1204 Commits

Author SHA1 Message Date
Julian Risch
a3147cae47
Add isolated node eval mode in pipeline eval (#1962)
* run predictions on ground-truth docs in reader

* build dataframe for closed/open domain eval

* fix looping through multilabel

* fix looping through multilabel's list of labels

* simplify collecting relevant docs

* switch closed-domain eval off by default

* Add latest docstring and tutorial changes

* handle edge case params not given

* renaming & generate pipeline eval report

* add test case for closed-domain eval metrics

* Add latest docstring and tutorial changes

* test  report of closed-domain eval

* report closed-domain metrics only for answer metrics not doc metrics

* refactoring

* fix mypy & remove comment

* add second for-loop & use answer as method input

* renaming & add separate loop building docs eval df

* Add latest docstring and tutorial changes

* source /home/tstad/miniconda3/bin/activatechange column order for evaluatation dataframe (#1957)
conda activate haystack-dev2

* change column order for evaluatation dataframe

* added missing eval column node_input

* generic order for both document and answer returning nodes; ensure no columns get lost

Co-authored-by: tstadel <60758086+tstadel@users.noreply.github.com>

* fix column reordering after renaming of node_input

* simplify tests &  add docu

* Add latest docstring and tutorial changes

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: ju-gu <87523290+ju-gu@users.noreply.github.com>
Co-authored-by: tstadel <60758086+tstadel@users.noreply.github.com>
Co-authored-by: Thomas Stadelmann <thomas.stadelmann@deepset.ai>
2022-01-14 14:37:16 +01:00
Sara Zan
e28bf618d7
Implement proper FK in MetaDocumentORM and MetaLabelORM to work on PostgreSQL (#1990)
* Properly fix MetaDocumentORM and MetaLabelORM with composite foreign key constraints

* update_document_meta() was not using index properly

* Exclude ES and Memory from the cosine_sanity_check test

* move ensure_ids_are_correct_uuids in conftest and move one test back to faiss & milvus suite

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2022-01-14 13:48:58 +01:00
MichelBartels
3e4dbbb32c
Align similarity scores across document stores (#1967)
* align document store similarity functions

* remove unnecessary imports

* undone accidental change

* stopped weaviate from pretending to support dot product similarity

* stopped weaviate from pretending to support dot product similarity

* Add latest docstring and tutorial changes

* fix fixture params for document stores

* use cosine similarity for most tests

* fix cosine similarity test

* fix faiss test

* fix weaviate test

* fix accidental deletion

* fix document_store fixture

* test fix; shouldn't be merged

* fix test_normalize_embeddings_diff_shapes

* probably a better fix

* fix for parameter combinations

* revert new pytest_generate_tests functionality

* simplify pytest_generate_tests

* normalize embeddings for test_dpr_embedding

* add to faiss doc that embeddings are normalized

* Add latest docstring and tutorial changes

* remove unnecessary parameters and add comments

* simplify two lines of memory.py into one

* test similarity scores with smaller language model

* fix test_similarity_score


Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2022-01-12 19:28:20 +01:00
Mathew Kuriakose
a44b6c18c0
Unify vector_dim and embedding_dim parameter in Document Store (#1922)
* Refactored code to unify vector_dim and embedding_dim parameter in DocumentStores

* Unit test cases updated to use `embedding_dim` instead of `vector_dim`

* Unit test case update to use embedding_dim instead of vector_dim

* Add latest docstring and tutorial changes

* Put usage of `vector_dim` param in same if-block as corresponding warning

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: bogdankostic <bogdankostic@web.de>
2022-01-10 18:10:32 +01:00
MichelBartels
0b0b9689a4
Add TinyBERT data augmentation (#1923)
* add tinybert data augmentation

* don't reload glove in tinybert data augmentation

* fix unnecessary load_glove call

* fix type hints

* add comments and type hints

* add batch_size argument

* don't predict subwords as alternative for words

* fix subword predictions

* limit sequence length

* actually limit sequence length

* improve performance by calculating nearest glove vector on gpu

* add model and tokenizer parameter

* fix type hints

* improve data augmentation performance

* explained limits of script

* corrected comment

* added data augmentation test

* don't label every question in augmented dataset as impossible

* add sample glove

* better handling of downloading of glove

* fix typo of last commit
2022-01-04 18:34:16 +01:00
bogdankostic
381fc302cb
Fix loading a saved FAISSDocumentStore (#1937)
* Remove faiss_index param from config

* Add Tests

* Add assertions to tests
2022-01-04 12:22:31 +01:00
bogdankostic
45df18c416
Add RCIReader for TableQA (#1909)
* Add RCIReader

* Add latest docstring and tutorial changes

* Add Doc Strings

* Add latest docstring and tutorial changes

* Add Tests

* Add Doc Strings

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2022-01-03 16:59:24 +01:00
Kristof Herrmann
6e8e3c68d9
Custom id hashing on documentstore level (#1910)
* adding dynamic id hashing

* Add latest docstring and tutorial changes

* added pr review

* Add latest docstring and tutorial changes

* fixed tests

* fix mypy error

* fix mypy issue

* ignore typing

* fixed correct check

* fixed tests

* try fixing the tests

* set id hash keys only if not none

* dont store id_hash_keys

* fix tests

* Add latest docstring and tutorial changes

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2022-01-03 16:58:19 +01:00
tstadel
a94c274134
Support custom headers per request in pipeline (#1861)
* chain headers param down to document_stores

