Pyserini: Anserini Integration with Python

Pyserini provides a simple Python interface to the Anserini IR toolkit via pyjnius.

A low-effort way to try out Pyserini is to look at our online notebooks, which will allow you to get started with just a few clicks. For convenience, we've pre-built a few common indexes, available to download here.

Pyserini versions adopt the convention of X.Y.Z.W, where X.Y.Z tracks the version of Anserini, and W is used to distinguish different releases on the Python end. The current stable release of Pyserini is v0.9.4.0 on PyPI. The current experimental release of Pyserini on TestPyPI is behind the current stable release (i.e., do not use). In general, documentation is kept up to date with the latest code in the repo.

If you're looking to work with the COVID-19 Open Research Dataset (CORD-19), start with this guide.

Package Installation

Install via PyPI:

pip install pyserini==0.9.4.0

Development Installation

If you're planning on just using Pyserini, then the pip instructions above are fine. However, if you're planning on contributing to the codebase or want to work with the latest not-yet-released features, you'll need a development installation. Clone our repo with the --recurse-submodules option to make sure the eval/ submodule also gets cloned.

The eval/ directory, which contains evaluation tools and scripts, is actually this repo, integrated as a Git submodule (so that it can be shared across related projects). Build as follows (you might get warnings, but okay to ignore):

cd tools/eval && tar xvfz trec_eval.9.0.4.tar.gz && cd trec_eval.9.0.4 && make && cd ../../..
cd tools/eval/ndeval && make && cd ../../..

Next, you'll need to clone and build Anserini. It makes sense to put both pyserini/ and anserini/ in a common folder. After you've successfully built Anserini, copy the fatjar, which will be target/anserini-X.Y.Z-SNAPSHOT-fatjar.jar into pyserini/resources/jars/. You can confirm everything is working by running the unit tests:

python -m unittest

Assuming all tests pass, you should be ready to go!

How Do I Search?

Here's a sample pre-built index on TREC Disks 4 & 5 to play with (used in the TREC 2004 Robust Track):

wget https://git.uwaterloo.ca/jimmylin/anserini-indexes/raw/master/index-robust04-20191213.tar.gz
tar xvfz index-robust04-20191213.tar.gz -C indexes
rm index-robust04-20191213.tar.gz

Use the SimpleSearcher for searching:

from pyserini.search import SimpleSearcher

searcher = SimpleSearcher('indexes/index-robust04-20191213/')
hits = searcher.search('hubble space telescope')

# Print the first 10 hits:
for i in range(0, 10):
    print(f'{i+1:2} {hits[i].docid:15} {hits[i].score:.5f}')

The results should be as follows:

 1 LA071090-0047   16.85690
 2 FT934-5418      16.75630
 3 FT921-7107      16.68290
 4 LA052890-0021   16.37390
 5 LA070990-0052   16.36460
 6 LA062990-0180   16.19260
 7 LA070890-0154   16.15610
 8 FT934-2516      16.08950
 9 LA041090-0148   16.08810
10 FT944-128       16.01920

To further examine the results:

# Grab the raw text:
hits[0].raw

# Grab the raw Lucene Document:
hits[0].lucene_document

Configure BM25 parameters and use RM3 query expansion:

searcher.set_bm25(0.9, 0.4)
searcher.set_rm3(10, 10, 0.5)

hits2 = searcher.search('hubble space telescope')

# Print the first 10 hits:
for i in range(0, 10):
    print(f'{i+1:2} {hits2[i].docid:15} {hits2[i].score:.5f}')

How Do I build searchers?

There are two ways to build searchers.

• To build a searcher with a path to a directory containing the index.

searcher = SimpleSearcher('indexes/index-robust04-20191213/')

• To build a searcher with the index's identifier name.

searcher = SimpleSearcher.from_prebuilt_index('trec45')

It currently supports:

• trec45 (TREC Disks 4 & 5)
• robust04 (TREC Disks 4 & 5)
• ms-marco-passage (MS MARCO Passage)
• ms-marco-doc (MS MARCO Doc)

How Do I Fetch a Document?

