Feature/vcf

.github/workflows/build.yaml

@@ -27,7 +27,7 @@ jobs:
 
         # Login to Quay.io and build image
         docker login quay.io
-        docker build -t $REPO:$BRANCH .
+        docker build --build-arg GITHUB_SHA=$GITHUB_SHA -t $REPO:$BRANCH .
 
         # Add 'latest' tag to 'main' image
         if [[ $BRANCH == 'main' ]]; then

Dockerfile

@@ -1,12 +1,21 @@
 FROM python:3.12
 
-WORKDIR /app
+ARG GITHUB_SHA
+ENV GITHUB_SHA=$GITHUB_SHA
 
-ADD "https://api.github.com/repos/ACED-IDP/image_viewer/commits?per_page=1" latest_commit
-
-RUN git clone  https://github.com/ACED-IDP/image_viewer
 WORKDIR /app/image_viewer
-RUN git checkout development
-RUN pip install --no-cache-dir .
-RUN git log --oneline
+# Copy the project files into the container
+COPY pyproject.toml  ./
+
+RUN pip install .
+
+# write git commit hash to a file
+RUN echo $GITHUB_SHA > git_commit_hash.txt
+
+# Copy the rest of the project files into the container
+COPY . .
+
+# Expose the port your app listens on
+EXPOSE 8000
+
 CMD ["uvicorn", "image_viewer.app:app", "--reload"]

image_viewer/__init__.py

@@ -0,0 +1,4 @@
+from cacheout import Cache
+
+cache = Cache(ttl=60)  # 1 second
+

image_viewer/app.py

@@ -3,12 +3,13 @@
 import threading
 
 import uvicorn
-from fastapi import FastAPI, HTTPException, Header, Cookie
+from fastapi import FastAPI, HTTPException, Header, Cookie, Request
 from fastapi.responses import RedirectResponse
 from pydantic import Field
 from pydantic_settings import BaseSettings, SettingsConfigDict
 
-from image_viewer.indexd_searcher import aviator_url
+from image_viewer import cache
+from image_viewer.indexd_searcher import redirection_url
 
 #AVIVATOR_URL = "https://avivator.gehlenborglab.org/?image_url="
 AVIVATOR_URL = "/aviator/?image_url="
@@ -44,7 +45,8 @@ async def health_check():
          summary="View Object",
          description="Redirects to a URL for the object.",
          responses={307: {"description": "Temporary Redirect"}})
-async def view_object(object_id: str, authorization: str = Header(None), access_token: str = Cookie(None)):
+async def view_object(object_id: str, request: Request, authorization: str = Header(None), access_token: str = Cookie(None)):
+    """Create a view for the object, render a redirect."""
 
     token = None
 
@@ -62,7 +64,7 @@ async def view_object(object_id: str, authorization: str = Header(None), access_
 
     try:
         logger.error(f"in view object {object_id} {settings.base_url}")
-        redirect_url = aviator_url(object_id, token, settings.base_url)
+        redirect_url = redirection_url(object_id, token, settings.base_url, request)
         logger.error(f"in view object {redirect_url}")
 
         return RedirectResponse(url=redirect_url)
@@ -71,6 +73,23 @@ async def view_object(object_id: str, authorization: str = Header(None), access_
         raise HTTPException(status_code=e.status_code, detail=str(e))
 
 
+@app.get("/ucsc/{token_hash}/{object_id}",
+         summary="UCSC Genome Browser Track definition",
+         description="Redirects to a URL for the object.",
+         responses={200: {"description": "Track config https://genome.ucsc.edu/goldenpath/help/trackDb/trackDbHub.html"}})
+async def ucsc_track(token_hash: str, object_id: str, authorization: str = Header(None), access_token: str = Cookie(None)):
+    urls: dict = cache.get(f"{object_id}_{token_hash}")
+    if not urls:
+        raise HTTPException(status_code=404, detail="No signed URL found")
+    source = urls.get("source")
+    tbi = urls.get("tbi")
+    if not source or not tbi:
+        raise HTTPException(status_code=404, detail="No signed URL found")
+    return f"""
+    track type=vcf name="vcf" description="vcf" visibility=full bigDataUrl="{source}" bigDataIndex="{tbi}"
+    """
+
+
 # Make the application multi-threaded
 def run_server():
     uvicorn.run(app, host="0.0.0.0", port=8000, workers=4)  # workers=4 makes the app multi-threaded.

image_viewer/indexd_searcher.py

@@ -1,18 +1,91 @@
+import hashlib
 import urllib
 
-from fastapi import HTTPException
+from fastapi import HTTPException, Request
 from gen3.auth import Gen3Auth
 from gen3.file import Gen3File
 from gen3.index import Gen3Index
+
+from image_viewer import cache
 from image_viewer.object_signer import get_signed_url
 import logging
+import re
+from dataclasses import dataclass
 