* Add latest docstring and tutorial changes

* fix InMemoryDocumentStore params

* Add latest docstring and tutorial changes

* fix TfidfRetriever params

* Add latest docstring and tutorial changes

* fix missing headers

* Add latest docstring and tutorial changes

* fix sparql client and update docs

* Add latest docstring and tutorial changes

* test for documentstores

* pipeline tests added

* update header param in docstrings

* Add latest docstring and tutorial changes

* refactoring: headers as implicit param

* Add latest docstring and tutorial changes

* remove unnecessary imports

* propagade batch_size correctly

* Add latest docstring and tutorial changes

* revert InMemoryDocumentStore.write_documents signature

* Add latest docstring and tutorial changes

* remove #type: ignore

* Add latest docstring and tutorial changes

* replace MutableMapping by Dict

* Add latest docstring and tutorial changes

* improve docstrings

* Add latest docstring and tutorial changes

* get rid of **kwargs

* Add latest docstring and tutorial changes

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2022-01-03 11:38:02 +01:00
bogdankostic
39573cf0a9
Add ParsrConverter (#1931)
* Add ParsrConverter

* Fix typing error + add Parsr to Linux CI

* Fix valid_language for all converters + fix context generation for ParsrConverter

* Remove ParsrConverter test from WindowsCI

* Add latest docstring and tutorial changes

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-12-30 10:15:11 +01:00
MichelBartels
f33c2b987a
Adding distillation loss functions from TinyBERT (#1879)
* initial tinybertdistill commit

* add tinybert distill loss

* remove teacher caching for tinybert

* add tinybert to distil_from method

* Add latest docstring and tutorial changes

* add dim mapping and fix type hints

* fix type hints

* fix dummy input

* fix dim mapping for tinybert loss and add comments/doc strings

* add test for tinybert loss

* Add latest docstring and tutorial changes

* add comment

* fix BERT forward parameters

* add doc string to AdaptiveModel forward method

* remove unnecessary data silo

* fix farm import

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-12-23 14:54:02 +01:00
tstadel
fc8df2163d
Fix Windows CI OOM (#1878)
* set fixture scope to "function"

* run FARMReader without multiprocessing

* dispose off ray after tests

* run most expensive tasks first in test files

* run expensive tests first

* run garbage collector between tests

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-12-22 17:20:23 +01:00
Fabrice Depaulis
77d52ad215
Rely api healthcheck on status code rather than json decoding (#1871)
* Rely api healthcheck on status code rather than json decoding

* Install UI dependencies on the Linux and Windows CI

Co-authored-by: Fabrice Depaulis <fabrice.depaulis@orange.com>
Co-authored-by: ZanSara <sarazanzo94@gmail.com>
2021-12-10 18:05:23 +01:00
KUNPENG GUO
160f81aaa3
Fix bug ranker: wrong lambda function (#1824)
* Fix bug ranker: wrong lambda function

The zip function used in line 110 intends to choose the logits array to be the key for the lambda function while it should be the first/second logit of the logit array which corresponds to the classification label (has_answer)

* Use label 1 as has_answer label

* generic ranker (add if-cond for logits vector shape)

* remove test code

* remove test code...

* add two_logits test case for ranker module.

* complete the documentation of ranker, support rankers with 1 or 2 logits as output
2021-12-06 17:13:57 +01:00
tstadel
9293a902d7
Fix OOM in test_eval.py Windows CI (#1830)
* diable problematic eval tests for windows ci

* move standard pipeline eval tests to separate test file

* switch to elasticsearch documentstore to reduce inproc mem

* Revert "switch to elasticsearch documentstore to reduce inproc mem"

This reverts commit 7a75871909c3317a252dff3a4df17e99eff69d05.

* get retiever from conftest

* use smaller embedding model for summarizer

* use smaller summarizer model

* remove queries param from pipeline.eval()

* isolate problematic tests

* rename separate test file

* Add latest docstring and tutorial changes

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-12-02 19:23:58 +01:00
tstadel
dc4cd49049
remove queries param from pipeline.eval() (#1836)
* remove queries param from pipeline.eval()

* Add latest docstring and tutorial changes

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-12-02 16:04:01 +01:00
Sara Zan
e39d015a59
Allow SQLDocumentStore to filter by many filters (#1776)
* Aliasing the join is not sufficient yet

* Update the filter query in some other functions of SQLDocumentStore - this functionality should be centralized

* Adding tests for get_all_documents, now failing

* Fix tests

* Fix typo spotted by mypy
2021-12-01 16:16:17 +01:00
tstadel
c5540d05ed
Calculation of metrics and presentation of eval results (#1760)
* retriever metrics added

* Add latest docstring and tutorial changes

* answer and document level matching metrics implemented

* Add latest docstring and tutorial changes

* answer related metrics for retriever

* basic reader metrics implemented

* handle no_answers

* fix typing

* fix tests

* fix tests without sas

* first draft for simulated top k

* rename sas and f1 columns in dataframe

* refactoring of EvaluationResult

* Add latest docstring and tutorial changes

* more eval tests added

* fix sas expected value precision

* distinction between ir and qa recall

* EvaluationResult.worst_queries() implemented

* print_evaluation_report() added

* eval report for QA Pipeline improved

* dynamic metrics for worst queries calc

* Add latest docstring and tutorial changes

* method names adjusted

* simple test for print_eval_report() added

* improved documentation

* Add latest docstring and tutorial changes

* minor formatting

* Add latest docstring and tutorial changes

* fix no_answer cases

* adjust one docstring

* Add latest docstring and tutorial changes

* fix no_answer cases for sas

* batchmode for sas implemented

* fix for retriever metrics if there are only no_answers

* fix multilabel tests

* improve documentation for pipeline.eval()

