From c0264fe2a46700886d05f69dfaf39482e43b7c86 Mon Sep 17 00:00:00 2001 From: ArturOle Date: Tue, 22 Oct 2024 12:03:57 +0200 Subject: [PATCH 01/33] make file and poetry build --- makefile | 46 + poetry.lock | 3036 ++++++++++++++++++++++++++++++++++++++++++++++++ pyproject.toml | 40 +- 3 files changed, 3111 insertions(+), 11 deletions(-) create mode 100644 makefile create mode 100644 poetry.lock diff --git a/makefile b/makefile new file mode 100644 index 0000000..c100106 --- /dev/null +++ b/makefile @@ -0,0 +1,46 @@ +# Use Poetry for dependency management and running tasks + +# Target to install dependencies +install: + poetry install + +# Target to update dependencies +update: + poetry update + +# Target to run tests (assuming you use pytest) +test: + poetry run pytest + +# Target to export requirements.txt for compatibility +requirements: + poetry export -f requirements.txt --output requirements/base.txt --without-hashes + +# Target to run linting (assuming you use flake8) +lint: + 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text = ["GPL-3.0"], file = "LICENSE" } +license = "GPL-3.0" readme = "README.md" keywords = ["semantic search", "ocr", "rag", "document-embedding", "contextual-search", "retrieval-augmented-generation", "pdf"] -dynamic = ["dependencies"] +packages = [{include = "context_search", from="src"}] -[build-system] -requires = ["setuptools>=42", "wheel"] -build-backend = "setuptools.build_meta" +[tool.poetry.dependencies] +python = "^3.10" +neo4j = "^5.25.0" +pdf2image = "^1.17.0" +pydantic = "^2.9.2" +PyMuPDF = "^1.24.10" +pytesseract = "^0.3.13" +pytextrank = "^3.3.0" +spacy = "^3.8.2" +tqdm = "^4.66.5" +transformers = "^4.45.1" +numpy = "^2.0.2" +torch = { version = "^2.3.1", source = "torch"} + +[tool.poetry.dev-dependencies] +pytest = "^8.3.2" +pytest-mock = "^3.14.0" +pytest-cov = "^5.0.0" -[tool.setuptools.dynamic] -dependencies = {file = ["requirements\base.txt"]} +[[tool.poetry.source]] +name = "torch" +url = "https://download.pytorch.org/whl/cpu" +secondary = true -[tool.setuptools.packages.find] -where = ["src"] +[build-system] +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" From 029189ca002c9147b026c42953862cc565832172 Mon Sep 17 00:00:00 2001 From: ArturOle Date: Tue, 22 Oct 2024 12:26:56 +0200 Subject: [PATCH 02/33] modification of dockerfiles --- docker/build_dev/dockerfile | 4 +--- docker/integration_tests/dockerfile | 5 +---- docker/unit_tests/dockerfile | 5 +---- pyproject.toml | 1 + 4 files changed, 4 insertions(+), 11 deletions(-) diff --git a/docker/build_dev/dockerfile b/docker/build_dev/dockerfile index a9c5e1d..100ee27 100644 --- a/docker/build_dev/dockerfile +++ b/docker/build_dev/dockerfile @@ -6,9 +6,7 @@ CMD ["bash"] RUN apt-get update RUN apt-get install -y python3 python3-pip -RUN pip3 install torch --index-url https://download.pytorch.org/whl/cpu -COPY ./requirements /ragger/requirements WORKDIR /ragger -RUN pip install -r requirements/test.txt +RUN make install COPY . /ragger diff --git a/docker/integration_tests/dockerfile b/docker/integration_tests/dockerfile index 4dca895..bacf0be 100644 --- a/docker/integration_tests/dockerfile +++ b/docker/integration_tests/dockerfile @@ -12,13 +12,10 @@ RUN apt install -y tesseract-ocr RUN apt install -y libtesseract-dev RUN apt install -y poppler-utils -COPY ./requirements /ragger/requirements WORKDIR /ragger RUN pip install --upgrade pip -RUN pip install -r requirements/test.txt -RUN python3 -m spacy download en_core_web_sm COPY . /ragger RUN touch logs.log -RUN pip install . +RUN make install RUN export GIT_PYTHON_GIT_EXECUTABLE=$(which git) diff --git a/docker/unit_tests/dockerfile b/docker/unit_tests/dockerfile index 8a23a2a..c227b76 100644 --- a/docker/unit_tests/dockerfile +++ b/docker/unit_tests/dockerfile @@ -11,13 +11,10 @@ RUN apt install -y tesseract-ocr RUN apt install -y libtesseract-dev RUN apt install -y poppler-utils -COPY ./requirements /ragger/requirements WORKDIR /ragger RUN pip install --upgrade pip -RUN pip install -r requirements/test.txt -RUN python3 -m spacy download en_core_web_sm COPY . /ragger RUN touch logs.log -RUN pip install . +RUN make install RUN export GIT_PYTHON_GIT_EXECUTABLE=$(which git) diff --git a/pyproject.toml b/pyproject.toml index 8f4a058..4de0f9b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,6 +23,7 @@ tqdm = "^4.66.5" transformers = "^4.45.1" numpy = "^2.0.2" torch = { version = "^2.3.1", source = "torch"} +it_core_news_sm = {url = "https://github.com/explosion/spacy-models/releases/download/it_core_news_sm-3.5.0/it_core_news_sm-3.5.0.tar.gz"} [tool.poetry.dev-dependencies] pytest = "^8.3.2" From e6450a750ce498efb47d72c4e81a2ffc53b64c0a Mon Sep 17 00:00:00 2001 From: ArturOle Date: Tue, 22 Oct 2024 12:52:13 +0200 Subject: [PATCH 03/33] Correction of dockerfiles --- docker/build_dev/dockerfile | 3 ++- docker/integration_tests/dockerfile | 1 + docker/unit_tests/dockerfile | 2 +- 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/docker/build_dev/dockerfile b/docker/build_dev/dockerfile index 100ee27..0efc616 100644 --- a/docker/build_dev/dockerfile +++ b/docker/build_dev/dockerfile @@ -6,7 +6,8 @@ CMD ["bash"] RUN apt-get update RUN apt-get install -y python3 python3-pip +RUN curl -sSL https://install.python-poetry.org | python3 - WORKDIR /ragger -RUN make install COPY . /ragger +RUN make install \ No newline at end of file diff --git a/docker/integration_tests/dockerfile b/docker/integration_tests/dockerfile index bacf0be..401167c 100644 --- a/docker/integration_tests/dockerfile +++ b/docker/integration_tests/dockerfile @@ -6,6 +6,7 @@ CMD ["bash"] RUN apt-get update --fix-missing RUN apt-get install -y python3 python3-pip git ca-certificates lsb-release ubuntu-keyring software-properties-common +RUN curl -sSL https://install.python-poetry.org | python3 - RUN update-ca-certificates --fresh RUN export SSL_CERT_DIR=/etc/ssl/certs RUN apt install -y tesseract-ocr diff --git a/docker/unit_tests/dockerfile b/docker/unit_tests/dockerfile index c227b76..df0569d 100644 --- a/docker/unit_tests/dockerfile +++ b/docker/unit_tests/dockerfile @@ -6,7 +6,7 @@ CMD ["bash"] RUN apt-get update RUN apt-get install -y python3 python3-pip git -RUN pip3 install torch --index-url https://download.pytorch.org/whl/cpu +RUN curl -sSL https://install.python-poetry.org | python3 - RUN apt install -y tesseract-ocr RUN apt install -y libtesseract-dev RUN apt install -y poppler-utils From 4df056ed5db3fcb2ad8bcbcf7dc45b00ffc9fc70 Mon Sep 17 00:00:00 2001 From: ArturOle Date: Tue, 22 Oct 2024 13:07:07 +0200 Subject: [PATCH 04/33] Adding curl to dockerfiles --- docker/build_dev/dockerfile | 2 +- docker/integration_tests/dockerfile | 2 +- docker/unit_tests/dockerfile | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docker/build_dev/dockerfile b/docker/build_dev/dockerfile index 0efc616..7c8f4e7 100644 --- a/docker/build_dev/dockerfile +++ b/docker/build_dev/dockerfile @@ -5,7 +5,7 @@ ENV DEBIAN_FRONTEND=noninteractive CMD ["bash"] RUN apt-get update -RUN apt-get install -y python3 python3-pip +RUN apt-get install -y python3 python3-pip curl RUN curl -sSL https://install.python-poetry.org | python3 - WORKDIR /ragger diff --git a/docker/integration_tests/dockerfile b/docker/integration_tests/dockerfile index 401167c..13816cd 100644 --- a/docker/integration_tests/dockerfile +++ b/docker/integration_tests/dockerfile @@ -5,7 +5,7 @@ ENV DEBIAN_FRONTEND=noninteractive CMD ["bash"] RUN apt-get update --fix-missing -RUN apt-get install -y python3 python3-pip git ca-certificates lsb-release ubuntu-keyring software-properties-common +RUN apt-get install -y python3 python3-pip git ca-certificates lsb-release ubuntu-keyring software-properties-common curl RUN curl -sSL https://install.python-poetry.org | python3 - RUN update-ca-certificates --fresh RUN export SSL_CERT_DIR=/etc/ssl/certs diff --git a/docker/unit_tests/dockerfile b/docker/unit_tests/dockerfile index df0569d..4c1842e 100644 --- a/docker/unit_tests/dockerfile +++ b/docker/unit_tests/dockerfile @@ -5,7 +5,7 @@ ENV DEBIAN_FRONTEND=noninteractive CMD ["bash"] RUN apt-get update -RUN apt-get install -y python3 python3-pip git +RUN apt-get install -y python3 python3-pip git curl RUN curl -sSL https://install.python-poetry.org | python3 - RUN apt install -y tesseract-ocr RUN apt install -y libtesseract-dev From 2da631290cee5db7435f2473767ecc9a96d30523 Mon Sep 17 00:00:00 2001 From: ArturOle Date: Tue, 22 Oct 2024 13:10:40 +0200 Subject: [PATCH 05/33] Adding poetry to the PATH --- docker/build_dev/dockerfile | 1 + docker/integration_tests/dockerfile | 2 ++ docker/unit_tests/dockerfile | 1 + 3 files changed, 4 insertions(+) diff --git a/docker/build_dev/dockerfile b/docker/build_dev/dockerfile index 7c8f4e7..66b7e9a 100644 --- a/docker/build_dev/dockerfile +++ b/docker/build_dev/dockerfile @@ -7,6 +7,7 @@ CMD ["bash"] RUN apt-get update RUN apt-get install -y python3 python3-pip curl RUN curl -sSL https://install.python-poetry.org | python3 - +RUN export PATH="/root/.local/bin:$PATH" WORKDIR /ragger COPY . /ragger diff --git a/docker/integration_tests/dockerfile b/docker/integration_tests/dockerfile index 13816cd..131fed0 100644 --- a/docker/integration_tests/dockerfile +++ b/docker/integration_tests/dockerfile @@ -7,6 +7,8 @@ CMD ["bash"] RUN apt-get update --fix-missing RUN apt-get install -y python3 python3-pip git ca-certificates lsb-release ubuntu-keyring software-properties-common curl RUN curl -sSL https://install.python-poetry.org | python3 - +RUN export PATH="/root/.local/bin:$PATH" + RUN update-ca-certificates --fresh RUN export SSL_CERT_DIR=/etc/ssl/certs RUN apt install -y tesseract-ocr diff --git a/docker/unit_tests/dockerfile b/docker/unit_tests/dockerfile index 4c1842e..f63ed5a 100644 --- a/docker/unit_tests/dockerfile +++ b/docker/unit_tests/dockerfile @@ -7,6 +7,7 @@ CMD ["bash"] RUN apt-get update RUN apt-get install -y python3 python3-pip git curl RUN curl -sSL https://install.python-poetry.org | python3 - +RUN export PATH="/root/.local/bin:$PATH" RUN apt install -y tesseract-ocr RUN apt install -y libtesseract-dev RUN apt install -y poppler-utils From bb64db80e646d8b33a338b52b1ced023f13bc947 Mon Sep 17 00:00:00 2001 From: ArturOle Date: Tue, 22 Oct 2024 13:16:51 +0200 Subject: [PATCH 06/33] Using Docker's ENV for env var passing --- docker/build_dev/dockerfile | 2 +- docker/integration_tests/dockerfile | 2 +- docker/unit_tests/dockerfile | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docker/build_dev/dockerfile b/docker/build_dev/dockerfile index 66b7e9a..e189899 100644 --- a/docker/build_dev/dockerfile +++ b/docker/build_dev/dockerfile @@ -7,7 +7,7 @@ CMD ["bash"] RUN apt-get update RUN apt-get install -y python3 python3-pip curl RUN curl -sSL https://install.python-poetry.org | python3 - -RUN export PATH="/root/.local/bin:$PATH" +ENV PATH="/opt/gtk/bin:$PATH" WORKDIR /ragger COPY . /ragger diff --git a/docker/integration_tests/dockerfile b/docker/integration_tests/dockerfile index 131fed0..e742fd2 100644 --- a/docker/integration_tests/dockerfile +++ b/docker/integration_tests/dockerfile @@ -7,7 +7,7 @@ CMD ["bash"] RUN apt-get update --fix-missing RUN apt-get install -y python3 python3-pip git ca-certificates lsb-release ubuntu-keyring software-properties-common curl RUN curl -sSL https://install.python-poetry.org | python3 - -RUN export PATH="/root/.local/bin:$PATH" +ENV PATH="/opt/gtk/bin:$PATH" RUN update-ca-certificates --fresh RUN export SSL_CERT_DIR=/etc/ssl/certs diff --git a/docker/unit_tests/dockerfile b/docker/unit_tests/dockerfile index f63ed5a..2788eb6 100644 --- a/docker/unit_tests/dockerfile +++ b/docker/unit_tests/dockerfile @@ -7,7 +7,7 @@ CMD ["bash"] RUN apt-get update RUN apt-get install -y python3 python3-pip git curl RUN curl -sSL https://install.python-poetry.org | python3 - -RUN export PATH="/root/.local/bin:$PATH" +ENV PATH="/opt/gtk/bin:$PATH" RUN apt install -y tesseract-ocr RUN apt install -y libtesseract-dev RUN apt install -y poppler-utils From ec482e4d45857743fba6c2099d15b4f7ac474dce Mon Sep 17 00:00:00 2001 From: ArturOle Date: Tue, 22 Oct 2024 13:20:23 +0200 Subject: [PATCH 07/33] path correction --- docker/build_dev/dockerfile | 2 +- docker/integration_tests/dockerfile | 2 +- docker/unit_tests/dockerfile | 3 ++- 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/docker/build_dev/dockerfile b/docker/build_dev/dockerfile index e189899..72733b3 100644 --- a/docker/build_dev/dockerfile +++ b/docker/build_dev/dockerfile @@ -7,7 +7,7 @@ CMD ["bash"] RUN apt-get update RUN apt-get install -y python3 python3-pip curl RUN curl -sSL https://install.python-poetry.org | python3 - -ENV PATH="/opt/gtk/bin:$PATH" +ENV PATH="/root/.local/bin:$PATH" WORKDIR /ragger COPY . /ragger diff --git a/docker/integration_tests/dockerfile b/docker/integration_tests/dockerfile index e742fd2..123c723 100644 --- a/docker/integration_tests/dockerfile +++ b/docker/integration_tests/dockerfile @@ -7,7 +7,7 @@ CMD ["bash"] RUN apt-get update --fix-missing RUN apt-get install -y python3 python3-pip git ca-certificates lsb-release ubuntu-keyring software-properties-common curl RUN curl -sSL https://install.python-poetry.org | python3 - -ENV PATH="/opt/gtk/bin:$PATH" +ENV PATH="/root/.local/bin:$PATH" RUN update-ca-certificates --fresh RUN export SSL_CERT_DIR=/etc/ssl/certs diff --git a/docker/unit_tests/dockerfile b/docker/unit_tests/dockerfile index 2788eb6..5369f08 100644 --- a/docker/unit_tests/dockerfile +++ b/docker/unit_tests/dockerfile @@ -7,7 +7,8 @@ CMD ["bash"] RUN apt-get update RUN apt-get install -y python3 python3-pip git curl RUN curl -sSL https://install.python-poetry.org | python3 - -ENV PATH="/opt/gtk/bin:$PATH" +ENV PATH="/root/.local/bin:$PATH" + RUN apt install -y tesseract-ocr RUN apt install -y libtesseract-dev RUN apt install -y poppler-utils From 79b6d1c4b946dd37914df59cc4699cb4a74e561f Mon Sep 17 00:00:00 2001 From: ArturOle Date: Tue, 22 Oct 2024 13:31:26 +0200 Subject: [PATCH 08/33] ENV not executing, trying different ordering --- docker/build_dev/dockerfile | 3 ++- docker/integration_tests/dockerfile | 3 ++- docker/unit_tests/dockerfile | 3 ++- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/docker/build_dev/dockerfile b/docker/build_dev/dockerfile index 72733b3..4ea566c 100644 --- a/docker/build_dev/dockerfile +++ b/docker/build_dev/dockerfile @@ -1,13 +1,14 @@ FROM ubuntu:22.04 ENV DEBIAN_FRONTEND=noninteractive +ENV POETRY_HOME="/root/.poetry" +ENV PATH="$POETRY_HOME/bin:$PATH" CMD ["bash"] RUN apt-get update RUN apt-get install -y python3 python3-pip curl RUN curl -sSL https://install.python-poetry.org | python3 - -ENV PATH="/root/.local/bin:$PATH" WORKDIR /ragger COPY . /ragger diff --git a/docker/integration_tests/dockerfile b/docker/integration_tests/dockerfile index 123c723..09c9bb8 100644 --- a/docker/integration_tests/dockerfile +++ b/docker/integration_tests/dockerfile @@ -1,13 +1,14 @@ FROM ubuntu:22.04 ENV DEBIAN_FRONTEND=noninteractive +ENV POETRY_HOME="/root/.poetry" +ENV PATH="$POETRY_HOME/bin:$PATH" CMD ["bash"] RUN apt-get update --fix-missing RUN apt-get install -y python3 python3-pip git ca-certificates lsb-release ubuntu-keyring software-properties-common curl RUN curl -sSL https://install.python-poetry.org | python3 - -ENV PATH="/root/.local/bin:$PATH" RUN update-ca-certificates --fresh RUN export SSL_CERT_DIR=/etc/ssl/certs diff --git a/docker/unit_tests/dockerfile b/docker/unit_tests/dockerfile index 5369f08..d88a6b5 100644 --- a/docker/unit_tests/dockerfile +++ b/docker/unit_tests/dockerfile @@ -1,13 +1,14 @@ FROM ubuntu:22.04 ENV DEBIAN_FRONTEND=noninteractive +ENV POETRY_HOME="/root/.poetry" +ENV PATH="$POETRY_HOME/bin:$PATH" CMD ["bash"] RUN apt-get update RUN apt-get install -y python3 python3-pip git curl RUN curl -sSL https://install.python-poetry.org | python3 - -ENV PATH="/root/.local/bin:$PATH" RUN apt install -y tesseract-ocr RUN apt install -y libtesseract-dev From 36461a3da6966b1b347a535ef231ce54c55d5858 Mon Sep 17 00:00:00 2001 From: ArturOle Date: Tue, 22 Oct 2024 13:43:27 +0200 Subject: [PATCH 09/33] Correction of poetry build --- poetry.lock | 16 +++++++++++++++- pyproject.toml | 4 ++-- 2 files changed, 17 insertions(+), 3 deletions(-) diff --git a/poetry.lock b/poetry.lock index 6cc983f..dc8cee7 100644 --- a/poetry.lock +++ b/poetry.lock @@ -484,6 +484,20 @@ files = [ {file = "cymem-2.0.8.tar.gz", hash = "sha256:8fb09d222e21dcf1c7e907dc85cf74501d4cea6c4ed4ac6c9e016f98fb59cbbf"}, ] +[[package]] +name = "en_core_web_sm" +version = "3.8.0" +description = "English pipeline optimized for CPU. Components: tok2vec, tagger, parser, senter, ner, attribute_ruler, lemmatizer." +optional = false +python-versions = "*" +files = [ + {file = "en_core_web_sm-3.8.0.tar.gz", hash = "sha256:14a2f31bc476af87019819ea8c9948fabdfd473a442edd6b1cba62bf0c2c0f55"}, +] + +[package.source] +type = "url" +url = "https://github.com/explosion/spacy-models/releases/download/en_core_web_sm-3.8.0/en_core_web_sm-3.8.0.tar.gz" + [[package]] name = "exceptiongroup" version = "1.2.2" @@ -3033,4 +3047,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = "^3.10" -content-hash = "e98de1bbd25f4d295f08d3088c26d8a4a8598b81f77f952e0d392264e6908341" +content-hash = "c22a6d58e82b390ccf486d9632768b0d6f074eb7a2c4ab12c6363977592b85aa" diff --git a/pyproject.toml b/pyproject.toml index 4de0f9b..7c3a248 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,7 +23,7 @@ tqdm = "^4.66.5" transformers = "^4.45.1" numpy = "^2.0.2" torch = { version = "^2.3.1", source = "torch"} -it_core_news_sm = {url = "https://github.com/explosion/spacy-models/releases/download/it_core_news_sm-3.5.0/it_core_news_sm-3.5.0.tar.gz"} +en_core_web_sm = {url = "https://github.com/explosion/spacy-models/releases/download/en_core_web_sm-3.8.0/en_core_web_sm-3.8.0.tar.gz"} [tool.poetry.dev-dependencies] pytest = "^8.3.2" @@ -33,7 +33,7 @@ pytest-cov = "^5.0.0" [[tool.poetry.source]] name = "torch" url = "https://download.pytorch.org/whl/cpu" -secondary = true +priority = "secondary" [build-system] requires = ["poetry-core>=1.0.0"] From cd922de2c3f5dc152f9ffd1d80796dcf0c590592 Mon Sep 17 00:00:00 2001 From: ArturOle Date: Tue, 22 Oct 2024 13:51:56 +0200 Subject: [PATCH 10/33] Changing execution of test --- docker/integration_tests/docker-compose.yml | 2 +- makefile | 7 +++---- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/docker/integration_tests/docker-compose.yml b/docker/integration_tests/docker-compose.yml index ca6c7a8..bedda72 100644 --- a/docker/integration_tests/docker-compose.yml +++ b/docker/integration_tests/docker-compose.yml @@ -23,5 +23,5 @@ services: environment: - SSL_CERT_DIR=/etc/ssl/certs command: > - bash -c "python3 -m pytest ./test/integration_tests || exit 1" + bash -c "make test ./test/integration_tests || exit 1" && docker-compose down diff --git a/makefile b/makefile index c100106..1055203 100644 --- a/makefile +++ b/makefile @@ -8,7 +8,7 @@ install: update: poetry update -# Target to run tests (assuming you use pytest) +# Target to run tests test: poetry run pytest @@ -16,12 +16,11 @@ test: requirements: poetry export -f requirements.txt --output requirements/base.txt --without-hashes -# Target to run linting (assuming you use flake8) +# Target to run linting lint: poetry run flake8 . -# Target to run the application (replace with your main script) -run: +# Target to run the application poetry run python src/main.py # Clean up cache files, etc. From cfa681938b4f661a61d051f318a6ffdd80573e04 Mon Sep 17 00:00:00 2001 From: ArturOle Date: Tue, 22 Oct 2024 13:56:27 +0200 Subject: [PATCH 11/33] Correction of docker compose for unit-tests --- docker/unit_tests/docker-compose.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/unit_tests/docker-compose.yml b/docker/unit_tests/docker-compose.yml index 3a08608..ba67690 100644 --- a/docker/unit_tests/docker-compose.yml +++ b/docker/unit_tests/docker-compose.yml @@ -6,5 +6,5 @@ services: dockerfile: docker/unit_tests/dockerfile container_name: ragger command: > - bash -c "python3 -m pytest ./test/unit_tests || exit 1" + bash -c "make test ./test/integration_tests || exit 1" && docker-compose down From 7b132db83850c62fc3f5d65159b0e0dae548725e Mon Sep 17 00:00:00 2001 From: ArturOle Date: Tue, 22 Oct 2024 14:12:24 +0200 Subject: [PATCH 12/33] Checking running poetry run pytest with directory --- docker/unit_tests/docker-compose.yml | 2 +- makefile | 5 ----- 2 files changed, 1 insertion(+), 6 deletions(-) diff --git a/docker/unit_tests/docker-compose.yml b/docker/unit_tests/docker-compose.yml index ba67690..2664dbb 100644 --- a/docker/unit_tests/docker-compose.yml +++ b/docker/unit_tests/docker-compose.yml @@ -6,5 +6,5 @@ services: dockerfile: docker/unit_tests/dockerfile container_name: ragger command: > - bash -c "make test ./test/integration_tests || exit 1" + bash -c "poetry run pytest ./test/integration_tests || exit 1" && docker-compose down diff --git a/makefile b/makefile index 1055203..9b7fce2 100644 --- a/makefile +++ b/makefile @@ -8,10 +8,6 @@ install: update: poetry update -# Target to run tests -test: - poetry run pytest - # Target to export requirements.txt for compatibility requirements: poetry export -f requirements.txt --output requirements/base.txt --without-hashes @@ -37,7 +33,6 @@ help: @echo "Available commands:" @echo " install Install project dependencies" @echo " update Update project dependencies" - @echo " test Run tests" @echo " requirements Export dependencies to requirements.txt" @echo " lint Run linting" @echo " run Run the application" From 0a38ed26735509f20dd6e2653863075cb8eec7bd Mon Sep 17 00:00:00 2001 From: ArturOle Date: Tue, 22 Oct 2024 14:17:52 +0200 Subject: [PATCH 13/33] Test path correction --- docker/integration_tests/docker-compose.yml | 2 +- docker/unit_tests/docker-compose.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docker/integration_tests/docker-compose.yml b/docker/integration_tests/docker-compose.yml index bedda72..703e67e 100644 --- a/docker/integration_tests/docker-compose.yml +++ b/docker/integration_tests/docker-compose.yml @@ -23,5 +23,5 @@ services: environment: - SSL_CERT_DIR=/etc/ssl/certs command: > - bash -c "make test ./test/integration_tests || exit 1" + bash -c "poetry run pytest ./test/integration_tests || exit 1" && docker-compose down diff --git a/docker/unit_tests/docker-compose.yml b/docker/unit_tests/docker-compose.yml index 2664dbb..a3402a7 100644 --- a/docker/unit_tests/docker-compose.yml +++ b/docker/unit_tests/docker-compose.yml @@ -6,5 +6,5 @@ services: dockerfile: docker/unit_tests/dockerfile container_name: ragger command: > - bash -c "poetry run pytest ./test/integration_tests || exit 1" + bash -c "poetry run pytest ./test/unit_tests || exit 1" && docker-compose down From fd41c46cffed5f33f715c8731e1c6f88f1e95212 Mon Sep 17 00:00:00 2001 From: ArturOle Date: Tue, 22 Oct 2024 14:24:51 +0200 Subject: [PATCH 14/33] deprecation correction --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 7c3a248..24ae880 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,7 +33,7 @@ pytest-cov = "^5.0.0" [[tool.poetry.source]] name = "torch" url = "https://download.pytorch.org/whl/cpu" -priority = "secondary" +priority = "supplemental" [build-system] requires = ["poetry-core>=1.0.0"] From 0ca69ab807816a358989d1679a683f5663a4af04 Mon Sep 17 00:00:00 2001 From: ArturOle Date: Tue, 22 Oct 2024 14:30:39 +0200 Subject: [PATCH 15/33] poetry lock update --- poetry.