Added requested changes for renaming, added amr_linking endpoint, cha…

…nges to pdf extractions endpoint.

.gitignore

@@ -5,3 +5,6 @@
 .env
 api.env
 *.env
+
+# Python
+__pycache__

Makefile

@@ -43,5 +43,5 @@ restart:docker-compose.yaml
 # No internal docker connection to TDS
 .PHONY:up-prod
 up-prod:docker-compose.yaml
- $(DOCKER_COMPOSE) compose up -f docker-compose.prod.yaml -d
+ $(DOCKER_COMPOSE) compose -f docker-compose.prod.yaml up -d
 

api.env.sample

@@ -1,7 +1,6 @@
 REDIS_HOST=redis
 REDIS_PORT=6379
-TDS_URL=http://data-service-api:8000
-SKEMA_RS_URL=http://skema-rs:8080
-TA1_UNIFIED_URL=http://skema-unified:8000
-INTEGRATED_TR_URL=http://integrated-tr:7778
-MIT_TR_URL=http://mit-tr:8000
+TDS_URL=http://data-service.staging.terarium.ai
+SKEMA_RS_URL=http://skema-rs.staging.terarium.ai
+TA1_UNIFIED_URL=http://skema-unified.staging.terarium.ai
+MIT_TR_URL=http://mit-tr.staging.terarium.ai

api/server.py

@@ -34,14 +34,14 @@ def build_api(*args) -> FastAPI:
 app = build_api()
 
 
-@app.get("/status/{simulation_id}")
-def get_status(simulation_id: str):
+@app.get("/status/{extraction_job_id}")
+def get_status(extraction_job_id: str):
  """
  Retrieve the status of a simulation
  """
  from utils import fetch_job_status
 
- status, result = fetch_job_status(simulation_id)
+ status, result = fetch_job_status(extraction_job_id)
  if not isinstance(status, str):
  return status
 
@@ -70,7 +70,7 @@ def mathml_to_amr(payload: List[str], model: str = "petrinet"):
 
 @app.post("/pdf_extractions")
 async def pdf_extractions(
- pdf: UploadFile = File(...),
+ artifact_id: str,
  annotate_skema: bool = True,
  annotate_mit: bool = True,
  name: str = None,
@@ -84,36 +84,14 @@ async def pdf_extractions(
 
  from utils import create_job
 
- # Create a file-like object from the file content
- filename = pdf.filename
- pdf_file = io.BytesIO(await pdf.read())
-
- if filename.split(".")[-1] == "pdf":
- # Open the PDF file and extract text content
- pdf_reader = pypdf.PdfReader(pdf_file)
- num_pages = len(pdf_reader.pages)
-
- text_content = ""
- for page_number in range(num_pages):
- page = pdf_reader.pages[page_number]
- text_content += page.extract_text()
- else:
- # Open the TXT file and extract text content
- with pdf_file as pdf:
- text_content = ""
- for page in pdf:
- text_content += page.decode("utf-8")
-
  operation_name = "operations.pdf_extractions"
 
  # text_content = text_content[: len(text_content) // 2]
  options = {
- "text_content": text_content,
+ "artifact_id": artifact_id,
  "annotate_skema": annotate_skema,
  "annotate_mit": annotate_mit,
- "bytes_obj": pdf_file.seek(0),
- "filename": filename,
- "name": filename.split(".")[0] if name is None else name,
+ "name": name,
  "description": description,
  }
 
@@ -136,3 +114,19 @@ def profile_dataset(dataset_id, document_text):
  resp = create_job(operation_name=operation_name, options=options)
 
  return resp
+
+
+@app.post("/link_amr")
+def link_amr(artifact_id, model_id):
+ from utils import create_job
+
+ operation_name = "operations.link_amr"
+
+ options = {
+ "artifact_id": artifact_id,
+ "model_id": model_id,
+ }
+
+ resp = create_job(operation_name=operation_name, options=options)
+
+ return resp