* streamline multilabel aggregates and docs

* Add latest docstring and tutorial changes

* fix multilabel tests

* unify document_id

* add dataframe schema description to EvaluationResult

* Add latest docstring and tutorial changes

* rename worst_queries to wrong_examples

* Add latest docstring and tutorial changes

* make query digesting standard pipelines work with pipeline.eval()

* Add latest docstring and tutorial changes

* tests for multi retriever pipelines added

* remove unnecessary import

* print_eval_report(): support all pipelines without junctions

* Add latest docstring and tutorial changes

* fix typos

* Add latest docstring and tutorial changes

* fix minor simulated_top_k bug and use memory documentstore throughout tests

* sas model param description improved

* Add latest docstring and tutorial changes

* rename recall metrics

* Add latest docstring and tutorial changes

* fix mean average precision link

* Add latest docstring and tutorial changes

* adjust sas description docstring

* Add latest docstring and tutorial changes

* Add latest docstring and tutorial changes

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Malte Pietsch <malte.pietsch@deepset.ai>
2021-11-30 19:26:34 +01:00
bogdankostic
eb5f7bb4c0
Add AzureConverter to support table parsing from documents (#1813)
* Add FormRecognizerConverter

* Change signature of convert method + change return type of all converters

* Adapt preprocessing util to new return type of converters

* Parametrize number of lines used for surrounding context of table

* Change name from FormRecognizerConverter to AzureConverter

* Set version of azure-ai-formrecognizer package

* Change tutorial 8 based on new return type of converters

* Add tests

* Add latest docstring and tutorial changes

* Fix typo

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Malte Pietsch <malte.pietsch@deepset.ai>
2021-11-29 18:44:20 +01:00
Sara Zan
c29f960c47
Fix UI demo feedback (#1816)
* Fix the feedback function of the demo with a workaround

* Some docstring

* Update tests and rename methods in feedback.py

* Fix tests

* Remove operation_ids

* Add a couple of status code checks
2021-11-29 17:03:54 +01:00
MichelBartels
84147edcca
Model Distillation (#1758)
* initial commit

* Add latest docstring and tutorial changes

* added comments and fixed bug

* fixed bugs, added benchmark and added documentation

* Add latest docstring and tutorial changes

* fix type: ignore comment

* fix logging in benchmark

* fixed distillation config

* Add latest docstring and tutorial changes

* added type annotations

* fixed distillation loss calculation

* added type annotations

* fixed distillation mse loss

* improved model distillation benchmark config loading

* added temperature for model distillation

* removed uncessary imports, added comments, added named parameter calls

* Add latest docstring and tutorial changes

* added some more comments

* added distillation test

* fixed distillation test

* removed unnecessary import

* fix softmax dimension

* add grid search

* improved model distillation benchmark config

* fixed model distillation hyperparameter search

* added doc strings and type hints for model distillation

* Add latest docstring and tutorial changes

* fixed type hints

* fixed type hints

* fixed type hints

* wrote out params instead of kwargs in DistillationDataSilo initializer

* fixed type hints

* fixed typo

* fixed typo

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-11-26 18:49:30 +01:00
Sowmiya Jaganathan
04d93ec247
Introduced an arg to add synonyms - Elasticsearch (#1625)
* Introduced an arg add synonyms to Elasticsearch

* Added the test code, removed the whitespace formatting changes, and overwrote the relevant parts from the already existing mapping instead of creating new mapping.

* Added the test code

* Remove whitespace change

* Added the doc_string with examples and link

* Removed unneccessary spaces

* Add latest docstring and tutorial changes

* fix text_field -> content_field

Co-authored-by: sowmiya-emplay <sowmiya.j@emplay.net>
Co-authored-by: Malte Pietsch <malte.pietsch@deepset.ai>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-11-23 19:10:34 +01:00
Sara Zan
600662b1f0
Hide 'no answer' responsed from the REST API tests (#1791) 2021-11-23 17:13:16 +01:00
MichelBartels
e80771f839
Adding yaml functionality to standard pipelines (save/load...) (#1735)
* adding yaml functionality to BaseStandardPipeline

fixes #1681

* Add latest docstring and tutorial changes

* Update API Reference Pages for v1.0 (#1729)

* Create new API pages and update existing ones

* Create query classifier page

* Remove Objects suffix

* Change answer aggregation key to doc_id, query instead of label_id, query (#1726)

* Add debugging example to tutorial (#1731)

* Add debugging example to tutorial

* Add latest docstring and tutorial changes

* Remove Objects suffix

* Add latest docstring and tutorial changes

* Revert "Remove Objects suffix"

This reverts commit 6681cb06510b080775994effe6a50bae42254be4.

* Revert unintentional commit

* Add third debugging option

* Add latest docstring and tutorial changes

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* Fix another self.device/s typo (#1734)

* Fix yet another self.device(s) typo

* Add typing to 'initialize_device_settings' to try prevent future issues

* Fix bug in Tutorial5

* Fix the same bug in the notebook

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* added test for saving and loading prebuilt pipelines

* fixed typo, changed variable name and added comments

* Add latest docstring and tutorial changes

* Fix a few details of some tutorials (#1733)

* Make Tutorial10 use print instead of logs and fix a typo in Tutoria15

* Add a type check in 'print_answers'

* Add same checks to print_documents and print_questions

* Make RAGenerator return Answers instead of dictionaries

* Fix RAGenerator tests

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* Fix `print_answers` (#1743)

* Fix a specific path of print_answers that was assuming answers are dictionaries

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* Split pipeline tests into three suites (#1755)

* Split pipeline tests into three suites

* Will this trigger the CI?