The other commonly used feature is to fetch a document given its docid. This is easy to do:

doc = searcher.doc('LA071090-0047')

From doc, you can access its contents as well as its raw representation. The contents hold the representation of what's actually indexed; the raw representation is usually the original "raw document". A simple example can illustrate this distinction: for an article from CORD-19, raw holds the complete JSON of the article, which obviously includes the article contents, but has metadata and other information as well. The contents are extracts from the article that's actually indexed (for example, the title and abstract). In most cases, contents can be deterministically reconstructed from the raw. When building the index, we specify flags to store contents and/or raw; it's rarely the case we store both, since it's usually a waste of space. In the case of this (Robust04) index, we only store raw. Thus:

# Document contents: what's actually indexed.
# Note, not stored in this index.
doc.contents()
                                                                                                   
# Raw document
doc.raw()

As you'd expected, doc.id() returns the docid, which is LA071090-0047 in this case. Finally, doc.lucene_document() returns the underlying Lucene Document (i.e., a Java object). With that, you get direct access to the complete Lucene API for manipulating documents.

Every document has a docid, of type string, assigned by the collection it is part of. In addition, Lucene assigns each document a unique internal id (confusingly, Lucene also calls this the docid), which is an integer numbered sequentially starting from zero to one less than the number of documents in the index. This can be a source of confusion but the meaning is usually clear from context. Where there may be ambiguity, we refer to the external collection docid and Lucene's internal docid to be explicit. Programmatically, the two are distinguished by type: the first is a string and the second is an integer.

As an important side note, Lucene's internal docids are not stable across different index instances. That is, in two different index instances of the same collection, Lucene is likely to have assigned different internal docids for the same document. This is because the internal docids are assigned based on document ingestion order; this will vary due to thread interleaving during indexing (which is usually performed on multiple threads).

The doc method in searcher takes either a string (interpreted as an external collection docid) or an integer (interpreted as Lucene's internal docid) and returns the corresponding document. Thus, a simple way to iterate through all documents in the collection (and for example, print out its external collection docid) is as follows:

for i in range(searcher.num_docs):
    print(searcher.doc(i).docid())

How Do I Search My Own Documents?

Pyserini (via Anserini) provides ingestors for document collections in many different formats. The simplest, however, is the following JSON format:

{
  "id": "doc1",
  "contents": "this is the contents."
}

A document is simply comprised of two fields, a docid and contents. Pyserini accepts collections comprised of these documents organized in three different ways:

• Folder with each JSON in its own file, like this.
• Folder with files, each of which contains an array of JSON documents, like this.
• Folder with files, each of which contains a JSON on an individual line, like this (often called JSONL format).

So, the quickest way to get started is to write a script that converts your documents into the above format. Then, you can invoke the indexer (here, we're indexing JSONL, but any of the other formats work as well):

python -m pyserini.index -collection JsonCollection -generator DefaultLuceneDocumentGenerator \
 -threads 1 -input integrations/resources/sample_collection_jsonl \
 -index indexes/sample_collection_jsonl -storePositions -storeDocvectors -storeRaw

Once this is done, you can use SimpleSearcher to search the index:

from pyserini.search import SimpleSearcher

searcher = SimpleSearcher('indexes/sample_collection_jsonl')
hits = searcher.search('document')

for i in range(len(hits)):
    print(f'{i+1:2} {hits[i].docid:15} {hits[i].score:.5f}')

Happy honking!

Additional Documentation

• Guide to working with the COVID-19 Open Research Dataset (CORD-19)
• Guide to running the BM25 baseline for the MS MARCO Passage Retrieval Task
• Guide to running the BM25 baseline for the MS MARCO Document Retrieval Task
• Usage of the Analyzer API
• Usage of the Index Reader API
• Usage of the Query Builder API
• Usage of the Collection API
• Direct Interaction via Pyjnius

Known Issues

Anserini is designed to work with JDK 11. There was a JRE path change above JDK 9 that breaks pyjnius 1.2.0, as documented in this issue, also reported in Anserini here and here. This issue was fixed with pyjnius 1.2.1 (released December 2019). The previous error was documented in this notebook and this notebook documents the fix.

Release History

• v0.9.4.0: June 26, 2020 [Release Notes]
• v0.9.3.1: June 11, 2020 [Release Notes]
• v0.9.3.0: May 27, 2020 [Release Notes]
• v0.9.2.0: May 15, 2020 [Release Notes]
• v0.9.1.0: May 6, 2020 [Release Notes]
• v0.9.0.0: April 18, 2020 [Release Notes]
• v0.8.1.0: March 22, 2020 [Release Notes]
• v0.8.0.0: March 12, 2020 [Release Notes]
• v0.7.2.0: January 25, 2020 [Release Notes]
• v0.7.1.0: January 9, 2020 [Release Notes]
• v0.7.0.0: December 13, 2019 [Release Notes]
• v0.6.0.0: November 2, 2019