v0.6.0-alpha

What's Changed

• Add literature review module and citation screening functionality (#171) by @WojciechKusa in #172
• Improve document search by adding available search engines to the database by @WojciechKusa in #173
• Refactor literature review database by @WojciechKusa in #174
• Add option to delete literature review by @WojciechKusa in #175
• Add automatic screening using prompt-based model predictions by @WojciechKusa in #176
• Implement papers import from bib file by @WojciechKusa in #177
• fix(google scholar): catch exception when not possible to import scholarly by @WojciechKusa in #178
• Test: update unit tests for literature review views by @WojciechKusa in #185
• Improve screening UI by @WojciechKusa in #186
• feat: add FAQ page by @WojciechKusa in #187
• Implement papers import from RIS files by @WojciechKusa in #189
• feat: prefill data from DB when editing screened review by @WojciechKusa in #190
• feat: add an infobox when user creates an account with the purpose of the data collection by @WojciechKusa in #191
• test(citation screening): fix base template path by @WojciechKusa in #197
• build(requirements): update Django and PyTorch by @WojciechKusa in #196
• feat(pubmed search): add search in PubMed using Entrez by @WojciechKusa in #194
• feat(ui): add app version to about page by @WojciechKusa in #199
• refactor: split literature review and citation screening apps by @WojciechKusa in #200
• feat(literature review): implement adding and removing users from review by @WojciechKusa in #201
• feat(citation screening): distribute screening tasks between reviewers by @WojciechKusa in #206
• feat(citation screening): multi-user screening with distributed tasks by @WojciechKusa in #208
• fix(screening): correctly filter tasks by id by @WojciechKusa in #209
• feat(review): add review types: review and annotation by @WojciechKusa in #210
• docs: update README.md by @WojciechKusa in #215
• feat: update new literature review form by @WojciechKusa in #216
• Update LICENSE by @WojciechKusa in #218
• v0.6.0 by @WojciechKusa in #217

Full Changelog: v0.4.0...v0.6.0

v0.5.0-alpha

What's Changed

Literature reviews module:

• feat(literature review): connects literature review with user
• feat(literature review): display all literature reviews in table
• feat(literature review): add main literature review subpage
• feat(literature review): add review fields, on save search semantic scholar
• feat(literature review): register models in django admin
• feat(literature review): add new django project with database routers
• feat(literature review): create review detailed page
• feat(literature review): add option for selecting search engines while creating new review
• feat(literature review): add option to screen any paper from the list
• feat(review search): add top_k parameter while creating review
• refactor(literature review): remove old sqlite connection code
• fix(literature review): always enable review details page button
• feat(literature review): allow for sorting the table with papers
• feat(literature review): display number of citations per paper
• feat(literature review): relax requirements on field names while creating new review
• feat(literature review): google scholar added to available search engines for literature review
• fix(literature review): remove unused favicons
• feat(literature review): update UI of screening and review display pages
• feat(literature review): update database models with new fields
• feat(seed studies): user can add seed studies to review from pdf URLs
• feat(literature review): add option for editing literature review parameters
• feat(literature review): merge papers based on the title
• fix(literature review): add review id to results export
• feat(literature review): add link to my reviews to the header
• feat(literature review): fix type mismatch when creating new review
• fix(literature review): remove duplicated key when deduplicating

Citation screening

• feat(citation screening): add new option to citation screening
• feat(citation screening): measure time spent on screening
• refactor(citation screening): refactor screen_papers()
• feat(citation screening): update results export with more fields
• refactor(citation screening): refactor with sourcery
• feat(citation screening): enable exporting screening results to json
• feat(citation screening): display decision count
• feat(citation screening): implement initial title and abstract screening
• feat(citation screening): add citation screening project stub
• docs(citation screening): add django project template
• docs(citation screening): add simple screening django model
• fix(citation screening): descriptive reason field made optional
• fix(citation screening): fix missing time in context data for screening papers
• fix(citation screening): update screening interface according to comments from Georgios
• feat(citation screening): update screening interface according to comments from Georgios
• docs(citation screening): add documentation to citation screening forms
• feat(citation screening): display asterisk for required elements during screening
• feat(citation screening): update citation screening page UI
• fix(citation screening): fix DOI display during screening
• fix(citation screening): fix ambiguity with questions about prior knowledge of paper/authors

Automatic citation screening

• feat(automatic classification): users can add new classifiers to the review
• feat(automatic classification): add document_classification models to django admin
• feat(automatic classification): add document_classification urls
• feat(automatic classification): update django settings.py with new apps
• feat(automatic classification): add ML algorithm registry
• test(automatic classification): add classifier and registry tests
• feat(automatic classification): add dummy classification algorithm
• feat(automatic classification): add base algorithm class and fasttext implementation
• feat(automatic classification): add views and serializers for ml algorithms
• feat(automatic classification): add django models for document classification
• feat(document screening): add can_screen_automatically flag
• feat(automatic classification): add django app template
• feat(automatic classification): update classifiers, automatic screening works with fasttext
• feat(automatic classification): automatic screening works with dummy model on review data
• feat(document classification): 'maybe' decisions treated as 'yes' for training model
• feat(document classification): improve fasttext classifier
• feat(document classification): fix import in document classification
• refactor(document classification): remove unused PredictView