* Rename duplicate test into test_most_similar_documents_pipeline

* Fixing a bug that was probably never noticed

* Capitalize starting letter in params (#1750)

* Capitalize starting letter in params

Capitalized the starting letter in code examples for params in keeping with the latest names for nodes where first letter is capitalized. 
Refer: https://github.com/deepset-ai/haystack/issues/1748

* Update standard_pipelines.py

Capitalized some starting letters in the docstrings in keeping with the updated node names for standard pipelines

* Multi query eval (#1746)

* add eval() to pipeline

* Add latest docstring and tutorial changes

* support multiple queries in eval()

* Add latest docstring and tutorial changes

* keep single query test

* fix EvaluationResult node_results default

* adjust docstrings

* Add latest docstring and tutorial changes

* minor improvements from comments

* Add latest docstring and tutorial changes

* move EvaluationResult and calculate_metrics to schema

* Add latest docstring and tutorial changes

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* Split summarizer tests in order to make windows CI work again (#1757)

* separate testfile for summarizer with translation

* Add latest docstring and tutorial changes

* import SPLIT_DOCS from test_summarizer

* add workflow_dispatch to windows_ci

* add worflow_dispatch to linux_ci

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* fix import of EvaluationResult in test case

* exclude test_summarizer_translation.py for windows_ci (#1759)

* Pipelines now tolerate custom _debug content (#1756)

* Pipelines now tolerate custom _debug content

* Support Tables in all DocumentStores (#1744)

* Add support for tables in SQLDocumentStore, FAISSDocumentStore and MilvuDocumentStore

* Add support for WeaviateDocumentStore

* Make sure that embedded meta fields are strings + add embedding_dim to WeaviateDocStore in test config

* Add latest docstring and tutorial changes

* Represent tables in WeaviateDocumentStore as nested lists

* Fix mypy

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* Allow TableReader models without aggregation classifier (#1772)

* Fix usage of filters in `/query` endpoint in REST API (#1774)

* WIP filter refactoring

* fix filter formatting

* remove inplace modification of filters

* Public demo (#1747)

* Queries now run only when pressing RUN. File upload hidden. Question is not sent if the textbox is empty.

* Add latest docstring and tutorial changes

* Tidy up: remove needless state, add comments, fix minor bugs

* Had to add results to the status to avoid some bugs in eval mode

* Added 'credits'

* Add footers, update requirements, some random questions for the evaluation

* Add requested changes

* Temporary rollback the UI to the old GoT dataset

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* Facilitate concurrent query / indexing in Elasticsearch with dense retrievers (new `skip_missing_embeddings` param) (#1762)

* Filtering records not having embeddings

* Added support for skip_missing_embeddings Flag. Default behavior is throw error when embeddings are missing. If skip_missing_embeddings=True then documents without embeddings are ignored for vector similarity

* Fix for below error:
haystack/document_stores/elasticsearch.py:852: error: Need type annotation for "script_score_query"

* docstring for skip_missing_embeddings parameter

* Raise exception where no documents with embeddings is found for Embedding retriever.

* Default skip_missing_embeddings to True

* Explicitly check if embeddings are present if no results are returned by EmbeddingRetriever for Elasticsearch

* Added test case for based on Julian's input

* Added test case for based on Julian's input. Fix pytest error on the testcase

* Added test case for based on Julian's input. Fix pytest error on the testcase

* Added test case for based on Julian's input. Fix pytest error on the testcase

* Simplify code by using get_embed_count

* Adjust docstring & error msg slightly

* Revert error msg

Co-authored-by: Malte Pietsch <malte.pietsch@deepset.ai>

* Huggingface private model support via API tokens (FARMReader) (#1775)

* passed kwargs to model loading

* Pass Auth token explicitly

* add use_auth_token to get_language_model_class

* added use_auth_token parameter at FARMReader

* Add latest docstring and tutorial changes

* added docs for parameter `use_auth_token`

* Add latest docstring and tutorial changes

* adding docs link

* Add latest docstring and tutorial changes

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* private hugging face models for retrievers (#1785)

* private dpr

* Add latest docstring and tutorial changes

* added parameters to child functions

* Add latest docstring and tutorial changes

* added tableextractor

* Add latest docstring and tutorial changes

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* ignore empty filters parameter (#1783)

* ignore empty filters parameter

* Add latest docstring and tutorial changes

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* initialize doc store with doc and label index in tutorial 5 (#1730)

* initialize doc store with doc and label index

* change ipynb according to py for tutorial 5

* Add latest docstring and tutorial changes

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* Small fixes to the public demo (#1781)

* Make strealit tolerant to haystack not knowing its version, and adding special error for docstore issues

* Add workaround for a Streamlit bug

* Make default filters value an empty dict

* Return more context for each answer in the rest api

* Make the hs_version call not-blocking by adding a very quick timeout

* Add disclaimer on low confidence answer

* Use the no-answer feature of the reader to highlight questions with no good answer

* Upgrade torch to v1.10.0 (#1789)