docker-compose.prod.yaml

@@ -39,59 +39,60 @@ services:
  - redis
  networks:
  - ta1-extraction-service
- mit-tr:
- extends:
- file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
- service: mit-tr
- networks:
- - ta1-extraction-service
- skema-tr:
- extends:
- file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
- service: skema-tr
- networks:
- - ta1-extraction-service
- integrated-tr:
- extends:
- file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
- service: integrated-tr
- networks:
- - ta1-extraction-service
- skema-py:
- extends:
- file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
- service: skema-py
- networks:
- - ta1-extraction-service
- skema-rs:
- extends:
- # Changed to port 8085
- file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
- service: skema-rs
- networks:
- - ta1-extraction-service
- graphdb:
- extends:
- # Changed to port 7688
- file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
- service: graphdb
- networks:
- - ta1-extraction-service
- eq2mml:
- extends:
- # Changed to port 8011
- file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
- service: eq2mml
- networks:
- - ta1-extraction-service
- mathjax:
- extends:
- file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
- service: mathjax
- networks:
- - ta1-extraction-service
 
 volumes:
  mg_lib:
  mg_log:
  mg_etc:
+
+ # mit-tr:
+ # extends:
+ # file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
+ # service: mit-tr
+ # networks:
+ # - ta1-extraction-service
+ # skema-tr:
+ # extends:
+ # file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
+ # service: skema-tr
+ # networks:
+ # - ta1-extraction-service
+ # integrated-tr:
+ # extends:
+ # file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
+ # service: integrated-tr
+ # networks:
+ # - ta1-extraction-service
+ # skema-py:
+ # extends:
+ # file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
+ # service: skema-py
+ # networks:
+ # - ta1-extraction-service
+ # skema-rs:
+ # extends:
+ # # Changed to port 8085
+ # file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
+ # service: skema-rs
+ # networks:
+ # - ta1-extraction-service
+ # graphdb:
+ # extends:
+ # # Changed to port 7688
+ # file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
+ # service: graphdb
+ # networks:
+ # - ta1-extraction-service
+ # eq2mml:
+ # extends:
+ # # Changed to port 8011
+ # file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
+ # service: eq2mml
+ # networks:
+ # - ta1-extraction-service
+ # mathjax:
+ # extends:
+ # file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
+ # service: mathjax
+ # networks:
+ # - ta1-extraction-service

docker-compose.yaml

@@ -43,54 +43,55 @@ services:
  networks:
  - ta1-extraction-service
  - data-api
- mit-tr:
- extends:
- file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
- service: mit-tr
- networks:
- - ta1-extraction-service
- skema-tr:
- extends:
- file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
- service: skema-tr
- networks:
- - ta1-extraction-service
- skema-py:
- extends:
- file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
- service: skema-py
- networks:
- - ta1-extraction-service
- skema-unified:
- extends:
- file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
- service: skema-unified
- skema-rs:
- extends:
- file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
- service: skema-rs
- networks:
- - ta1-extraction-service
- graphdb:
- extends:
- file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
- service: graphdb
- networks:
- - ta1-extraction-service
- eq2mml:
- extends:
- file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
- service: eq2mml
- networks:
- - ta1-extraction-service
- mathjax:
- extends:
- file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
- service: mathjax
- networks:
- - ta1-extraction-service
 
 volumes:
  mg_lib:
  mg_log:
  mg_etc:
+
+ # mit-tr:
+ # extends:
+ # file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
+ # service: mit-tr
+ # networks:
+ # - ta1-extraction-service
+ # skema-tr:
+ # extends:
+ # file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
+ # service: skema-tr
+ # networks:
+ # - ta1-extraction-service
+ # skema-py:
+ # extends:
+ # file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
+ # service: skema-py
+ # networks:
+ # - ta1-extraction-service
+ # skema-unified:
+ # extends:
+ # file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
+ # service: skema-unified
+ # skema-rs:
+ # extends:
+ # file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
+ # service: skema-rs
+ # networks:
+ # - ta1-extraction-service
+ # graphdb:
+ # extends:
+ # file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
+ # service: graphdb
+ # networks:
+ # - ta1-extraction-service
+ # eq2mml:
+ # extends:
+ # file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
+ # service: eq2mml
+ # networks:
+ # - ta1-extraction-service
+ # mathjax:
+ # extends:
+ # file: ./askem-ta1-dockervm/end-to-end-rest/docker-compose.yml
+ # service: mathjax
+ # networks:
+ # - ta1-extraction-service