more integration complete

compose.development.override.yaml

@@ -6,6 +6,14 @@ services:
       dockerfile: ./external_components/rtransparent/Dockerfile
     volumes:
       - ./external_components/rtransparent:/app
+  llm_extraction:
+    environment:
+      - OPENAI_API_KEY=${OPENAI_API_KEY:-NOKEY}
+    build:
+      context: .
+      dockerfile: ./external_components/llm_extraction/Dockerfile
+    volumes:
+      - ./external_components/llm_extraction:/app
 
   web_api:
     container_name: web_api

compose.yaml

@@ -9,3 +9,8 @@ services:
     image: nimhdsst/rtransparent:staging
     ports:
       - "8071:8071"
+  llm_extraction:
+    container_name: llm_extraction
+    image: nimhdsst/llm_extraction:staging
+    ports:
+      - "8072:8072"

external_components/llm_extraction/Dockerfile

@@ -3,22 +3,25 @@ SHELL ["/bin/bash", "--login", "-c"]
 # Set working directory
 WORKDIR /app
 
-COPY external_components/rtransparent/environment.yaml /app
+COPY external_components/llm_extraction/environment.yaml /app
 
 # Create the environment
 RUN conda env create -f environment.yaml
 
 # Ensure the conda environment is activated
 RUN echo "source /opt/conda/etc/profile.d/conda.sh && conda activate osm" | tee -a ~/.bashrc /etc/profile /etc/profile.d/conda.sh /etc/skel/.bashrc /etc/skel/.profile > /dev/null
 
-RUN R -e '\
-devtools::install_github("quest-bih/oddpub",ref="c5b091c7e82ed6177192dc380a515b3dc6304863"); \
-devtools::install_github("serghiou/rtransparent", build_vignettes = F)'
+RUN mkdir -p /opt/osm
+COPY pyproject.toml /opt/osm
+COPY osm /opt/osm/osm
+ARG PSEUDO_VERSION=0.0.1 # strongly recommended to update based on git describe
+RUN SETUPTOOLS_SCM_PRETEND_VERSION_FOR_OSM=${PSEUDO_VERSION} pip install -e /opt/osm
+RUN --mount=source=.git,target=/opt/osm/.git,type=bind pip install -e /opt/osm
 
 # # Copy the project files and install the package
-COPY external_components/rtransparent/app.py /app
+COPY external_components/llm_extraction/app.py /app
 
 # Make entrypoint etc. convenient for users
 COPY external_components/_entrypoint.sh /usr/local/bin/_entrypoint.sh
 ENTRYPOINT ["/usr/local/bin/_entrypoint.sh"]
-CMD ["fastapi", "dev", "--host", "0.0.0.0", "--port", "8071"]
+CMD ["fastapi", "dev", "--host", "0.0.0.0", "--port", "8072"]

external_components/llm_extraction/environment.yaml

@@ -7,41 +7,11 @@ dependencies:
   - lxml
   - pandas
   - pip
-  - psutil
   - python
   - requests
-  - rpy2
   - uvicorn
-  # Dependencies for rtransparent
-  - r-crul
-  - r-devtools
-  - r-dplyr
-  - r-furrr
-  - r-future
-  - r-globals
-  - r-hoardr
-  - r-httpcode
-  - r-lazyeval
-  - r-lubridate
-  - r-magrittr
-  - r-pbapply
-  - r-pdftools
-  - r-plyr
-  - r-purrr
-  - r-qpdf
-  - r-readr
-  # - r-rentrez
-  - r-rlang
-  - r-stringr
-  - r-tibble
-  - r-tidyr
-  - r-tidyselect
-  - r-timechange
-  - r-tokenizers
-  - r-triebeard
-  - r-urltools
-  - r-utf8
-  # - r-XML
-  - r-xml2
+  - llama-index
+  - llama-index-llms-openai
   - pip:
-    - metapub
+    - odmantic
+    - llama-index-program-openai

osm/cli.py

@@ -2,7 +2,7 @@
 
 from osm._utils import DEFAULT_OUTPUT_DIR, _existing_file, _setup, compose_down
 from osm.pipeline.core import Pipeline, Savers
-from osm.pipeline.extractors import RTransparentExtractor
+from osm.pipeline.extractors import LLMExtractor, RTransparentExtractor
 from osm.pipeline.parsers import NoopParser, PMCParser, ScienceBeamParser
 from osm.pipeline.savers import FileSaver, JSONSaver, OSMSaver
 
@@ -13,6 +13,7 @@
 }
 EXTRACTORS = {
     "rtransparent": RTransparentExtractor,
+    "llm_extractor": LLMExtractor,
 }
 
 
@@ -51,6 +52,11 @@ def parse_args():
         nargs="+",
         help="Select the tool for extracting the output metrics. Default is 'rtransparent'.",
     )
+    parser.add_argument(
+        "--llm_model",
+        default="gpt-4o-2024-08-06",
+        help="Specify the model to use for LLM extraction.",
+    )
     parser.add_argument(
         "--comment",
         required=False,