* Upgrade torch to v1.10.0

* Adapt torch version for torch-scatter in TableQA tutorial

* Add latest docstring and tutorial changes

* Make torch version more flexible

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* adding yaml functionality to BaseStandardPipeline

fixes #1681

* Add latest docstring and tutorial changes

* added test for saving and loading prebuilt pipelines

* fixed typo, changed variable name and added comments

* Add latest docstring and tutorial changes

* fix code rendering for example

* Add latest docstring and tutorial changes

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Branden Chan <33759007+brandenchan@users.noreply.github.com>
Co-authored-by: Julian Risch <julian.risch@deepset.ai>
Co-authored-by: Sara Zan <sara.zanzottera@deepset.ai>
Co-authored-by: nishanthcgit <5066268+nishanthcgit@users.noreply.github.com>
Co-authored-by: tstadel <60758086+tstadel@users.noreply.github.com>
Co-authored-by: bogdankostic <bogdankostic@web.de>
Co-authored-by: Malte Pietsch <malte.pietsch@deepset.ai>
Co-authored-by: C V Goudar <cvgoudar@users.noreply.github.com>
Co-authored-by: Kristof Herrmann <37148029+ArzelaAscoIi@users.noreply.github.com>
2021-11-23 17:01:39 +01:00
C V Goudar
a9a379784a
Facilitate concurrent query / indexing in Elasticsearch with dense retrievers (new skip_missing_embeddings param) (#1762)
* Filtering records not having embeddings

* Added support for skip_missing_embeddings Flag. Default behavior is throw error when embeddings are missing. If skip_missing_embeddings=True then documents without embeddings are ignored for vector similarity

* Fix for below error:
haystack/document_stores/elasticsearch.py:852: error: Need type annotation for "script_score_query"

* docstring for skip_missing_embeddings parameter

* Raise exception where no documents with embeddings is found for Embedding retriever.

* Default skip_missing_embeddings to True

* Explicitly check if embeddings are present if no results are returned by EmbeddingRetriever for Elasticsearch

* Added test case for based on Julian's input

* Added test case for based on Julian's input. Fix pytest error on the testcase

* Added test case for based on Julian's input. Fix pytest error on the testcase

* Added test case for based on Julian's input. Fix pytest error on the testcase

* Simplify code by using get_embed_count

* Adjust docstring & error msg slightly

* Revert error msg

Co-authored-by: Malte Pietsch <malte.pietsch@deepset.ai>
2021-11-19 14:50:23 +01:00
Malte Pietsch
c0892717a0
Fix usage of filters in /query endpoint in REST API (#1774)
* WIP filter refactoring

* fix filter formatting

* remove inplace modification of filters
2021-11-18 18:13:03 +01:00
bogdankostic
5e36988b31
Support Tables in all DocumentStores (#1744)
* Add support for tables in SQLDocumentStore, FAISSDocumentStore and MilvuDocumentStore

* Add support for WeaviateDocumentStore

* Make sure that embedded meta fields are strings + add embedding_dim to WeaviateDocStore in test config

* Add latest docstring and tutorial changes

* Represent tables in WeaviateDocumentStore as nested lists

* Fix mypy

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-11-17 16:41:04 +01:00
Sara Zan
faf41df65c
Pipelines now tolerate custom _debug content (#1756)
* Pipelines now tolerate custom _debug content
2021-11-17 15:50:56 +01:00
Julian Risch
f3e46b8cc7
fix import of EvaluationResult in test case 2021-11-16 09:55:09 +01:00
tstadel
956d5bba43
Split summarizer tests in order to make windows CI work again (#1757)
* separate testfile for summarizer with translation

* Add latest docstring and tutorial changes

* import SPLIT_DOCS from test_summarizer

* add workflow_dispatch to windows_ci

* add worflow_dispatch to linux_ci

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-11-15 18:49:49 +01:00
tstadel
59e04cba05
Multi query eval (#1746)
* add eval() to pipeline

* Add latest docstring and tutorial changes

* support multiple queries in eval()

* Add latest docstring and tutorial changes

* keep single query test

* fix EvaluationResult node_results default

* adjust docstrings

* Add latest docstring and tutorial changes

* minor improvements from comments

* Add latest docstring and tutorial changes

* move EvaluationResult and calculate_metrics to schema

* Add latest docstring and tutorial changes

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-11-15 14:51:11 +01:00
Sara Zan
1a10de506c
Split pipeline tests into three suites (#1755)
* Split pipeline tests into three suites

* Will this trigger the CI?

* Rename duplicate test into test_most_similar_documents_pipeline

* Fixing a bug that was probably never noticed
2021-11-15 12:16:27 +01:00
Sara Zan
ea3abd305b
Fix a few details of some tutorials (#1733)
* Make Tutorial10 use print instead of logs and fix a typo in Tutoria15

* Add a type check in 'print_answers'

* Add same checks to print_documents and print_questions

* Make RAGenerator return Answers instead of dictionaries

* Fix RAGenerator tests

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-11-12 16:44:28 +01:00
tstadel
158460504b
Make FAISSDocumentStore work with yaml (#1727)
* add faiss_index_path and faiss_config_path

* Add latest docstring and tutorial changes

* remove duplicate cleaning stuff

* refactoring + test for invalid param combination

* adjust type hints

* Add latest docstring and tutorial changes

* add documentation to @preload_index

* Add latest docstring and tutorial changes

* recursive __init__ instead of decorator

* Add latest docstring and tutorial changes

* validate instead of check

* combine ifs

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-11-11 11:02:22 +01:00
Sara Zan
42c8edca54
Simplify logs management (#1696)
* Move each haystack module's logger configuration into the respective file and configure the handlers properly

* Implement most changes from #1714

* Remove accidentally committed git merge tags ':D

* Remove the debug logs capture feature

* Remove more references to debug_logs

* Fix issue with FARMReader that somehow made it to master

* Add devices parameter to Inferencer

* Change log of APEX message to DEBUG and lower the 'Starting <docstore>...' messages to DEBUG as well

* Change log level of a few logs from modeling

* Silence the transformers warning

* Remove empty line below the workers :)

* Fix two more levels in the tutorials logs

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: bogdankostic <bogdankostic@web.de>
2021-11-11 10:16:25 +01:00
tstadel
14515a861b
Tutorial for DocumentClassifier at Index Time (#1697)
* basic example of document classifier in preprocessing logic