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/poetry.lock b/poetry.lock index dc8cee7..6767479 100644 --- a/poetry.lock +++ b/poetry.lock @@ -3047,4 +3047,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = "^3.10" -content-hash = "c22a6d58e82b390ccf486d9632768b0d6f074eb7a2c4ab12c6363977592b85aa" +content-hash = "c921953644a627375f053eed8bb7823aa2667a37f4795775c3e51c0d61579850" From 92f56a9d7bee99b3bf771892bcbf44f80d828945 Mon Sep 17 00:00:00 2001 From: ArturOle Date: Tue, 22 Oct 2024 15:22:31 +0200 Subject: [PATCH 16/33] Deletion of reqs dir --- requirements/base.txt | 13 ------------- requirements/test.txt | 4 ---- 2 files changed, 17 deletions(-) delete mode 100644 requirements/base.txt delete mode 100644 requirements/test.txt diff --git a/requirements/base.txt b/requirements/base.txt deleted file mode 100644 index 62a07ac..0000000 --- a/requirements/base.txt +++ /dev/null @@ -1,13 +0,0 @@ -neo4j==5.25.0 -pdf2image==1.17.0 -pydantic==2.9.2 -PyMuPDF==1.24.10 -pytesseract -pytextrank -spacy -tqdm -transformers==4.45.1 -numpy -scipy ---find-links https://download.pytorch.org/whl/torch_stable.html -torch==2.3.1+cpu \ No newline at end of file diff --git a/requirements/test.txt b/requirements/test.txt deleted file mode 100644 index 9927db3..0000000 --- a/requirements/test.txt +++ /dev/null @@ -1,4 +0,0 @@ --r base.txt -pytest >= 8.3.2 -pytest-mock -pytest-cov \ No newline at end of file From 77d0682efdf32cc3b357c00ad35f4af803203605 Mon Sep 17 00:00:00 2001 From: ArturOle Date: Sun, 27 Oct 2024 11:52:33 +0100 Subject: [PATCH 17/33] Deploy version for arm server deployment --- poetry.lock | 1621 +---------------- pyproject.toml | 3 - src/context_search/preprocessor/extractor.py | 14 +- .../preprocessor/preprocessor.py | 3 +- .../preprocessor_test/preprocessor_test.py | 9 +- .../literature_dataclass_test.py | 2 +- .../preprocessor_test/extractor_test.py | 16 - 7 files changed, 73 insertions(+), 1595 deletions(-) delete mode 100644 test/unit_tests/data_manager_test/preprocessor_test/extractor_test.py diff --git a/poetry.lock b/poetry.lock index 6767479..9fb64d4 100644 --- a/poetry.lock +++ b/poetry.lock @@ -11,76 +11,6 @@ files = [ {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, ] -[[package]] -name = "asttokens" -version = "2.4.1" -description = "Annotate AST trees with source code positions" -optional = false -python-versions = "*" -files = [ - {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"}, - {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"}, -] - 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self.nlp = spacy.load("en_core_web_sm") - self.nlp.add_pipe("textrank") + # self.nlp = spacy.load("en_core_web_sm") + # self.nlp.add_pipe("textrank") def extract_keywords(self, text_list: List[str]) -> list: ranked_phrases = [] - doc = self.nlp(''.join(text_list)) - for phrase in doc._.phrases: - ranked_phrases.append([phrase.text, phrase.rank]) + # # doc = self.nlp(''.join(text_list)) + # for phrase in doc._.phrases: + # ranked_phrases.append([phrase.text, phrase.rank]) return ranked_phrases diff --git a/src/context_search/preprocessor/preprocessor.py b/src/context_search/preprocessor/preprocessor.py index 888b710..fbf9a77 100644 --- a/src/context_search/preprocessor/preprocessor.py +++ b/src/context_search/preprocessor/preprocessor.py @@ -15,7 +15,8 @@ def __init__(self): self.splitter = TextSplitter( order="any", separators=['\.', '\n\n', '\n', '\s'], - is_separator_regex=True + is_separator_regex=True, + chunk_overlap=128 ) def process(self, literatures: list[LiteratureDTO]): diff --git a/test/integration_tests/data_manager_test/preprocessor_test/preprocessor_test.py b/test/integration_tests/data_manager_test/preprocessor_test/preprocessor_test.py index fb9e2e8..be727d0 100644 --- a/test/integration_tests/data_manager_test/preprocessor_test/preprocessor_test.py +++ b/test/integration_tests/data_manager_test/preprocessor_test/preprocessor_test.py @@ -3,7 +3,7 @@ from context_search.data_classes import LiteratureDTO import numpy as np import random -import pytest +import pytest # noqa: F401 random.seed(0) np.random.seed(0) @@ -23,13 +23,6 @@ def test_preprocessing_steps(): assert len(literature.chunks) == 1 assert literature.chunks[0].text == "This is a test text" assert literature.chunks[0].page_number == 0 - assert len(literature.tags) == 2 - assert literature.tags[0].text == "a test text" - assert pytest.approx(literature.tags[0].embeddings[:2], 1e-3) ==\ - [-0.23820725, -0.3175099] - assert literature.relation_weights[0].literature == "name" - assert literature.relation_weights[0].tag == "a test text" - assert literature.relation_weights[0].weight == 0.25 def test_multiple_file_processing(): diff --git a/test/unit_tests/data_manager_test/literature_dataclass_test.py b/test/unit_tests/data_manager_test/literature_dataclass_test.py index b79aed3..394711c 100644 --- a/test/unit_tests/data_manager_test/literature_dataclass_test.py +++ b/test/unit_tests/data_manager_test/literature_dataclass_test.py @@ -140,7 +140,7 @@ def test_literature_graph_creation_incorrect(): filepath=r'f:\ile\pat.h' ), chunks=[Chunk(text='text')], - tags=[Chunk(text='text')], # should be a list of Tag + tags=[Chunk(text='text')], # should be a list of Tag relation_weights=[RelationWeight( literature='literature', tag='tag', diff --git a/test/unit_tests/data_manager_test/preprocessor_test/extractor_test.py b/test/unit_tests/data_manager_test/preprocessor_test/extractor_test.py deleted file mode 100644 index 0294347..0000000 --- a/test/unit_tests/data_manager_test/preprocessor_test/extractor_test.py +++ /dev/null @@ -1,16 +0,0 @@ - -from context_search.preprocessor.extractor import Extractor - - -def test_extractor_extract_keywords(): - correct_ranks = [ - "a test text 0.25", - "This 0.0" - ] - extractor = Extractor() - text = "This is a test text. This is a test text. This is a test text." - ranks = extractor.extract_keywords(text) - - for i, rank in enumerate(ranks): - assert ' '.join((str(r) for r in rank)) == correct_ranks[i] - assert len(rank) == 2 From 96e7708cfaf9a9779e08c3e5a02c060b803f6a46 Mon Sep 17 00:00:00 2001 From: ArturOle Date: Sun, 27 Oct 2024 18:03:15 +0100 Subject: [PATCH 18/33] correcting indentation error --- src/context_search/preprocessor/extractor.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/context_search/preprocessor/extractor.py b/src/context_search/preprocessor/extractor.py index 163bf2d..7890e5b 100644 --- a/src/context_search/preprocessor/extractor.py +++ b/src/context_search/preprocessor/extractor.py @@ -9,8 +9,7 @@ class Extractor: def __init__(self): - # self.nlp = spacy.load("en_core_web_sm") - # self.nlp.add_pipe("textrank") + pass def extract_keywords(self, text_list: List[str]) -> list: ranked_phrases = [] From 8ab7ed2f657c065f2f31422c225306fab135bd93 Mon Sep 17 00:00:00 2001 From: ArturOle Date: Sun, 27 Oct 2024 18:10:11 +0100 Subject: [PATCH 19/33] Correcting text splitter parameters --- src/context_search/preprocessor/preprocessor.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/src/context_search/preprocessor/preprocessor.py b/src/context_search/preprocessor/preprocessor.py index fbf9a77..c10fef5 100644 --- a/src/context_search/preprocessor/preprocessor.py +++ b/src/context_search/preprocessor/preprocessor.py @@ -13,10 +13,12 @@ def __init__(self): self.embedder = Embedder() self.extractor = Extractor() self.splitter = TextSplitter( - order="any", - separators=['\.', '\n\n', '\n', '\s'], + order="sequential", + separators=['\n\n', '\n', '\.', '\s'], is_separator_regex=True, - chunk_overlap=128 + chunk_size=1024, + chunk_overlap=128, + margin=128 ) def process(self, literatures: list[LiteratureDTO]): From a40dd28ab96f258cae925e072ab465b7994fb4f7 Mon Sep 17 00:00:00 2001 From: ArturOle Date: Wed, 30 Oct 2024 10:11:57 +0100 Subject: [PATCH 20/33] Replacing pytorch and transformers with fastembed --- poetry.lock | 1100 ++++++++--------- pyproject.toml | 12 +- src/context_search/preprocessor/embedder.py | 46 +- .../preprocessor/preprocessor.py | 4 +- 4 files changed, 535 insertions(+), 627 deletions(-) diff --git a/poetry.lock b/poetry.lock index 9fb64d4..ae067c7 100644 --- a/poetry.lock +++ b/poetry.lock @@ -147,6 +147,23 @@ files = [ {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"}, ] +[[package]] +name = "coloredlogs" +version = "15.0.1" +description = "Colored terminal output for Python's logging module" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +files = [ + {file = "coloredlogs-15.0.1-py2.py3-none-any.whl", hash = "sha256:612ee75c546f53e92e70049c9dbfcc18c935a2b9a53b66085ce9ef6a6e5c0934"}, + {file = "coloredlogs-15.0.1.tar.gz", hash = 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["fugashi (>=1.0)", "ipadic (>=1.0.0,<2.0)", "rhoknp (>=1.1.0,<1.3.1)", "sudachidict-core (>=20220729)", "sudachipy (>=0.6.6)", "unidic (>=1.0.2)", "unidic-lite (>=1.0.7)"] -modelcreation = ["cookiecutter (==1.7.3)"] -natten = ["natten (>=0.14.6,<0.15.0)"] -onnx = ["onnxconverter-common", "onnxruntime (>=1.4.0)", "onnxruntime-tools (>=1.4.2)", "tf2onnx"] -onnxruntime = ["onnxruntime (>=1.4.0)", "onnxruntime-tools (>=1.4.2)"] -optuna = ["optuna"] -quality = ["GitPython (<3.1.19)", "datasets (!=2.5.0)", "isort (>=5.5.4)", "libcst", "rich", "ruff (==0.5.1)", "urllib3 (<2.0.0)"] -ray = ["ray[tune] (>=2.7.0)"] -retrieval = ["datasets (!=2.5.0)", "faiss-cpu"] -ruff = ["ruff (==0.5.1)"] -sagemaker = ["sagemaker (>=2.31.0)"] -sentencepiece = ["protobuf", "sentencepiece (>=0.1.91,!=0.1.92)"] -serving = ["fastapi", "pydantic", "starlette", "uvicorn"] -sigopt = ["sigopt"] -sklearn = ["scikit-learn"] -speech = ["kenlm", "librosa", "phonemizer", "pyctcdecode (>=0.4.0)", "torchaudio"] -testing = ["GitPython (<3.1.19)", "beautifulsoup4", "cookiecutter (==1.7.3)", "datasets (!=2.5.0)", "dill (<0.3.5)", "evaluate (>=0.2.0)", "faiss-cpu", "nltk (<=3.8.1)", "parameterized", "psutil", "pydantic", "pytest (>=7.2.0,<8.0.0)", "pytest-rich", "pytest-timeout", "pytest-xdist", "rjieba", "rouge-score (!=0.0.7,!=0.0.8,!=0.1,!=0.1.1)", "ruff (==0.5.1)", "sacrebleu (>=1.4.12,<2.0.0)", "sacremoses", "sentencepiece (>=0.1.91,!=0.1.92)", "tensorboard", "timeout-decorator"] -tf = ["keras-nlp (>=0.3.1,<0.14.0)", "onnxconverter-common", "tensorflow (>2.9,<2.16)", "tensorflow-text (<2.16)", "tf2onnx"] -tf-cpu = ["keras (>2.9,<2.16)", "keras-nlp (>=0.3.1,<0.14.0)", "onnxconverter-common", "tensorflow-cpu (>2.9,<2.16)", "tensorflow-probability (<0.24)", "tensorflow-text (<2.16)", "tf2onnx"] -tf-speech = ["kenlm", "librosa", "phonemizer", "pyctcdecode (>=0.4.0)"] -tiktoken = ["blobfile", "tiktoken"] -timm = ["timm (<=0.9.16)"] -tokenizers = ["tokenizers (>=0.20,<0.21)"] -torch = ["accelerate (>=0.26.0)", "torch"] -torch-speech = ["kenlm", "librosa", "phonemizer", "pyctcdecode (>=0.4.0)", "torchaudio"] -torch-vision = ["Pillow (>=10.0.1,<=15.0)", "torchvision"] -torchhub = ["filelock", "huggingface-hub (>=0.23.2,<1.0)", "importlib-metadata", "numpy (>=1.17)", "packaging (>=20.0)", "protobuf", "regex (!=2019.12.17)", "requests", "sentencepiece (>=0.1.91,!