Organisations:

• feat(organisations): display all reviews from organisation
• feat(organisations): enable adding reviews to organisation
• feat(organisations): adding/removing member and deleting organisation requires permissions
• feat(organisations): enable permissions for editing and viewing organisations
• feat(organisations): display user organisations on user profile page
• feat(organisations): filter users part of organisation
• feat(organisations): implement remove organisation and member delete
• feat(organisations): implement removing user from organisation
• feat(organisations): display organisation details
• feat(organisations): admin can create new organisation
• feat(organisations): create organisations django app with db model

Document search

• fix(CORE search): fix URL in CORE search API call
• feat(CORE search): add CORE API search function
• feat(search): update aminer search with new fields
• docs(SemanticScholar search): update type annotations
• feat(SemanticScholar search): add function for searching with S2 API
• fix(search documents): remove checkbox for searching with taxonomies
• fix(search results): if abstract not available display only snippet
• feat(google scholar): add script for searching GS with scholarly
• fix(search): fix order of search request
• feat(search): speed up search by naive concurrency
• fix(google scholar): fix publication date in google scholar search
• fix(google scholar): fix google scholar publication date type
• feat(document search): rename internal search function to search_cruise

Taxonomy search

• feat(CSO classifier): add CSO classifier for single article
• fix(CSO classifier): fix keywords parameter in CSO classifier
• feat(CSO classifier search): CSO classifier API works on both titles and abstracts
• feat(CSO classifier): CSO concepts are classified only after clicking 'CSO keywords' button
• feat(CSO concepts): CSO concepts for empty docs classified on page load
• feat(search): disable taxonomy search

Database

• feat(postgresql): add django database configuration with postgresql
• feat(postgresql): add readme and requirements for running postgresql database

Front-end

• feat(frontend): add item in navbar with link to user profile
• feat(pdf icon): add pdf icon
• feat(frontend): display new fields on the result page
• fix(UI): change height of main page so it fits into screen without scrolling
• feat(favicon): add cruise favicon
• fix(UI): hide my reviews for non authenticated users

Other

• feat(article): add DOI to article class, update search functions accordingly
• fix(users): add login required to user_profile view
• feat(utils): add Author dataclass, update Article fields
• fix(imports): fix relative package imports

Full Changelog: ProjectDossier/cruise-literature@v0.4.0...v0.5.0

v0.4.0-alpha

What's Changed

New features

• feat(search): replacing pyterrier by elastic search indices by @ospitia in https://github.com/ProjectDossier/cruise-literature/pull/127
• feat(display results): add two buttons to hide abstract and keywords by @WojciechKusa in https://github.com/ProjectDossier/cruise-literature/pull/124
• feat(backend): improve backend search by @WojciechKusa in https://github.com/ProjectDossier/cruise-literature/pull/132
• feat(concepts): Concept display by @ospitia in https://github.com/ProjectDossier/cruise-literature/pull/121
• feat(taxonomy): taxonomy search separated from the document search by @WojciechKusa in https://github.com/ProjectDossier/cruise-literature/pull/137
• feat(search): add CORE and SemanticScholar search API connection, parallelise search by @WojciechKusa in https://github.com/ProjectDossier/cruise-literature/pull/152

Bug fixes

• fix: Avoiding loading models and embeddings to the GPU by default by @ospitia in https://github.com/ProjectDossier/cruise-literature/pull/128
• fix(add docs): show max docs in add with tqdm by @WojciechKusa in https://github.com/ProjectDossier/cruise-literature/pull/122
• fix: Delete src/dossier_search directory by @WojciechKusa in https://github.com/ProjectDossier/cruise-literature/pull/145
• fix: collection updates by @ospitia in https://github.com/ProjectDossier/cruise-literature/pull/134
• fix: missing imports from last merge by @ospitia in https://github.com/ProjectDossier/cruise-literature/pull/147
• fix: limit elastic search memory usage by @ospitia in https://github.com/ProjectDossier/cruise-literature/pull/133

Refactoring

• refactor: cleanup code from old files by @WojciechKusa in https://github.com/ProjectDossier/cruise-literature/pull/125
• refactor: rename django project to cruise_literature by @WojciechKusa in https://github.com/ProjectDossier/cruise-literature/pull/126

Documentation

• Create CODEOWNERS by @WojciechKusa in https://github.com/ProjectDossier/cruise-literature/pull/123
• Update README.md by @AyahSoufan in https://github.com/ProjectDossier/cruise-literature/pull/131, https://github.com/ProjectDossier/cruise-literature/pull/140, https://github.com/ProjectDossier/cruise-literature/pull/141 and https://github.com/ProjectDossier/cruise-literature/pull/139

New Contributors

• @AyahSoufan made their first contribution in https://github.com/ProjectDossier/cruise-literature/pull/131

Full Changelog: ProjectDossier/cruise-literature@v0.3.0...v0.4.0

1st cruise-dev workshop

Backend search highlight 003 (#45)

* feat: update search_app.py for highlight (initial update).

* highlight sentences based on lexical matches with queries

* fix: lowercase added. snippet is taken from highlighted abstract

* fix: balanced highlight tag for snippet

Co-authored-by: Tobias Fink <[email protected]>