* add batch_size to TransformersDocumentClassifier

* complete tutorial16

* Add latest docstring and tutorial changes

* fix missing batch_size

* add notebook

* test for batch_size use added

* add tutorial 16 to headers.py

* Add latest docstring and tutorial changes

* make DocumentClassifier indexing pipeline rdy

* Add latest docstring and tutorial changes

* flexibility improvements for DocumentClassifier in Pipelines

* Add latest docstring and tutorial changes

* fix index time usage

* remove query from documentclassifier tests

* improve classification_field resolving + minor fixes

* Add latest docstring and tutorial changes

* tutorial 16 extended with zero shot and pipelines

* Add latest docstring and tutorial changes

* install graphviz in notebook

* Add latest docstring and tutorial changes

* remove convert_to_dicts

* Add latest docstring and tutorial changes

* Fix typo

* Add latest docstring and tutorial changes

* remove retriever from indexing pipeline

* Add latest docstring and tutorial changes

* fix save_to_yaml when using FileTypeClassifier

* emphasize the impact with zero shot classification

* Add latest docstring and tutorial changes

* adjust use_gpu to boolean in test

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Malte Pietsch <malte.pietsch@deepset.ai>
2021-11-09 18:43:00 +01:00
bogdankostic
cd8666f904
Standardize initialisation of device settings (#1683)
* Use initialize_device_settings in all nodes

* Set StreamHandler level to INFO

* Add latest docstring and tutorial changes

* work in progress

* Standardize device initialization

* Add latest docstring and tutorial changes

* Adapt device initialization in Reader's train method

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-11-09 12:44:20 +01:00
Julian Risch
892ce4a760
Make weaviate more compliant to other doc stores (UUIDs and dummy embedddings) (#1656)
* create uuid and dummy embeddding in weaviate doc store

* handle and test for duplicate non-uuid-formatted ids in weaviate

* add uuid and dummy embedding to doc strings

* Add latest docstring and tutorial changes

* Upgrade weaviate

* Include weaviate in common doc store test cases

* Add latest docstring and tutorial changes

* Exclude weaviate doc store from eval tests

* Incorporate index name in uuid generation

* Ignore mypy error

* Fix typo

* Restore DOCS without uuid and embeddings generated by weaviate

* Supply docs for retriever tests as fixture

* Limit scope of fixture to function instead of session

* Add comments

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-11-04 09:27:12 +01:00
fingoldo
27793814cf
Cosine similarity for the rest of DocStores. (#1569)
* Added uniform normalization method to each of the DocStores (implemented), so that now Milvus and Weaviate doc stores can use cosine similarity, plus future method for making existing embeddings normaziled (empty for now).

* Fixed a typo.

* Fixed lots of stuff. Performed local tests.

* Fixed scores representation for cosine. Assuming Weavieate's rep needs no change.

* fixes as per discussion

* Trigger CI

* resolving conflicts

* small typo

* fixed a param type

* cleaned some conflicts resolving left overs

* commented out fastmath for a moment

* fixing tests

* added docstore for small vectors

* test

* fixed document_store_cosine_small

* cosine tests fixes

* fixed document_store_cosine_small

* fixed weaviate index name and lowered rtol for ES

* increased rtol

* added explicit doc_ids for weaviate, excluded ES, included Inmemory

* resolving mismatch

* fixing a typo

* flatten normalize_embedding()

* fix import for test

* standardize normalize_embeddings across doc stores

* Add latest docstring and tutorial changes

* going for the faster plain dot prod

Co-authored-by: fingoldo <fingoldo@gmail.com>
Co-authored-by: Malte Pietsch <malte.pietsch@deepset.ai>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-11-01 13:42:32 +01:00
Lalit Pagaria
e5b4b62d75
Add CI for windows runner (#1458)
* Feat: Removing use of temp file while downloading archive from url along with adding CI for windows and mac platform

* Windows CI by default installing pytorch gpu hence updating CI to pick cpu version

* fixing mac cache build issue

* updating windows pip install command for torch

* another attempt

* updating ci

* Adding sudo

* fixing ls failure on windows

* another attempt to fix build issue

* Saving env variable of test files

* Adding debug log

* Github action differ on windows

* adding debug

* anohter attempt

* Windows have different ways to receive env

* fixing template

* minor fx

* Adding debug

* Removing use of json

* Adding back fromJson

* addin toJson

* removing print

* anohter attempt

* disabling parallel run at least for testing

* installing docker for mac runner

* correcting docker install command

* Linux dockers are not suported in windows

* Removing mac changes

* Upgrading pytorch

* using lts pytorch

* Separating win and ubuntu

* Install java 11

* enabling linux container env

* docker cli command

* docker cli command

* start elastic service

* List all service

* correcting service name

* Attempt to fix multiple test run

* convert to json

* another attempt to check

* Updating build cache step

* attempt

* Add tika

* Separating windows CI

* Changing CI name

* Skipping test which does not work in windows

* Skipping tests for windows

* create cleanup function in conftest

* adding skipif marker on tests

* Run windows PR on only push to master

* Addressing review comments

* Enabling windows ci for this PR

* Tika init is being called when importing tika function

* handling tika import issue

* handling tika import issue in test

* Fixing import issue

* removing tika fixure

* Removing fixture from tests

* Disable windows ci on pull request

* Add back extra pytorch install step

Co-authored-by: Malte Pietsch <malte.pietsch@deepset.ai>
2021-10-29 10:22:28 +02:00
Julian Risch
33b2663fdc
ensure tf-idf matrix calculation before retrieval (#1665)
* ensure tf-idf matrix calculation before retrieval