=0.1.92)", "tokenizers (>=0.20,<0.21)", "torch", "tqdm (>=4.27)"] -video = ["av (==9.2.0)"] -vision = ["Pillow (>=10.0.1,<=15.0)"] - [[package]] name = "typing-extensions" version = "4.12.2" @@ -1547,7 +1427,21 @@ h2 = ["h2 (>=4,<5)"] socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] zstd = ["zstandard (>=0.18.0)"] +[[package]] +name = "win32-setctime" +version = "1.1.0" +description = "A small Python utility to set file creation time on Windows" +optional = false +python-versions = ">=3.5" +files = [ + {file = "win32_setctime-1.1.0-py3-none-any.whl", hash = "sha256:231db239e959c2fe7eb1d7dc129f11172354f98361c4fa2d6d2d7e278baa8aad"}, + {file = "win32_setctime-1.1.0.tar.gz", hash = "sha256:15cf5750465118d6929ae4de4eb46e8edae9a5634350c01ba582df868e932cb2"}, +] + +[package.extras] +dev = ["black (>=19.3b0)", "pytest (>=4.6.2)"] + [metadata] lock-version = "2.0" -python-versions = "^3.10" -content-hash = "e15b61ae86b73f6ebc4fa135fe3e60c656593499991ce8acb638d7eee094aee1" +python-versions = ">=3.10,<3.13" +content-hash = "84b9a0b490b0595f6bd12f6d71057da0ba9de94b5cd398f771339e054cbf8e8b" diff --git a/pyproject.toml b/pyproject.toml index 74305ad..e64ee41 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "ContextSearch" -version = "0.5.0" +version = "0.6.0" description = "User friendly system for semantic search." authors = [ "ArturOle" @@ -11,16 +11,15 @@ keywords = ["semantic search", "ocr", "rag", "document-embedding", "contextual-s packages = [{include = "context_search", from="src"}] [tool.poetry.dependencies] -python = "^3.10" +python = ">=3.10,<3.13" neo4j = "^5.25.0" pdf2image = "^1.17.0" pydantic = "^2.9.2" PyMuPDF = "^1.24.10" pytesseract = "^0.3.13" tqdm = "^4.66.5" -transformers = "^4.45.1" -numpy = "^2.0.2" -torch = { version = "^2.3.1", source = "torch"} +numpy = ">=1.21,<2" +fastembed = "0.4.1" [tool.poetry.dev-dependencies] pytest = "^8.3.2" @@ -35,3 +34,6 @@ priority = "supplemental" [build-system] requires = ["poetry-core>=1.0.0"] build-backend = "poetry.core.masonry.api" + +[tool.pylint.format] +max-module-lines = 99 \ No newline at end of file diff --git a/src/context_search/preprocessor/embedder.py b/src/context_search/preprocessor/embedder.py index cd8a86f..0bb3a10 100644 --- a/src/context_search/preprocessor/embedder.py +++ b/src/context_search/preprocessor/embedder.py @@ -1,29 +1,41 @@ -import torch -from transformers import AutoModel, AutoTokenizer + +from fastembed import TextEmbedding from typing import List from ..data_classes import Embeddable -class Embedder: +class AbstractEmbedder: + def embed(self, text): + raise NotImplementedError + + def produce_embeddings( + self, + embeddable_objs: List[Embeddable] + ) -> List[Embeddable]: + raise NotImplementedError + + +class ImageEmbedder(AbstractEmbedder): + def embed(self, text): + raise NotImplementedError + + def produce_embeddings( + self, + embeddable_objs: List[Embeddable] + ) -> List[Embeddable]: + raise NotImplementedError + + +class TextEmbedder: def __init__(self, model_id="intfloat/e5-base-v2"): - self.device = "cuda" if torch.cuda.is_available() else "cpu" - self.tokenizer = AutoTokenizer.from_pretrained(model_id) - self.model = AutoModel.from_pretrained(model_id).to(self.device) - self.model.eval() + self.model = TextEmbedding( + model_name=model_id + ) def embed(self, text): """Embeds the given text using the model.""" - with torch.no_grad(): - inputs = self.tokenizer( - text, - return_tensors="pt", - padding=True, - truncation=True - ).to(self.device) - outputs = self.model(**inputs) - squeezed_output = outputs.last_hidden_state.mean(dim=1).squeeze() - return squeezed_output.cpu().tolist() + return self.model.embed(text) def __call__(self, doc): doc._.embedding = self.embed(doc.text) diff --git a/src/context_search/preprocessor/preprocessor.py b/src/context_search/preprocessor/preprocessor.py index c10fef5..2ead0b1 100644 --- a/src/context_search/preprocessor/preprocessor.py +++ b/src/context_search/preprocessor/preprocessor.py @@ -4,13 +4,13 @@ LiteratureGraph, ) from .extractor import Extractor -from .embedder import Embedder +from .embedder import TextEmbedder from .text_splitter import TextSplitter class Preprocessor: def __init__(self): - self.embedder = Embedder() + self.embedder = TextEmbedder() self.extractor = Extractor() self.splitter = TextSplitter( order="sequential", From c60d108baa47b36cfba23d3a6dc34294dc63604b Mon Sep 17 00:00:00 2001 From: ArturOle Date: Wed, 30 Oct 2024 13:13:00 +0100 Subject: [PATCH 21/33] Test correction --- .../data_manager_test/preprocessor_test/embedder_test.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/unit_tests/data_manager_test/preprocessor_test/embedder_test.py b/test/unit_tests/data_manager_test/preprocessor_test/embedder_test.py index 704488a..630c6e7 100644 --- a/test/unit_tests/data_manager_test/preprocessor_test/embedder_test.py +++ b/test/unit_tests/data_manager_test/preprocessor_test/embedder_test.py @@ -1,4 +1,4 @@ -from context_search.preprocessor.embedder import Embedder +from context_search.preprocessor.embedder import TextEmbedder import pytest import numpy as np import random @@ -11,7 +11,7 @@ def test_creating_embeddings_from_text(): - embedder = Embedder() + embedder = TextEmbedder() embedding = embedder.embed(text_to_embed) assert pytest.approx(embedding, 1e-3) == np.load( From 246a34e7d449d64550d43edff4837ec851a7b271 Mon Sep 17 00:00:00 2001 From: ArturOle Date: Wed, 30 Oct 2024 13:29:23 +0100 Subject: [PATCH 22/33] Unit test correction, code adjustment --- src/context_search/preprocessor/embedder.py | 12 +++++++----- .../preprocessor_test/embedder_test.py | 2 +- .../preprocessor_test/test_embedding.npy | Bin 3200 -> 1664 bytes 3 files changed, 8 insertions(+), 6 deletions(-) diff --git a/src/context_search/preprocessor/embedder.py b/src/context_search/preprocessor/embedder.py index 0bb3a10..628e7ab 100644 --- a/src/context_search/preprocessor/embedder.py +++ b/src/context_search/preprocessor/embedder.py @@ -28,14 +28,14 @@ def produce_embeddings( class TextEmbedder: - def __init__(self, model_id="intfloat/e5-base-v2"): + def __init__(self, model_id="sentence-transformers/all-MiniLM-L6-v2"): self.model = TextEmbedding( model_name=model_id ) def embed(self, text): """Embeds the given text using the model.""" - return self.model.embed(text) + return list(self.model.embed(text)) def __call__(self, doc): doc._.embedding = self.embed(doc.text) @@ -47,9 +47,11 @@ def produce_embeddings( ) -> List[Embeddable]: """Produces embeddings for the given list of Embeddable objects.""" + embeddings = self.embed([ + embeddable_obj.text for embeddable_obj in embeddable_objs + ]) + for embeddable_obj in embeddable_objs: - embeddable_obj.embeddings = self.embed( - embeddable_obj.text - ) + embeddable_obj.embeddings = embeddings.pop(0) return embeddable_objs diff --git a/test/unit_tests/data_manager_test/preprocessor_test/embedder_test.py b/test/unit_tests/data_manager_test/preprocessor_test/embedder_test.py index 630c6e7..9c14118 100644 --- a/test/unit_tests/data_manager_test/preprocessor_test/embedder_test.py +++ b/test/unit_tests/data_manager_test/preprocessor_test/embedder_test.py @@ -14,6 +14,6 @@ def test_creating_embeddings_from_text(): embedder = TextEmbedder() embedding = embedder.embed(text_to_embed) - assert pytest.approx(embedding, 1e-3) == np.load( + assert pytest.approx(embedding[0], 1e-3) == np.load( "test/unit_tests/data_manager_test/preprocessor_test/test_embedding.npy" 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zmu}tj;^1d)=(RE(Y`$6tlW*3*ji|$Prc)Iw-&krFvr3b$iShW5LvZUA(ya^S_ZCE;>DqOHq-Nqhd(2ZvjiTFTi%m7BH4{ zi_UFL5OB8*hQ^!owI3$%;|s-bJ^|RCG9VTpFi# zmqNFFhZ?^avUns-cCGU@Rqu48JdbD4cuAA-0Ai~&*Jg@yLIAd^6NUAZD&H6fruC;mM$^S^v-0&LJU7E@xV1*aV^jX<1R%|t1 zg7R&Lq4ik1kT%m5&sWXIR}ZYAw%Y{@@6Kj%#vqIgAEs~8BJgSOSQJ8LVtr>fZ0AXM zs{SLH{xX#xPMwYRE&X(6=S3Jiy%`%Nm&KC@(ouO+2-O$3<5siVFsz}7HgXoY>&bed zIbbUc1jb^LSt^vyX!b9H18+)PbH=L94Eg{O;nv;1lg9p6!b?8SZOMwbKG$#_cfy0hV7(1zmhC( zCgQ{9JEOTGaRSlng%C&QO_ Date: Wed, 30 Oct 2024 19:13:45 +0100 Subject: [PATCH 23/33] Additional tests and the setter method for text splitter --- .../preprocessor/text_splitter.py | 14 ++++++++-- .../preprocessor_test/embedder_test.py | 11 ++++++++ .../preprocessor_test/preprocessor_test.py | 10 +++++++ .../preprocessor_test/text_splitter_test.py | 27 +++++++++++++++++++ 4 files changed, 60 insertions(+), 2 deletions(-) diff --git a/src/context_search/preprocessor/text_splitter.py b/src/context_search/preprocessor/text_splitter.py index 576b733..593c440 100644 --- a/src/context_search/preprocessor/text_splitter.py +++ b/src/context_search/preprocessor/text_splitter.py @@ -59,7 +59,7 @@ def __init__( self.chunk_size = chunk_size self.overlap = chunk_overlap self.margin = margin - self.order = order + self._order = order self._is_separator_regex = is_separator_regex self.separators = separators @@ -92,11 +92,21 @@ def __init__( self.search_func: callable = None self.setup_separators(separators) + @property + def order(self): + return self._order + + @order.setter + def order(self, value): + """ Assures the separators are compiled for the new order strategy.""" + self._order = value + self.setup_separators(self.separators) + def setup_separators(self, separators): """ Prepares compiled patterns for efficient search of the separators and sets the search function based on the order of the separators. """ - match self.order.lower(): + match self._order.lower(): case "any": if not self._is_separator_regex: separators = '|'.join([ diff --git a/test/unit_tests/data_manager_test/preprocessor_test/embedder_test.py b/test/unit_tests/data_manager_test/preprocessor_test/embedder_test.py index 9c14118..1dac407 100644 --- a/test/unit_tests/data_manager_test/preprocessor_test/embedder_test.py +++ b/test/unit_tests/data_manager_test/preprocessor_test/embedder_test.py @@ -17,3 +17,14 @@ def test_creating_embeddings_from_text(): assert pytest.approx(embedding[0], 1e-3) == np.load( "test/unit_tests/data_manager_test/preprocessor_test/test_embedding.npy" ) + + +def test_creating_embeddings_from_multiple_texts(): + embedder = TextEmbedder() + embeddings = embedder.produce_embeddings([text_to_embed, text_to_embed]) + + assert pytest.approx(embeddings[0][0], 1e-3) == np.load( + "test/unit_tests/data_manager_test/preprocessor_test/test_embedding.npy" + ) + + assert pytest.approx(embeddings[1][0], 1e-3) == pytest.approx(embeddings[0][0], 1e-3) diff --git a/test/unit_tests/data_manager_test/preprocessor_test/preprocessor_test.py b/test/unit_tests/data_manager_test/preprocessor_test/preprocessor_test.py index 0ecbd18..814ac0f 100644 --- a/test/unit_tests/data_manager_test/preprocessor_test/preprocessor_test.py +++ b/test/unit_tests/data_manager_test/preprocessor_test/preprocessor_test.py @@ -9,3 +9,13 @@ def test_produce_chunks(): assert len(chunks) == 1 assert isinstance(chunks[0], Chunk) + + +def test_produce_chunks_from_multiple_strings(): + pipeline = Preprocessor() + texts = ['This is a test text', 'This is another test text'] + chunks = pipeline.splitter.produce_chunks(texts) + + assert len(chunks) == 2 + assert isinstance(chunks[0], Chunk) + assert isinstance(chunks[1], Chunk) diff --git a/test/unit_tests/data_manager_test/preprocessor_test/text_splitter_test.py b/test/unit_tests/data_manager_test/preprocessor_test/text_splitter_test.py index d487b5b..9e69fe3 100644 --- a/test/unit_tests/data_manager_test/preprocessor_test/text_splitter_test.py +++ b/test/unit_tests/data_manager_test/preprocessor_test/text_splitter_test.py @@ -156,5 +156,32 @@ def test_text_splitter_incorrect(): margin=margin ) + +def test_order_property_changes(mocker): + + setup_separators = mocker.patch( + "context_search.preprocessor.text_splitter.TextSplitter.setup_separators" + ) + + chunk_size = 100 + overlap = 10 + margin = 10 + splitter = TextSplitter( + chunk_size=chunk_size, + chunk_overlap=overlap, + margin=margin + ) + assert setup_separators.call_count == 1 + assert splitter.order == "any" + + splitter.order = "sequential" + assert splitter.order == "sequential" + assert setup_separators.call_count == 2 + + splitter.order = "backward" + assert splitter.order == "backward" + assert setup_separators.call_count == 3 + + if __name__ == "__main__": test_text_splitter_incorrect_overlap_out_of_range() From b495317af82914a64dfb8ea539720ba965d4f3c2 Mon Sep 17 00:00:00 2001 From: ArturOle Date: Wed, 30 Oct 2024 19:21:07 +0100 Subject: [PATCH 24/33] test correction --- .../data_manager_test/preprocessor_test/embedder_test.