counts for a given title and year of data or content-item 
   # eg. rebuilt counts could be: {"issues": 45, "content_items_out": 9110, "ft_tokens": 1545906} 
   
   # add the counts to the manifest
   manifest.add_by_title_year("title_x", "year_y", counts)
   # OR
   manifest.add_by_ci_id("content-item-id_z", counts)

   • Note that it can be useful to only add counts for items or title-year pairs for which it's certain that the processing was successful. For instance, if the resulting output is written in files and uplodaded to S3, it would be preferable to add the counts corresponding to each file only once the upload is over without any exceptions or issues. This ensures the manifest's counts actually reflect the result of the processing.

3. Computation, validation and export of the manifest: Finally, after all counts have been added to the manifest, its lazy computation can be triggered. This corresponds to a series of processing steps that:

   • compare the provided counts to the ones of previous versions,
   • compute title and corpus-level statistics,
   • serialize the generated manifest to JSON and
   • upload it to S3 (optionally Git).
   • This computation is triggered as follows:

   [...] # instantiate the manifest, and add all counts for processed objects
   
   # To compute the manifest, upload to S3 AND push to GitHub
   manifest.compute(export_to_git_and_s3=True) 
   
   # OR
   
   # To compute the manifest, without exporting it directly
   manifest.compute(export_to_git_and_s3=False)
   # Then one can explore/verify the generated manifest with
   print(manifest.manifest_data)
   # To export it to S3, and optionally push it to Git if it's ALREADY BEEN GENERATED
   manifest.validate_and_export_manifest(push_to_git=[True or False])

Versions and version increments

The manifests use semantic versioning, where increments are automatically deduced based on the changes made to the data during a given processing or since the last manifest computation on a bucket. There are two main "modes" in which the manifest computation can be configured:

• Documenting an update (only_counting=False):
  • By default, any data "shown"/added to the manifest (so to be taken into account in the statistics) is considered to have been "modified" or re-generated.
  • If one desires to generate a manifest after a partial update of the data of a given stage, without taking the whole corpus into consideration, the best approach is to provide the exact list of media titles to include in the versioning.
• Documenting the contents of a bucket independently of a processing (only_counting=True):
  • However, the option has also been added to compute a manifest on a given bucket to simply count and document its contents (after data was copied from one bucket ot he next for instance).
  • In such cases, only modifications in the statistics for a given title-year pair will result in updates/modifications in the final manifest generated (in particular, the "last_modification_date" field of the manifest, associated to statistics would stay the same for any title for which no changes were identified).

When the computing of a manifest is launched, the following will take place to determine the version to give to the resulting manifest:

• _If a an existing version of the manifest for a given data stage exists in the output_bucket provided_, this manifest will be read and updated. Its version will be the basis to identify what the version increment should be based on the type of modifications.
• _If no such manifest exists and no manifest can be found in the output_bucket provided_, the there are two possibilities:
  • The argument previous_mft_s3_path is provided, with the path to a previously computed manifest which is present in another bucket. This manifest is used as the previous one like described above to update the data and compute the next verison.
  • The argument previous_mft_s3_path is not provided, then this is the original manifest for a given data stage, and the version in this case is 0.0.1. This is the case for your first manifest.

Based on the information that was updated, the version increment varies:

• Major version increment if new title-year pairs have been added that were not present in the previous manifest.
• Minor version increment if:
  • No new title-year pairs have been provided as part of the new manifest's data, and the processing was not a patch.
  • This is in particular the version increment if we re-ingest or re-generate a portion of the corpus, where the underlying stats do not change. If a part of the corpus only was modified/reingested, the specific newspaper titles should be provided within the newspapers parameter to indicate which data (within the media_list) to consider and update.
• Patch version increment if:
  • The _is_patch or patched_fields parameters are set to True_. The processing or ingestion versioned in this case is a patch, and the patched_fields will be updated according to the values provided as parameters.
  • The _only_counting parameter is set to True_.
  • This parameter is exactly made for the case scenarios where one wants to recompute the manifest on an entire bucket of existing data which has not necessarily been recomputed or changed (for instance if data was copied, or simply to recount etc).
  • The computation of the manifest in this context is meant more as a sanity-check of the bucket's contents.
  • The counts and statistics will be computed like in other cases, but the update information (modification date, updated years, git commit url etc) will not be updated unless a change in the statstics is identified (in which case the resulting manifest version is incremented accordingly).