* Run fit() automatically if new documents have been added

* Add latest docstring and tutorial changes

* Fix type error

* Add test case for tfidf retriever yaml pipeline

* Use InMemoryDocStore and add 2nd test case

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-10-28 16:48:06 +02:00
Sara Zan
eab475bb5d
Rename every occurrence of 'embed_passages' with 'embed_documents' (#1667)
* Rename every occurrence of 'embed_passages' with 'embed_documents'

* Remove aliased method embed_documents

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-10-28 12:17:56 +02:00
Sara Zan
13510aa753
Refactoring of the haystack package (#1624)
* Files moved, imports all broken

* Fix most imports and docstrings into

* Fix the paths to the modules in the API docs

* Add latest docstring and tutorial changes

* Add a few pipelines that were lost in the inports

* Fix a bunch of mypy warnings

* Add latest docstring and tutorial changes

* Create a file_classifier module

* Add docs for file_classifier

* Fixed most circular imports, now the REST API can start

* Add latest docstring and tutorial changes

* Tackling more mypy issues

* Reintroduce  from FARM and fix last mypy issues hopefully

* Re-enable old-style imports

* Fix some more import from the top-level  package in an attempt to sort out circular imports

* Fix some imports in tests to new-style to prevent failed class equalities from breaking tests

* Change document_store into document_stores

* Update imports in tutorials

* Add latest docstring and tutorial changes

* Probably fixes summarizer tests

* Improve the old-style import allowing module imports (should work)

* Try to fix the docs

* Remove dedicated KnowledgeGraph page from autodocs

* Remove dedicated GraphRetriever page from autodocs

* Fix generate_docstrings.sh with an updated list of yaml files to look for

* Fix some more modules in the docs

* Fix the document stores docs too

* Fix a small issue on Tutorial14

* Add latest docstring and tutorial changes

* Add deprecation warning to old-style imports

* Remove stray folder and import Dict into dense.py

* Change import path for MLFlowLogger

* Add old loggers path to the import path aliases

* Fix debug output of convert_ipynb.py

* Fix circular import on BaseRetriever

* Missed one merge block

* re-run tutorial 5

* Fix imports in tutorial 5

* Re-enable squad_to_dpr CLI from the root package and move get_batches_from_generator into document_stores.base

* Add latest docstring and tutorial changes

* Fix typo in utils __init__

* Fix a few more imports

* Fix benchmarks too

* New-style imports in test_knowledge_graph

* Rollback setup.py

* Rollback squad_to_dpr too

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-10-25 15:50:23 +02:00
bogdankostic
51acf779f2
Add TableTextRetriever (#1529)
* first draft / notes on new primitives

* wip label / feedback refactor

* rename doc.text -> doc.content. add doc.content_type

* add datatype for content

* remove faq_question_field from ES and weaviate. rename text_field -> content_field in docstores. update tutorials for content field

* update converters for . Add warning for empty

* renam label.question -> label.query. Allow sorting of Answers.

* WIP primitives

* update ui/reader for new Answer format

* Improve Label. First refactoring of MultiLabel. Adjust eval code

* fixed workflow conflict with introducing new one (#1472)

* Add latest docstring and tutorial changes

* make add_eval_data() work again

* fix reader formats. WIP fix _extract_docs_and_labels_from_dict

* fix test reader

* Add latest docstring and tutorial changes

* fix another test case for reader

* fix mypy in farm reader.eval()

* fix mypy in farm reader.eval()

* WIP ORM refactor

* Add latest docstring and tutorial changes

* fix mypy weaviate

* make label and multilabel dataclasses

* bump mypy env in CI to python 3.8

* WIP refactor Label ORM

* WIP refactor Label ORM

* simplify tests for individual doc stores

* WIP refactoring markers of tests

* test alternative approach for tests with existing parametrization

* WIP refactor ORMs

* fix skip logic of already parametrized tests

* fix weaviate behaviour in tests - not parametrizing it in our general test cases.

* Add latest docstring and tutorial changes

* fix some tests

* remove sql from document_store_types

* fix markers for generator and pipeline test

* remove inmemory marker

* remove unneeded elasticsearch markers

* add dataclasses-json dependency. adjust ORM to just store JSON repr

* ignore type as dataclasses_json seems to miss functionality here

* update readme and contributing.md

* update contributing

* adjust example

* fix duplicate doc handling for custom index

* Add latest docstring and tutorial changes

* fix some ORM issues. fix get_all_labels_aggregated.

* update drop flags where get_all_labels_aggregated() was used before

* Add latest docstring and tutorial changes

* add to_json(). add + fix tests

* fix no_answer handling in label / multilabel

* fix duplicate docs in memory doc store. change primary key for sql doc table

* fix mypy issues

* fix mypy issues

* haystack/retriever/base.py

* fix test_write_document_meta[elastic]

* fix test_elasticsearch_custom_fields

* fix test_labels[elastic]

* fix crawler

* fix converter

* fix docx converter

* fix preprocessor

* fix test_utils

* fix tfidf retriever. fix selection of docstore in tests with multiple fixtures / parameterizations

* Add latest docstring and tutorial changes

* fix crawler test. fix ocrconverter attribute

* fix test_elasticsearch_custom_query

* fix generator pipeline

* fix ocr converter

* fix ragenerator

* Add latest docstring and tutorial changes

* fix test_load_and_save_yaml for elasticsearch

* fixes for pipeline tests

* fix faq pipeline

* fix pipeline tests

* Add latest docstring and tutorial changes

* Add MultimodalRetriever

* Add latest docstring and tutorial changes

* fix weaviate

* Add latest docstring and tutorial changes

* trigger CI

* satisfy mypy

* Add latest docstring and tutorial changes

* satisfy mypy

* Add latest docstring and tutorial changes

* trigger CI

* fix question generation test

* fix ray. fix Q-generation

* fix translator test

* satisfy mypy

* wip refactor feedback rest api

* fix rest api feedback endpoint

* fix doc classifier

* remove relation of Labels -> Docs in SQL ORM

* fix faiss/milvus tests

* fix doc classifier test

* fix eval test

* fixing eval issues

* Add latest docstring and tutorial changes

* fix mypy

* WIP replace dataclasses-json with manual serialization

* Add methods to MultimodalRetriever

* Add latest docstring and tutorial changes

* revert to dataclass-json serialization for now. remove debug prints.