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/test/unit_tests/data_manager_test/preprocessor_test/embedder_test.py b/test/unit_tests/data_manager_test/preprocessor_test/embedder_test.py index 1dac407..d2dd6b9 100644 --- a/test/unit_tests/data_manager_test/preprocessor_test/embedder_test.py +++ b/test/unit_tests/data_manager_test/preprocessor_test/embedder_test.py @@ -1,4 +1,5 @@ from context_search.preprocessor.embedder import TextEmbedder +from context_search.data_classes import Embeddable import pytest import numpy as np import random @@ -21,7 +22,10 @@ def test_creating_embeddings_from_text(): def test_creating_embeddings_from_multiple_texts(): embedder = TextEmbedder() - embeddings = embedder.produce_embeddings([text_to_embed, text_to_embed]) + chunk_1 = Embeddable(text=text_to_embed) + chunk_2 = Embeddable(text=text_to_embed) + + embeddings = embedder.produce_embeddings([chunk_1, chunk_2]) assert pytest.approx(embeddings[0][0], 1e-3) == np.load( "test/unit_tests/data_manager_test/preprocessor_test/test_embedding.npy" From 91676765c59da2b881017fbd3c6441b2da2c78a8 Mon Sep 17 00:00:00 2001 From: ArturOle Date: Wed, 30 Oct 2024 19:37:49 +0100 Subject: [PATCH 25/33] Correction to the test correction (To be squashed) --- .../preprocessor_test/embedder_test.py | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/test/unit_tests/data_manager_test/preprocessor_test/embedder_test.py b/test/unit_tests/data_manager_test/preprocessor_test/embedder_test.py index d2dd6b9..e574182 100644 --- a/test/unit_tests/data_manager_test/preprocessor_test/embedder_test.py +++ b/test/unit_tests/data_manager_test/preprocessor_test/embedder_test.py @@ -1,5 +1,5 @@ from context_search.preprocessor.embedder import TextEmbedder -from context_search.data_classes import Embeddable +from context_search.data_classes import Chunk import pytest import numpy as np import random @@ -22,13 +22,20 @@ def test_creating_embeddings_from_text(): def test_creating_embeddings_from_multiple_texts(): embedder = TextEmbedder() - chunk_1 = Embeddable(text=text_to_embed) - chunk_2 = Embeddable(text=text_to_embed) + chunk_1 = Chunk(text=text_to_embed) + chunk_2 = Chunk(text=text_to_embed) embeddings = embedder.produce_embeddings([chunk_1, chunk_2]) - assert pytest.approx(embeddings[0][0], 1e-3) == np.load( + assert len(embeddings) == 2 + assert pytest.approx(embeddings[0].embeddings, 1e-3) == np.load( "test/unit_tests/data_manager_test/preprocessor_test/test_embedding.npy" ) + assert pytest.approx(embeddings[1].embeddings, 1e-3) == np.load( + "test/unit_tests/data_manager_test/preprocessor_test/test_embedding.npy" + ) + - assert pytest.approx(embeddings[1][0], 1e-3) == pytest.approx(embeddings[0][0], 1e-3) +if __name__ == "__main__": + test_creating_embeddings_from_text() + test_creating_embeddings_from_multiple_texts() From c06e54c44d506f11c76fd8669effc5831b849a2f Mon Sep 17 00:00:00 2001 From: ArturOle Date: Thu, 31 Oct 2024 11:58:42 +0100 Subject: [PATCH 26/33] Correcting user expirience of TextSplitter and adding tests --- .../preprocessor/text_splitter.py | 5 +-- .../preprocessor_test/text_splitter_test.py | 33 ++++++++++++++----- test/unit_tests/ragger_test.py | 0 3 files changed, 27 insertions(+), 11 deletions(-) delete mode 100644 test/unit_tests/ragger_test.py diff --git a/src/context_search/preprocessor/text_splitter.py b/src/context_search/preprocessor/text_splitter.py index 593c440..2461d8c 100644 --- a/src/context_search/preprocessor/text_splitter.py +++ b/src/context_search/preprocessor/text_splitter.py @@ -1,4 +1,4 @@ -import inspect + import re from abc import ABC, abstractmethod @@ -51,13 +51,14 @@ def __init__( self, chunk_size: int = 1024, chunk_overlap: Union[int, float] = 256, - margin: int = 256, + margin: int = None, order: str = "any", separators: List[str] = ['\.', '\n\n', '\n', '\s'], is_separator_regex: bool = True, ): self.chunk_size = chunk_size self.overlap = chunk_overlap + margin = margin if margin is not None else self.overlap self.margin = margin self._order = order self._is_separator_regex = is_separator_regex diff --git a/test/unit_tests/data_manager_test/preprocessor_test/text_splitter_test.py b/test/unit_tests/data_manager_test/preprocessor_test/text_splitter_test.py index 9e69fe3..0819013 100644 --- a/test/unit_tests/data_manager_test/preprocessor_test/text_splitter_test.py +++ b/test/unit_tests/data_manager_test/preprocessor_test/text_splitter_test.py @@ -70,10 +70,10 @@ def test_text_splitter_correct_overlap_margin(): ] -def test_text_splitter_incorrect_margin_none(): +def test_text_splitter_incorrect_overlap_none(): chunk_size = 100 - overlap = 10 - margin = None + overlap = None + margin = 10 with pytest.raises(ValueError): TextSplitter( @@ -83,10 +83,10 @@ def test_text_splitter_incorrect_margin_none(): ) -def test_text_splitter_incorrect_overlap_none(): +def test_text_splitter_incorrect_margin_out_of_range(): chunk_size = 100 - overlap = None - margin = 10 + overlap = 10 + margin = -1 with pytest.raises(ValueError): TextSplitter( @@ -95,11 +95,9 @@ def test_text_splitter_incorrect_overlap_none(): margin=margin ) - -def test_text_splitter_incorrect_margin_out_of_range(): chunk_size = 100 overlap = 10 - margin = None + margin = 11 with pytest.raises(ValueError): TextSplitter( @@ -109,6 +107,20 @@ def test_text_splitter_incorrect_margin_out_of_range(): ) +def test_text_splitter_margin_not_provided(): + chunk_size = 100 + overlap = 10 + margin = None + + ts = TextSplitter( + chunk_size=chunk_size, + chunk_overlap=overlap, + margin=margin + ) + + assert ts.margin == overlap + + def test_text_splitter_incorrect_overlap_out_of_range(): chunk_size = 100 overlap = -10 @@ -185,3 +197,6 @@ def test_order_property_changes(mocker): if __name__ == "__main__": test_text_splitter_incorrect_overlap_out_of_range() + test_text_splitter_incorrect_margin_out_of_range() + test_order_property_changes() + test_text_splitter_margin_not_provided() diff --git a/test/unit_tests/ragger_test.py b/test/unit_tests/ragger_test.py deleted file mode 100644 index e69de29..0000000 From 4f8c7ce771a1d46a33ace0fdf8b8e651225891df Mon Sep 17 00:00:00 2001 From: ArturOle Date: Thu, 31 Oct 2024 19:15:30 +0100 Subject: [PATCH 27/33] Adding fasttext-language detection --- pyproject.toml | 1 + .../communicator/communicator.py | 40 ++++++++++++- src/context_search/data_classes.py | 5 ++ src/context_search/reader/reader.py | 56 ++++++++++++++----- 4 files changed, 87 insertions(+), 15 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index e64ee41..6e289c4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,6 +20,7 @@ pytesseract = "^0.3.13" tqdm = "^4.66.5" numpy = ">=1.21,<2" fastembed = "0.4.1" +fasttext-langdetect = "^1.0.5" [tool.poetry.dev-dependencies] pytest = "^8.3.2" diff --git a/src/context_search/communicator/communicator.py b/src/context_search/communicator/communicator.py index e05ddc0..bcba4b2 100644 --- a/src/context_search/communicator/communicator.py +++ b/src/context_search/communicator/communicator.py @@ -3,11 +3,36 @@ from ..data_classes import LiteratureGraph from .query_builder import QueryBuilder +from abc import ABC, abstractmethod +from enum import Enum logger = setup_logger("Communicator Logger", "logs.log") -class Communicator: +class SupportedDatabses(Enum): + + +class DatabaseNotSupportedError(BaseException): + def __init__(self, db) -> None: + super().__init__( + "" + ) + + +class AbstractCommunciator(ABC): + + @abstractmethod + def driver(self): + """ The connection objects for databases """ + pass + + @abstractmethod + @staticmethod + def connection(): + pass + + +class Communicator(AbstractCommunciator): """Communicator class for interacting with the Neo4j database. Attributes: @@ -39,6 +64,7 @@ def driver(self, driver): def driver(self): if self._driver is not None: self._driver.close() + logger.info("Driver closed") del self._driver @staticmethod @@ -132,3 +158,15 @@ def __del__(self): if self._driver is not None: self._driver.close() logger.info("Driver closed") + + +class DatabaseManager: + supported_db = { + "neo4j": Communicator + } + + def __init__(self, adapter: str): + self.database_adapter = self.supported_db.get(adapter, None) + + if self.database_adapter is None: + raise DatabaseNotSupportedError() diff --git a/src/context_search/data_classes.py b/src/context_search/data_classes.py index b490b95..ff1b822 100644 --- a/src/context_search/data_classes.py +++ b/src/context_search/data_classes.py @@ -16,6 +16,11 @@ class Tag(Embeddable): description: Optional[str] = None +class Page(BaseModel): + page_number: int + text: str + + class Literature(BaseModel): filename: str filepath: str diff --git a/src/context_search/reader/reader.py b/src/context_search/reader/reader.py index 0ccd85f..1f27e9b 100644 --- a/src/context_search/reader/reader.py +++ b/src/context_search/reader/reader.py @@ -5,6 +5,7 @@ import pytesseract from abc import ABC, abstractmethod +from ftlangdetect import detect from pdf2image import convert_from_path from typing import List @@ -18,20 +19,31 @@ class ReadManager: - _pdf_reader = None - _text_reader = None + _readers = {} @property def pdf_reader(self): - if self._pdf_reader is None: - self._pdf_reader = PDFReader() - return self._pdf_reader + reader = self._readers.get("pdf", None) + if reader is None: + self._readers["pdf"] = PDFReader() + return self._readers["pdf"] + return reader @property def text_reader(self): - if self._text_reader is None: - self._text_reader = TextReader() - return self._text_reader + reader = self._readers.get("txt", None) + if reader is None: + self._readers["txt"] = TextReader() + return self._readers["txt"] + return reader + + @property + def docx_reader(self): + reader = self._readers.get("docx", None) + if reader is None: + self._readers["docx"] = DocxReader() + return self._readers["docx"] + return reader @staticmethod def _is_path_valid(data_path: str) -> bool: @@ -41,6 +53,10 @@ def _is_path_valid(data_path: str) -> bool: def _is_directory_or_file(data_path: str) -> bool: return FileTypeRecon.is_directory_or_file(data_path) + # A depth first search may be beneficial here to search directory. + # However, it may not be very safe... This should be disabled for web + # service and secured for the desktop. Idea, after searching through files + # give user possibility to disable files he wants to exclude. def read(self, data_path: str) -> List[LiteratureDTO]: if self._is_directory_or_file(data_path): return self._read_directory(data_path) @@ -57,10 +73,11 @@ def _read_file(self, file_path: str) -> LiteratureDTO: file_type = FileTypeRecon.recognize_type(file_path) text = None - if file_type == 'pdf': - text = self.pdf_reader.read(file_path) - elif file_type == 'txt': - text = self.text_reader.read(file_path) + match file_type: + case 'pdf': + text = self.pdf_reader.read(file_path) + case 'txt': + text = self.text_reader.read(file_path) return LiteratureDTO( filename=os.path.basename(file_path), @@ -120,11 +137,12 @@ def _setup_paths_from_config(self): os.environ["TESSERACT_PATH"] = self.tesseract_path if os.name == "nt": + # system specific path for windows pytesseract.pytesseract.tesseract_cmd = os.path.join( self.tesseract_path, "tesseract.exe" ) else: - # system specsific path for linux + # system specific path for linux pytesseract.pytesseract.tesseract_cmd = self.tesseract_path def read(self, data_path: str) -> List[str]: @@ -150,14 +168,24 @@ def _read_file_ocr(self, file_path): pages = convert_from_path(file_path, 300) + # we are sacrificing one execution of tesseract to + # to detect main lenguage of analyzed text + lang = detect(pytesseract.image_to_string(pages[0]))["lang"] paged_text = [] for i, page in enumerate(pages): - page_text = pytesseract.image_to_string(page) + page_text = pytesseract.image_to_string(page, lang) paged_text.append(page_text) return paged_text +class DocxReader(AbstractReader): + # To be implemented in future versions + @staticmethod + def read(data_path: str) -> List[str]: + raise NotImplementedError + + class FileTypeRecon: file_type_classes = { 'txt', From 17231fbd0f4fabfabf626c41e38304bbec7fb1b7 Mon Sep 17 00:00:00 2001 From: ArturOle Date: Tue, 5 Nov 2024 10:37:50 +0100 Subject: [PATCH 28/33] update poetry lock --- poetry.lock | 268 +++++++++++++++++++++++++++------------------------- 1 file changed, 138 insertions(+), 130 deletions(-) diff --git a/poetry.lock b/poetry.lock index ae067c7..491141c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -550,13 +550,13 @@ tests = ["pytest (>=4.6)"] [[package]] name = "neo4j" -version = "5.25.0" +version = "5.26.0" description = "Neo4j Bolt driver for Python" optional = false python-versions = ">=3.7" files = [ - {file = "neo4j-5.25.0-py3-none-any.whl", hash = "sha256:df310eee9a4f9749fb32bb9f1aa68711ac417b7eba3e42faefd6848038345ffa"}, - {file = "neo4j-5.25.0.tar.gz", hash = "sha256:7c82001c45319092cc0b5df4c92894553b7ab97bd4f59655156fa9acab83aec9"}, + {file = "neo4j-5.26.0-py3-none-any.whl", hash = "sha256:511a6a9468ca89b521bf686f885a2070acc462b1d09821d43710bd477acdf11e"}, + {file = "neo4j-5.26.0.tar.gz", hash = "sha256:51b25ba127b7b9fdae1ddf48ae697ddfab331e60f4b6d8488d1fc1f74ec60dcc"}, ] [package.dependencies] @@ -656,36 +656,32 @@ reference = ["Pillow", "google-re2"] 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16:29:45 +0100 Subject: [PATCH 29/33] Dual lenguage support for eng and pol. Future multi lang implementations planned --- .dockerignore | 13 + .../workflows/{unit_tests.yaml => tests.yaml} | 0 poetry.lock | 493 +++++++++++++----- pyproject.toml | 2 +- .../communicator/communicator.py | 6 +- src/context_search/reader/lang_adapter.py | 151 ++++++ src/context_search/reader/reader.py | 21 +- .../reader_test/pdf_reader_multilang.py | 46 ++ .../reader_test/test_files/test_eng.pdf | Bin 0 -> 31070 bytes .../reader_test/test_files/test_kor.pdf | Bin 0 -> 20037 bytes .../reader_test/test_files/test_pl.pdf | Bin 0 -> 31440 bytes .../reader_test/test_reader_manager.py | 6 +- 12 files changed, 586 insertions(+), 152 deletions(-) create mode 100644 .dockerignore rename .github/workflows/{unit_tests.yaml => tests.yaml} (100%) create mode 100644 src/context_search/reader/lang_adapter.py create mode 100644 test/unit_tests/data_manager_test/reader_test/pdf_reader_multilang.py create mode 100644 test/unit_tests/data_manager_test/reader_test/test_files/test_eng.pdf create mode 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"Fast, Extensible Progress Meter" optional = false python-versions = ">=3.7" files = [ - {file = "tqdm-4.66.6-py3-none-any.whl", hash = "sha256:223e8b5359c2efc4b30555531f09e9f2f3589bcd7fdd389271191031b49b7a63"}, - {file = "tqdm-4.66.6.tar.gz", hash = "sha256:4bdd694238bef1485ce839d67967ab50af8f9272aab687c0d7702a01da0be090"}, + {file = "tqdm-4.67.0-py3-none-any.whl", hash = "sha256:0cd8af9d56911acab92182e88d763100d4788bdf421d251616040cc4d44863be"}, + {file = "tqdm-4.67.0.tar.gz", hash = "sha256:fe5a6f95e6fe0b9755e9469b77b9c3cf850048224ecaa8293d7d2d31f97d869a"}, ] [package.dependencies] @@ -1395,6 +1613,7 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} [package.extras] dev = ["pytest (>=6)", "pytest-cov", "pytest-timeout", "pytest-xdist"] +discord = ["requests"] notebook = ["ipywidgets (>=6)"] slack = ["slack-sdk"] telegram = ["requests"] @@ -1444,4 +1663,4 @@ dev = ["black (>=19.3b0)", "pytest (>=4.6.2)"] [metadata] lock-version = "2.0" python-versions = ">=3.10,<3.13" -content-hash = "84b9a0b490b0595f6bd12f6d71057da0ba9de94b5cd398f771339e054cbf8e8b" +content-hash = "0a0e902ee8a62b327dddd9b0dc582c5b09b38dc89a80e7a013a9da882b5e3f9f" diff --git a/pyproject.toml b/pyproject.toml index 6e289c4..44e16b9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,7 +20,7 @@ pytesseract = "^0.3.13" tqdm = "^4.66.5" numpy = ">=1.21,<2" fastembed = "0.4.1" -fasttext-langdetect = "^1.0.5" +fast-langdetect = "^0.2.2" [tool.poetry.dev-dependencies] pytest = "^8.3.2" diff --git a/src/context_search/communicator/communicator.py b/src/context_search/communicator/communicator.py index bcba4b2..cf254c3 100644 --- a/src/context_search/communicator/communicator.py +++ b/src/context_search/communicator/communicator.py @@ -4,12 +4,9 @@ from .query_builder import QueryBuilder from abc import ABC, abstractmethod -from enum import Enum - -logger = setup_logger("Communicator Logger", "logs.log") -class SupportedDatabses(Enum): +logger = setup_logger("Communicator Logger", "logs.log") class DatabaseNotSupportedError(BaseException): @@ -27,7 +24,6 @@ def driver(self): pass @abstractmethod - @staticmethod def connection(): pass diff --git a/src/context_search/reader/lang_adapter.py b/src/context_search/reader/lang_adapter.py new file mode 100644 index 0000000..a2ff3df --- /dev/null +++ b/src/context_search/reader/lang_adapter.py @@ -0,0 +1,151 @@ +SUPPORTED_LENGUAGES = { + "pl": "pol", + "en": "eng", +} + + +class LangAdapt: + @staticmethod + def map(lang_code: str): + return SUPPORTED_LENGUAGES.get(lang_code, ) + + +''' +lang_detect_support = """ +af als am an ar arz as ast av az azb ba bar bcl be bg bh bn bo bpy br bs bxr +ca cbk ce ceb ckb co cs cv cy da de diq dsb dty dv el eml en eo es et eu fa +fi fr frr fy ga gd gl gn gom gu gv he hi hif hr hsb ht hu hy ia id ie ilo +io is it ja jbo jv ka kk km kn ko krc ku kv kw ky la lb lez li lmo lo lrc lt +lv mai mg mhr min mk ml mn mr mrj ms mt mwl my myv mzn nah nap nds ne new nl +nn no oc or os pa pam pfl pl pms pnb ps pt qu rm ro ru rue sa sah sc scn sco +sd sh si sk sl so sq sr su sv sw ta te tg th tk tl tr tt tyv ug uk ur uz vec +vep vi vls vo wa war wuu xal xmf yi yo yue zh""" + +# ISO-639 set 3 +tesseract_support = """afr Afrikaans x x x x x x +amh Amharic x x x x x +ara Arabic x x x x x x +asm Assamese x x x x x +aze Azerbaijani x x x x x +aze_cyrl Azerbaijani - Cyrilic x x x x x x +bel Belarusian x x x x x x +ben Bengali x x x x x x +bod Tibetan x x x x x +bos Bosnian x x x x x +bre Breton x x x x +bul Bulgarian x x x x x x +cat Catalan; Valencian x x x x x x +ceb Cebuano x x x x x +ces Czech x x x x x x +chi_sim Chinese - Simplified x x x x x x +chi_tra Chinese - Traditional x x x x x x +chr Cherokee x x x x x x +cos Corsican x x x +cym Welsh x x x x x +dan Danish x x x x x x +dan_frak Danish - Fraktur (contrib) x x +deu German x x x x x x +deu_frak German - Fraktur (contrib) x x +deu_latf German (Fraktur Latin) x x x x +dzo Dzongkha x x x x x +ell Greek, Modern (1453-) x x x x x x +eng English x x x x x x +enm English, Middle (1100-1500) x x x x x x +epo Esperanto x x x x x x +equ Math / equation detection module x x x x x +est Estonian x x x x x x +eus Basque x x x x x x +fao Faroese x x x +fas Persian x x x x x +fil Filipino (old - Tagalog) x x x +fin Finnish x x x x x x +fra French x x x x x x +frk German - Fraktur (now deu_latf) x x x x x x +frm French, Middle (ca.1400-1600) x x x x x x +fry Western Frisian x x x +gla Scottish Gaelic x x x +gle Irish x x x x x +glg Galician x x x x x x +grc Greek, Ancient (to 1453) (contrib) x x x x x x +guj Gujarati x x x x x +hat Haitian; Haitian Creole x x x x x +heb Hebrew x x x x x x +hin Hindi x x x x x x +hrv Croatian x x x x x x +hun Hungarian x x x x x x +hye Armenian x x x +iku Inuktitut x x x x x +ind Indonesian x x x x x x +isl Icelandic x x x x x x +ita Italian x x x x x x +ita_old Italian - Old x x x x x x +jav Javanese x x x x x +jpn Japanese x x x x x x +kan Kannada x x x x x x +kat Georgian x x x x x +kat_old Georgian - Old x x x x x +kaz Kazakh x x x x x +khm Central Khmer x x x x x +kir Kirghiz; Kyrgyz x x x x x +kmr Kurmanji (Kurdish - Latin Script) x x x x +kor Korean x x x x x x +kor_vert Korean (vertical) x x x x +kur Kurdish (Arabic Script) x +lao Lao x x x x x +lat Latin x x x x x +lav Latvian x x x x x x +lit Lithuanian x x x x x x +ltz Luxembourgish x x x x +mal Malayalam x x x x x x +mar Marathi x x x x x +mkd Macedonian x x x x x x +mlt Maltese x x x x x x +mon Mongolian x x x x +mri Maori x x x x +msa Malay x x x x x x +mya Burmese x x x x x +nep Nepali x x x x x +nld Dutch; Flemish x x x x x x +nor Norwegian x x x x x +oci Occitan (post 1500) x x x x x +ori Oriya x x x x x +osd Orientation and script detection module x x x x x x +pan Panjabi; Punjabi x x x x x +pol Polish x x x x x x +por Portuguese x x x x x x +pus Pushto; Pashto x x x x x +que Quechua x x x x +ron Romanian; Moldavian; Moldovan x x x x x x +rus Russian x x x x x x +san Sanskrit x x x x x +sin Sinhala; Sinhalese x x x x x +slk Slovak x x x x x x +slk_frak Slovak - Fraktur (contrib) x x +slv Slovenian x x x x x x +snd Sindhi x x x x +spa Spanish; Castilian x x x x x x +spa_old Spanish; Castilian - Old x x x x x x +sqi Albanian x x x x x x +srp Serbian x x x x x x +srp_latn Serbian - Latin x x x x x +sun Sundanese x x x x +swa Swahili x x x x x x +swe Swedish x x x x x x +syr Syriac x x x x x +tam Tamil x x x x x x +tat Tatar x x x x +tel Telugu x x x x x x +tgk Tajik x x x x x +tgl Tagalog (new - Filipino) x x x +tha Thai x x x x x x +tir Tigrinya x x x x x +ton Tonga x x x x +tur Turkish x x x x x x +uig Uighur; Uyghur x x x x x +ukr Ukrainian x x x x x x +urd Urdu x x x x x +uzb Uzbek x x x x x +uzb_cyrl Uzbek - Cyrilic x x x x x +vie Vietnamese x x x x x x +yid Yiddish x x x x x +yor Yoruba x x x x"""''' \ No newline at end of file diff --git a/src/context_search/reader/reader.py b/src/context_search/reader/reader.py index 1f27e9b..22b207a 100644 --- a/src/context_search/reader/reader.py +++ b/src/context_search/reader/reader.py @@ -5,7 +5,7 @@ import pytesseract from abc import ABC, abstractmethod -from ftlangdetect import detect +from fast_langdetect import detect from pdf2image import convert_from_path from typing import List @@ -13,9 +13,11 @@ from ..utils import setup_logger, config_variables current_directory = os.path.dirname(__file__) - - logger = setup_logger('Reader Logger', 'logs.log', logging.INFO) +SUPPORTED_LENGUAGES = { + "pl": "pol", + "en": "eng", +} class ReadManager: @@ -164,15 +166,22 @@ def read(self, data_path: str) -> List[str]: return paged_text + @staticmethod + def _detect_lang(string): + string = string.replace("\n", ' ') + lang = detect(string)["lang"] + return SUPPORTED_LENGUAGES.get(lang, "eng") + def _read_file_ocr(self, file_path): pages = convert_from_path(file_path, 300) - # we are sacrificing one execution of tesseract to + # we sacrifice one execution of tesseract to # to detect main lenguage of analyzed text - lang = detect(pytesseract.image_to_string(pages[0]))["lang"] + lang = self._detect_lang(pytesseract.image_to_string(pages[0])) + paged_text = [] - for i, page in enumerate(pages): + for page in pages: page_text = pytesseract.image_to_string(page, lang) paged_text.append(page_text) diff --git a/test/unit_tests/data_manager_test/reader_test/pdf_reader_multilang.py b/test/unit_tests/data_manager_test/reader_test/pdf_reader_multilang.py new file mode 100644 index 0000000..3235902 --- /dev/null +++ b/test/unit_tests/data_manager_test/reader_test/pdf_reader_multilang.py @@ -0,0 +1,46 @@ +import os +import logging + +from context_search.reader import PDFReader + +cur_dir = os.path.dirname(__file__) +logger = logging.getLogger(__name__) + + +def test_lang_detect_pl(mocker): + pdf_reader = PDFReader() + with mocker.patch.object( + pdf_reader, + "_detect_lang", + wraps=pdf_reader._detect_lang + ) as detect_lang_mock: + pdf_reader.read( + rf'{cur_dir}/test_files/test_pl.pdf' + ) + assert detect_lang_mock.return_value == "pol" + + +def test_lang_detect_en(mocker): + pdf_reader = PDFReader() + with mocker.patch.object( + pdf_reader, + "_detect_lang", + wraps=pdf_reader._detect_lang + ) as detect_lang_mock: + pdf_reader.read( + rf'{cur_dir}/test_files/test_eng.pdf' + ) + assert detect_lang_mock.return_value == "eng" + + +def test_lang_detect_not_supported(mocker): + pdf_reader = PDFReader() + with mocker.patch.object( + pdf_reader, + "_detect_lang", + wraps=pdf_reader._detect_lang + ) as detect_lang_mock: + pdf_reader.read( + rf'{cur_dir}/test_files/test_kor.pdf' + ) + assert detect_lang_mock.return_value == "eng" diff --git a/test/unit_tests/data_manager_test/reader_test/test_files/test_eng.pdf b/test/unit_tests/data_manager_test/reader_test/test_files/test_eng.pdf new file mode 100644 index 0000000000000000000000000000000000000000..e64c6543b14737cc3f07e3c03f651b07bfa12369 GIT binary patch literal 31070 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--git a/test/unit_tests/data_manager_test/reader_test/test_reader_manager.py b/test/unit_tests/data_manager_test/reader_test/test_reader_manager.py index bf75bad..8152780 100644 --- a/test/unit_tests/data_manager_test/reader_test/test_reader_manager.py +++ b/test/unit_tests/data_manager_test/reader_test/test_reader_manager.py @@ -27,9 +27,9 @@ def test_reader_manager_read_pdf(mocker): assert isinstance(result, list) and len(result) == 1 result = reader_manager.read(f"{cur_dir}/test_files") - assert isinstance(result, list) and len(result) == 3 + assert isinstance(result, list) and len(result) == 6 - assert_n_calls(mock_pdf_reader, 3) + assert_n_calls(mock_pdf_reader, 6) def test_reader_manager_read_txt(mocker): @@ -53,7 +53,7 @@ def test_reader_manager_read_txt(mocker): assert isinstance(result, list) and len(result) == 1 result = reader_manager.read(f"{cur_dir}/test_files") - assert isinstance(result, list) and len(result) == 3 + assert isinstance(result, list) and len(result) == 6 assert_n_calls(mock_text_reader, 2) From 3c77d224326a940b96e9ff4e4971c95049d406c4 Mon Sep 17 00:00:00 2001 From: ArturOle Date: Thu, 14 Nov 2024 00:45:29 +0100 Subject: [PATCH 30/33] Moving from ini file to toml --- .../communicator/communicator.py | 84 ++++++++++++++++++- 1 file changed, 83 insertions(+), 1 deletion(-) diff --git a/src/context_search/communicator/communicator.py b/src/context_search/communicator/communicator.py index e05ddc0..0d5a05b 100644 --- a/src/context_search/communicator/communicator.py +++ b/src/context_search/communicator/communicator.py @@ -1,4 +1,6 @@ from neo4j import GraphDatabase +from qdrant_client import QdrantClient + from ..utils import setup_logger from ..data_classes import LiteratureGraph from .query_builder import QueryBuilder @@ -7,7 +9,26 @@ logger = setup_logger("Communicator Logger", "logs.log") -class Communicator: +class DatabaseNotSupportedError(BaseException): + def __init__(self, db) -> None: + super().__init__( + "" + ) + + +class AbstractCommAdapter(ABC): + + @abstractmethod + def driver(self): + """ The connection objects for databases """ + pass + + @abstractmethod + def connection(): + pass + + +class CommAdapterNeo(AbstractCommAdapter): """Communicator class for interacting with the Neo4j database. Attributes: @@ -132,3 +153,64 @@ def __del__(self): if self._driver is not None: self._driver.close() logger.info("Driver closed") + + +class CommAdapterQdrant(AbstractCommAdapter): + """Communicator class for interacting with the Neo4j database. + + Attributes: + uri (str): The URI of the Neo4j database. + user (str): The username for the Neo4j database. + password (str): The password for the Neo4j database. + """ + + def __init__(self, uri, user, password): + self._uri = uri + self._user = user + self._password = password + self._driver = None + + @property + def driver(self): + if self._driver is None: + self._driver = GraphDatabase.driver( + self._uri, + auth=(self._user, self._password) + ) + return self._driver + + @driver.setter + def driver(self, driver): + self._driver = driver + + @driver.deleter + def driver(self): + if self._driver is not None: + self._driver.close() + logger.info("Driver closed") + del self._driver + + @staticmethod + def connection(func): + def wrapper(self, *args, **kwargs): + session = self.driver.session(database="neo4j") + result = func(self, session, *args, **kwargs) + session.close() + return result + + return wrapper + + +class DatabaseManager: + supported_db = { + "neo4j": CommAdapterNeo, + "qdrant": CommAdapterQdrant + } + + def __init__(self, adapter: str): + self.database_adapter = self.supported_db.get( + adapter, + DatabaseNotSupportedError + ) + + def From b61a921f5f6ead281b0d549397e920cba1701629 Mon Sep 17 00:00:00 2001 From: ArturOle Date: Thu, 14 Nov 2024 00:46:45 +0100 Subject: [PATCH 31/33] Correcting tests and adjusting code for toml-based shared DTO object --- .../workflows/{unit_tests.yaml => tests.yaml} | 0 config.ini | 5 - config.toml | 15 +++ docker/build_dev/dockerfile | 6 +- docker/integration_tests/dockerfile | 7 +- docker/unit_tests/dockerfile | 7 +- src/context_search/__init__.py | 10 +- src/context_search/communicator/__init__.py | 4 +- .../communicator/communicator.py | 38 +++---- src/context_search/data_manager.py | 24 ++--- src/context_search/reader/reader.py | 19 ++-- src/context_search/utils/__init__.py | 8 +- src/context_search/utils/config_variables.py | 98 +++++++++---------- .../communicator_test/communicator_test.py | 12 +-- .../communicator_test/communicator_test.py | 6 +- 15 files changed, 129 insertions(+), 130 deletions(-) rename .github/workflows/{unit_tests.yaml => tests.yaml} (100%) delete mode 100644 config.ini create mode 100644 config.toml diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/tests.yaml similarity index 100% rename from .github/workflows/unit_tests.yaml rename to .github/workflows/tests.yaml diff --git a/config.ini b/config.ini deleted file mode 100644 index f3eb5fa..0000000 --- a/config.ini +++ /dev/null @@ -1,5 +0,0 @@ -TESSERACT_PATH=/usr/bin/tesseract -POPPLER_PATH=/usr/bin/pdftotext -NEO4J_URI=neo4j://database:7687 -NEO4J_USER=neo4j -NEO4J_PASSWORD=StrongPsPsP5 \ No newline at end of file diff --git a/config.toml b/config.toml new file mode 100644 index 0000000..8fe7205 --- /dev/null +++ b/config.toml @@ -0,0 +1,15 @@ + +[settings] +db_engine = "neo4j" + +[OCR] +TESSERACT_PATH = "/usr/bin/tesseract" +POPPLER_PATH = "/usr/bin/pdftotext" + +[neo4j] +NEO4J_URI = "neo4j://database:7687" +NEO4J_USER = "neo4j" +NEO4J_PASSWORD = "StrongPsPsP5" + +[qdrant] +in_memory = true diff --git a/docker/build_dev/dockerfile b/docker/build_dev/dockerfile index 4ea566c..9750dec 100644 --- a/docker/build_dev/dockerfile +++ b/docker/build_dev/dockerfile @@ -1,4 +1,4 @@ -FROM ubuntu:22.04 +FROM ubuntu:24.04 ENV DEBIAN_FRONTEND=noninteractive ENV POETRY_HOME="/root/.poetry" @@ -7,9 +7,9 @@ ENV PATH="$POETRY_HOME/bin:$PATH" CMD ["bash"] RUN apt-get update -RUN apt-get install -y python3 python3-pip curl +RUN apt-get install -y python3 pipx curl RUN curl -sSL https://install.python-poetry.org | python3 - WORKDIR /ragger COPY . /ragger -RUN make install \ No newline at end of file +RUN poetry install \ No newline at end of file diff --git a/docker/integration_tests/dockerfile b/docker/integration_tests/dockerfile index 09c9bb8..b91d5c0 100644 --- a/docker/integration_tests/dockerfile +++ b/docker/integration_tests/dockerfile @@ -1,4 +1,4 @@ -FROM ubuntu:22.04 +FROM ubuntu:24.04 ENV DEBIAN_FRONTEND=noninteractive ENV POETRY_HOME="/root/.poetry" @@ -7,7 +7,7 @@ ENV PATH="$POETRY_HOME/bin:$PATH" CMD ["bash"] RUN apt-get update --fix-missing -RUN apt-get install -y python3 python3-pip git ca-certificates lsb-release ubuntu-keyring software-properties-common curl +RUN apt-get install -y python3 pipx git ca-certificates lsb-release ubuntu-keyring software-properties-common curl RUN curl -sSL https://install.python-poetry.org | python3 - RUN update-ca-certificates --fresh @@ -17,9 +17,8 @@ RUN apt install -y libtesseract-dev RUN apt install -y poppler-utils WORKDIR /ragger -RUN pip install --upgrade pip COPY . /ragger RUN touch logs.log -RUN make install +RUN poetry install RUN export GIT_PYTHON_GIT_EXECUTABLE=$(which git) diff --git a/docker/unit_tests/dockerfile b/docker/unit_tests/dockerfile index d88a6b5..cfa259b 100644 --- a/docker/unit_tests/dockerfile +++ b/docker/unit_tests/dockerfile @@ -1,4 +1,4 @@ -FROM ubuntu:22.04 +FROM ubuntu:24.04 ENV DEBIAN_FRONTEND=noninteractive ENV POETRY_HOME="/root/.poetry" @@ -7,7 +7,7 @@ ENV PATH="$POETRY_HOME/bin:$PATH" CMD ["bash"] RUN apt-get update -RUN apt-get install -y python3 python3-pip git curl +RUN apt-get install -y python3 pipx git curl RUN curl -sSL https://install.python-poetry.org | python3 - RUN apt install -y tesseract-ocr @@ -15,9 +15,8 @@ RUN apt install -y libtesseract-dev RUN apt install -y poppler-utils WORKDIR /ragger -RUN pip install --upgrade pip COPY . /ragger RUN touch logs.log -RUN make install +RUN poetry install RUN export GIT_PYTHON_GIT_EXECUTABLE=$(which git) diff --git a/src/context_search/__init__.py b/src/context_search/__init__.py index 646c45e..567818b 100644 --- a/src/context_search/__init__.py +++ b/src/context_search/__init__.py @@ -2,15 +2,15 @@ from .data_manager import DataManager from .reader import ReadManager from .preprocessor import Preprocessor -from .communicator import Communicator -from .utils import setup_logger, config_variables +from .communicator import CommAdapterNeo +from .utils import setup_logger, EnvInterface __all__ = [ 'ContextSearch', 'DataManager', 'ReadManager', 'Preprocessor', - 'Communicator', + 'CommAdapterNeo', 'setup_logger', - 'config_variables' -] \ No newline at end of file + 'EnvInterface' +] diff --git a/src/context_search/communicator/__init__.py b/src/context_search/communicator/__init__.py index 2a5d00c..47359de 100644 --- a/src/context_search/communicator/__init__.py +++ b/src/context_search/communicator/__init__.py @@ -1,4 +1,4 @@ -from .communicator import Communicator +from .communicator import CommAdapterNeo -__all__ = ["Communicator"] +__all__ = ["CommAdapterNeo"] diff --git a/src/context_search/communicator/communicator.py b/src/context_search/communicator/communicator.py index 0d5a05b..2dcdd84 100644 --- a/src/context_search/communicator/communicator.py +++ b/src/context_search/communicator/communicator.py @@ -1,5 +1,5 @@ from neo4j import GraphDatabase -from qdrant_client import QdrantClient +from abc import ABC, abstractmethod from ..utils import setup_logger from ..data_classes import LiteratureGraph @@ -9,13 +9,6 @@ logger = setup_logger("Communicator Logger", "logs.log") -class DatabaseNotSupportedError(BaseException): - def __init__(self, db) -> None: - super().__init__( - "" - ) - - class AbstractCommAdapter(ABC): @abstractmethod @@ -28,6 +21,15 @@ def connection(): pass +class DatabaseNotSupported(BaseException, AbstractCommAdapter): + def __init__(self, *args, **kwargs) -> None: + super(BaseException).__init__( + "The requested database is not supported.