* update docstrings

* fix extractor. fix Answer Span init

* fix api test

* keep meta data of answers in reader.run()

* fix meta handling

* adress review feedback

* Add latest docstring and tutorial changes

* make document=None for open domain labels

* add import

* fix print utils

* fix rest api

* Add methods and tests

* Add latest docstring and tutorial changes

* Fix mypy

* Add latest docstring and tutorial changes

* Add type hints and doc strings

* Make use of initialize_device_settings

* Move serialization of pd.DataFrame to schema.py

* Fix mypy

* Adapt Document's from_dict method

* Update docstrings

* Add latest docstring and tutorial changes

* Fix mypy

* Fix mypy

* Fix Document's from_dict method

* Fix Document's to_dict method

* Change handling of table metadata

* Add latest docstring and tutorial changes

* Change naming from Multimodal to TableText

* Turn off tokenizers_parallelism in retriever tests

* Add latest docstring and tutorial changes

* Remove turning off tokenizers_parallelism in retriever tests

* Adapt convert_es_hit_to_document

* Change embed_surrounding_context to embed_meta_fields

* Add latest docstring and tutorial changes

* Add check if torch.distributed is available

* Set n_gpu to 0 in training test

* Set HIP_LAUNCH_BLOCKING to 1

* Set HIP_LAUNCH_BLOCKING to "1"

* Set use_gpu to False

* Use DataParallel only if more than one device

* Remove --find-links=https://download.pytorch.org/whl/torch_stable.html

Co-authored-by: Malte Pietsch <malte.pietsch@deepset.ai>
Co-authored-by: Markus Paff <markuspaff.mp@gmail.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-10-25 12:27:02 +02:00
Lalit Pagaria
5dbd899a93
Experimental changes to support Milvus 2.x (#1473)
* Experimental changes to support Milvus 2.x

* Milvus 2.0 need other containers hence adding them

* Add latest docstring and tutorial changes

* Fixing tests

* Correcting use of list collections

* correcting connection close

* Removing connection close logic

* removing flush

* using collection instead of connection

* fixing describe collection

* Fixing insert, query and search based on new signature

* Making mypy happy

* Fixing one test case

* Fixing search and embedding fetch based on newer api

* Implementing delete vector id function

* Wrapping up final changes

* Add latest docstring and tutorial changes

* Correcting requirements.txt

* removing empty line in requirements.txt

* add docstring and exception for delete

* add docstring. condition import on env var. raise exception for deletion

* fix typo

* change delete signature

* ignore typing for import

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Malte Pietsch <malte.pietsch@deepset.ai>
2021-10-25 10:39:48 +02:00
Julian Risch
9de140110f
Use smaller model for one generator test case (#1622)
* Use smaller model for one generator test case

* Reduce max_length of generated sequences in tests
2021-10-20 17:57:15 +02:00
Julian Risch
4ed2b90bca
Add delete_labels() except for weaviate doc store (#1604)
* Add delete_labels() except for weaviate doc store

* Add latest docstring and tutorial changes

* Add test for delete_labels()

* Adapt filter for label deletion to different doc stores in test

* Allow delete labels by _id in elasticsearch

* Add latest docstring and tutorial changes

* Add latest docstring and tutorial changes

* re-add bugfix after merge

* Add ids as optional parameter

* Add latest docstring and tutorial changes

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-10-19 17:20:28 +02:00
Sara Zan
96c05c34e4
Pipeline node names validation (#1601)
* Add node names validation

* Add tests

* Improve test and test that params exists before validating

* Fix the REST API

* Use minilm-uncased-squad2 instead of roberta-base-squad2

* Use roberta model for test_pipeline.yaml

* Turn off TOKENIZERS_PARALLELISM in generator tests (#1605)

* Account for non-targeted parameters

* Restore previous parameters handling in the rest api

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Julian Risch <julian.risch@deepset.ai>
2021-10-19 15:22:44 +02:00
Malte Pietsch
3a7d029fdd
Fix Opensearch field type (flattened -> nested) (#1609)
* fix field type flattened -> nested. change default port from 9201 to 9200

* change port in benchmarks
2021-10-19 14:40:53 +02:00
Sara Zan
575e64333c
Delete documents by ID in all document stores (#1606)
* Modify BaseDocumentStore.delete_documents() signature, implement ElasticSearch, and add tests

* Add implementation for InMemory

* Implement for SQL, FAISS and Milvus too

* Add tests for faiss and milvus

* Fix delete_all_documents

* Implement deletion by ID for weaviate

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

Co-authored-by: sarthakj2109 <54064348+sarthakj2109@users.noreply.github.com>

Co-authored-by: prafgup <prafulgupta6@gmail.com>

Co-authored-by: ankh6 <andynzemokalumu@live.be>
2021-10-19 12:30:15 +02:00