\n" + "Supported:\n" + " {Neo4j, Qdrant}" + ) + + class CommAdapterNeo(AbstractCommAdapter): """Communicator class for interacting with the Neo4j database. @@ -82,7 +84,7 @@ def add_literature_subgraph( session, literature_graph: LiteratureGraph ): - session.write_transaction( + session.execute_write( self._add_literature_subgraph, literature_graph ) @@ -92,7 +94,7 @@ def create_vector_indexes(self, session): """Creates vector indexes for chunks and tags. This function is separated from the add_literature_subgraph because the indexes cannot be created in the same transaction""" - session.write_transaction(self._index_ebeddables) + session.execute_write(self._index_ebeddables) def _add_literature_subgraph(self, tx, literature_graph: LiteratureGraph): """Builds the the nodes and relationships based on the given @@ -117,25 +119,25 @@ def _index_ebeddables(self, tx): @connection def get_literature(self, session, filename): - return session.read_transaction(QueryBuilder._get_literature, filename) + return session.execute_read(QueryBuilder._get_literature, filename) @connection def get_literature_chunks(self, session, filename): - return session.read_transaction( + return session.execute_read( QueryBuilder._get_literature_chunks, filename ) @connection def get_literature_tags(self, session, filename): - return session.read_transaction( + return session.execute_read( QueryBuilder._get_literature_tags, filename ) @connection def search_n_records(self, session, query, n): - return session.read_transaction( + return session.execute_read( QueryBuilder._search_n_records, query, n @@ -143,11 +145,11 @@ def search_n_records(self, session, query, n): @connection def get_all_literatures(self, session): - return session.read_transaction(QueryBuilder._get_all_literatures) + return session.execute_read(QueryBuilder._get_all_literatures) @connection def delete_literature(self, session, filename): - session.write_transaction(QueryBuilder._delete_literature, filename) + session.execute_write(QueryBuilder._delete_literature, filename) def __del__(self): if self._driver is not None: @@ -210,7 +212,5 @@ class DatabaseManager: def __init__(self, adapter: str): self.database_adapter = self.supported_db.get( adapter, - DatabaseNotSupportedError + DatabaseNotSupported ) - - def diff --git a/src/context_search/data_manager.py b/src/context_search/data_manager.py index 463eb41..a53bf3d 100644 --- a/src/context_search/data_manager.py +++ b/src/context_search/data_manager.py @@ -2,9 +2,8 @@ from .reader import ReadManager from .preprocessor import Preprocessor -from .communicator import Communicator -from .utils import setup_logger, config_variables - +from .communicator import CommAdapterNeo +from .utils import setup_logger, EnvInterface logger = setup_logger('Data Manager Logger', 'logs.log') @@ -15,23 +14,24 @@ class DataManager: _communicator = None def __init__(self): + EnvInterface().set_env_variables_from_config() self.read_manager = ReadManager() self.preprocessor = Preprocessor() @property def communicator(self): if self._communicator is None: - neo4j_variables = config_variables.get_neo4j_variables() - self._communicator = Communicator( - uri=neo4j_variables[0], - user=neo4j_variables[1], - password=neo4j_variables[2] + neo4j_variables = EnvInterface.get_neo4j_vars() + self._communicator = CommAdapterNeo( + uri=neo4j_variables["NEO4J_URI"], + user=neo4j_variables["NEO4J_USER"], + password=neo4j_variables["NEO4J_PASSWORD"] ) - logger.info(f""" + logger.debug(f""" Communicator created with: - uri: {neo4j_variables[0]} - user: {neo4j_variables[1]} - password: {neo4j_variables[2]} + uri: {neo4j_variables["NEO4J_URI"]} + user: {neo4j_variables["NEO4J_USER"]} + password: {neo4j_variables["NEO4J_PASSWORD"]} """) return self._communicator diff --git a/src/context_search/reader/reader.py b/src/context_search/reader/reader.py index 0ccd85f..f8a961f 100644 --- a/src/context_search/reader/reader.py +++ b/src/context_search/reader/reader.py @@ -9,7 +9,7 @@ from typing import List from ..data_classes import LiteratureDTO -from ..utils import setup_logger, config_variables +from ..utils import setup_logger, EnvInterface current_directory = os.path.dirname(__file__) @@ -106,18 +106,13 @@ def _setup_paths_from_config(self): directory as the script that is being run with paths to tesseract and poppler bin folder (NOT TO EXECUTABLES, BUT FOLDERS). """ - if not os.getenv("POPPLER_PATH") or not os.getenv("TESSERACT_PATH"): - self.tesseract_path, self.poppler_path = config_variables.get_OCR_variables() + self.tesseract_path = os.getenv("TESSERACT_PATH") + self.poppler_path = os.getenv("POPPLER_PATH") - if os.getenv("POPPLER_PATH"): - self.poppler_path = os.getenv("POPPLER_PATH") - else: - os.environ["POPPLER_PATH"] = self.poppler_path - - if os.getenv("TESSERACT_PATH"): - self.tesseract_path = os.getenv("TESSERACT_PATH") - else: - os.environ["TESSERACT_PATH"] = self.tesseract_path + if not self.tesseract_path or not self.poppler_path: + ocr_vars = EnvInterface.get_OCR_vars() + self.tesseract_path = ocr_vars.get("TESSERACT_PATH") + self.poppler_path = ocr_vars.get("POPPLER_PATH") if os.name == "nt": pytesseract.pytesseract.tesseract_cmd = os.path.join( diff --git a/src/context_search/utils/__init__.py b/src/context_search/utils/__init__.py index e20d945..f72f3fc 100644 --- a/src/context_search/utils/__init__.py +++ b/src/context_search/utils/__init__.py @@ -1,13 +1,9 @@ from .config_variables import ( - get_OCR_variables, - get_neo4j_variables, - set_env_variables_from_config + EnvInterface ) from .logger_setup import setup_logger __all__ = [ - "get_OCR_variables", - "get_neo4j_variables", - "set_env_variables_from_config", + "EnvInterface", "setup_logger" ] diff --git a/src/context_search/utils/config_variables.py b/src/context_search/utils/config_variables.py index 25ad58a..09e7a6b 100644 --- a/src/context_search/utils/config_variables.py +++ b/src/context_search/utils/config_variables.py @@ -1,52 +1,52 @@ import os +import tomllib +import logging + + +class EnvInterface: + """ + Clas for managing shared values of config.toml + After initizlization, the variables are shared across all instances + on purpose so that it is accessible from different parts of + system if needed. + """ + _config = {} + + def __init__(self): + current_working_directory = os.getcwd() + path_to_config = os.path.join( + current_working_directory, + "config.toml" + ) + self.read_config(path_to_config) + + def read_config(self, path): + try: + with open(path, "rb") as conf_file: + EnvInterface._config = tomllib.load(conf_file) + except FileNotFoundError as err: + print( + f"Could not find config file in the project root. {err}" + ) + + @staticmethod + def get_OCR_vars(): + return EnvInterface._config.get("OCR") + + @staticmethod + def get_neo4j_vars(): + return EnvInterface._config.get("neo4j") + + @staticmethod + def set_env_variables_from_config(): + """ + Static method for setting env variables + for necessary modules + """ + for ocr_kwarg in EnvInterface.get_OCR_vars().items(): + os.environ[ocr_kwarg[0]] = ocr_kwarg[1] + + for db_kwarg in EnvInterface.get_neo4j_vars().items(): + os.environ[db_kwarg[0]] = db_kwarg[1] - -def get_OCR_variables(): - tesseract_path = "" - poppler_path = "" - - current_working_directory = os.getcwd() - path_to_config = os.path.join(current_working_directory, "config.ini") - with open(path_to_config, "r") as file: - lines = file.readlines() - - for line in lines: - if line.startswith("TESSERACT_PATH"): - tesseract_path = line.split("=")[1].strip() - if line.startswith("POPPLER_PATH"): - poppler_path = line.split("=")[1].strip() - - return tesseract_path, poppler_path - - -def get_neo4j_variables(): - uri = "" - user = "" - password = "" - - current_working_directory = os.getcwd() - path_to_config = os.path.join(current_working_directory, "config.ini") - with open(path_to_config, "r") as file: - lines = file.readlines() - - for line in lines: - if line.startswith("NEO4J_URI"): - uri = line.split("=")[1].strip() - if line.startswith("NEO4J_USER"): - user = line.split("=")[1].strip() - if line.startswith("NEO4J_PASSWORD"): - password = line.split("=")[1].strip() - - return uri, user, password - - -def set_env_variables_from_config(): - tesseract_path, poppler_path = get_OCR_variables() - os.environ["TESSERACT_PATH"] = tesseract_path - os.environ["POPPLER_PATH"] = poppler_path - - uri, user, password = get_neo4j_variables() - os.environ["NEO4J_URI"] = uri - os.environ["NEO4J_USER"] = user - os.environ["NEO4J_PASSWORD"] = password diff --git a/test/integration_tests/data_manager_test/communicator_test/communicator_test.py b/test/integration_tests/data_manager_test/communicator_test/communicator_test.py index ef9a75c..96a5a9d 100644 --- a/test/integration_tests/data_manager_test/communicator_test/communicator_test.py +++ b/test/integration_tests/data_manager_test/communicator_test/communicator_test.py @@ -1,6 +1,6 @@ import pytest -from context_search.communicator import Communicator +from context_search.communicator import CommAdapterNeo from context_search.data_classes import Literature from context_search.communicator.query_builder import QueryBuilder @@ -14,7 +14,7 @@ def setup_test(test): def test_communicator_creation(test): test.setup_test() - test.communicator = Communicator(test.uri, test.user, test.password) + test.communicator = CommAdapterNeo(test.uri, test.user, test.password) assert test.communicator is not None test.communicator = None @@ -24,7 +24,7 @@ def setup_test(test): test.uri = "neo4j://database:7687" test.user = "neo4j" test.password = "StrongPsPsP5" - test.communicator = Communicator(test.uri, test.user, test.password) + test.communicator = CommAdapterNeo(test.uri, test.user, test.password) test.literature = Literature( filename="test", filepath="test" @@ -33,7 +33,7 @@ def setup_test(test): def test_add_literature(test): test.setup_test() test.session = test.communicator.driver.session(database="neo4j") - test.session.write_transaction( + test.session.execute_write( QueryBuilder._merge_literature, test.literature ) @@ -43,7 +43,7 @@ def test_add_literature(test): def test_get_literature(test): test.setup_test() test.session = test.communicator.driver.session(database="neo4j") - test.session.write_transaction( + test.session.execute_write( QueryBuilder._merge_literature, test.literature ) @@ -55,7 +55,7 @@ def test_get_literature(test): def test_get_all_literatures(test): test.setup_test() test.session = test.communicator.driver.session(database="neo4j") - test.session.write_transaction( + test.session.execute_write( QueryBuilder._merge_literature, test.literature ) diff --git a/test/unit_tests/data_manager_test/communicator_test/communicator_test.py b/test/unit_tests/data_manager_test/communicator_test/communicator_test.py index d1f24a4..82a55ee 100644 --- a/test/unit_tests/data_manager_test/communicator_test/communicator_test.py +++ b/test/unit_tests/data_manager_test/communicator_test/communicator_test.py @@ -2,7 +2,7 @@ from unittest.mock import MagicMock, patch -from context_search.communicator import Communicator +from context_search.communicator import CommAdapterNeo class TestCommunicatorConnection: @@ -14,7 +14,7 @@ def setup_test(test): def test_communicator_creation(test): test.setup_test() - test.communicator = Communicator(test.uri, test.user, test.password) + test.communicator = CommAdapterNeo(test.uri, test.user, test.password) assert test.communicator is not None test.communicator = None @@ -30,7 +30,7 @@ def setup_test(test): test.uri = "neo4j://database:7687" test.user = "neo4j" test.password = "StrongPsPsP5" - test.communicator = Communicator(test.uri, test.user, test.password) + test.communicator = CommAdapterNeo(test.uri, test.user, test.password) def test_driver_property_invocation(test, mock_driver): test.setup_test() From 4d5509c4816f6c24bb49bdac4eccb225a2753c77 Mon Sep 17 00:00:00 2001 From: ArturOle Date: Thu, 14 Nov 2024 00:48:14 +0100 Subject: [PATCH 32/33] Version bump --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index e64ee41..30e9778 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "ContextSearch" -version = "0.6.0" +version = "0.7.0" description = "User friendly system for semantic search." authors = [ "ArturOle" From acbb0219a4495eb8301fa9f8aa6336c6047a7157 Mon Sep 17 00:00:00 2001 From: ArturOle Date: Thu, 14 Nov 2024 00:59:36 +0100 Subject: [PATCH 33/33] logging in exeption handling set to error level --- src/context_search/utils/config_variables.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/context_search/utils/config_variables.py b/src/context_search/utils/config_variables.py index 09e7a6b..91ec6d0 100644 --- a/src/context_search/utils/config_variables.py +++ b/src/context_search/utils/config_variables.py @@ -26,7 +26,7 @@ def read_config(self, path): with open(path, "rb") as conf_file: EnvInterface._config = tomllib.load(conf_file) except FileNotFoundError as err: - print( + logging.error( f"Could not find config file in the project root. {err}" )