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.DEBUG)
 
 
-def aviator_url(object_id: str, access_token: str, base_url: str) -> str:
-    """Return the URL for the Aviator image viewer.
+@dataclass
+class RegexEqual(str):
+    string: str
+    match: re.Match = None
+
+    def __eq__(self, pattern):
+        self.match = re.search(pattern, self.string)
+        return self.match is not None
+
+
+def aviator_url(source_record, base_url, file_service, index_service):
+    """Return the URL for the Aviator image viewer."""
+    source_file_name = source_record["file_name"]
+
+    offset_file_name = source_file_name.replace("ome.tiff", "offsets.json")
+    offset_file_name = offset_file_name.replace("ome.tif", "offsets.json")
+    offsets_records = index_service.query_urls(offset_file_name)
+    if not isinstance(offsets_records, list) or len(offsets_records) != 1:
+        raise HTTPException(status_code=404,
+                            detail=f"Could not find object with file_name {offset_file_name} {offsets_records}")
+    offsets_record = offsets_records[0]
+    if "did" not in offsets_record:
+        raise HTTPException(status_code=404, detail=f"Could not find did within {offsets_record}")
+    offsets_object_id = offsets_record["did"]
+
+    # get the signed url for the source object
+    object_id = source_record["did"]
+    source_signed_url = get_signed_url(object_id, file_service)
+    offsets_signed_url = get_signed_url(offsets_object_id, file_service)
+
+    # Use the configurable base_url from settings
+    # we encode the signed url because it will contain special characters
+    redirect_url = f"{base_url}{urllib.parse.quote_plus(source_signed_url)}&offsets_url={urllib.parse.quote_plus(offsets_signed_url)}"
+    return redirect_url
+
+
+def genome_browser_url(source_record, base_url, access_token, file_service, index_service):
+    """Return the URL for the genome browser."""
+    vcf_file_name = source_record["file_name"]
+
+    tbi_file_name = vcf_file_name + ".tbi"
+    tbi_records = index_service.query_urls(tbi_file_name)
+    if not isinstance(tbi_records, list) or len(tbi_records) != 1:
+        raise HTTPException(status_code=404,
+                            detail=f"Could not find object with file_name {tbi_file_name} {tbi_records}")
+    tbi_record = tbi_records[0]
+    if "did" not in tbi_record:
+        raise HTTPException(status_code=404, detail=f"Could not find did within {tbi_record}")
+    tbi_object_id = tbi_record["did"]
+
+    # get the signed url for the source object
+    object_id = source_record["did"]
+    source_signed_url = get_signed_url(object_id, file_service)
+    tbi_signed_url = get_signed_url(tbi_object_id, file_service)
+
+    # Use the configurable base_url from settings
+    # we encode the signed url because it will contain special characters
+    access_token_hash = hashlib.md5(access_token.encode()).hexdigest()
+    cache.set(f"{object_id}_{access_token_hash}", {
+        "source": source_signed_url,
+        "tbi": tbi_signed_url
+    })
+    # coordinate
+    hub_url = f"{base_url}/ucsc/{access_token_hash}/{object_id}"
+    redirect_url = f"http://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl={urllib.parse.quote_plus(hub_url)}"
+    return redirect_url
+
+
+def redirection_url(object_id: str, access_token: str, base_url: str, request: Request) -> str:
+    """Return the URL for the object.
     object_id: str The object ID of an ome.tif file to view
     access_token: str The access token to use for authentication
     base_url: str The base URL for the Aviator image viewer
@@ -30,32 +103,25 @@ def aviator_url(object_id: str, access_token: str, base_url: str) -> str:
     file_service = Gen3File(auth)
     index_service = Gen3Index(auth)
 
+    logger.error(f"in redirection_url")
+
     source_record = index_service.get(object_id)
     if not isinstance(source_record, dict):
-        raise HTTPException(status_code=500, detail=f"Could not find object with id {object_id} {source_record}")
-    logger.error(f"aviator_url source_record {source_record}")
+        raise HTTPException(status_code=404, detail=f"Could not find object with id {object_id} {source_record}")
+
+    logger.error(f"redirection_url source_record {source_record}")
+
     if "file_name" not in source_record:
         raise HTTPException(status_code=500, detail=f"Could not find file_name within {source_record}")
-    if "ome.tif" not in source_record["file_name"]:
-        raise HTTPException(status_code=500, detail=f"Expected file_name to contain 'ome.tif' {source_record}")
-    source_file_name = source_record["file_name"]
 
-    offset_file_name = source_file_name.replace("ome.tiff", "offsets.json")
-    offset_file_name = offset_file_name.replace("ome.tif", "offsets.json")
-    offsets_records = index_service.query_urls(offset_file_name)
-    if not isinstance(offsets_records, list) or len(offsets_records) != 1:
-        raise HTTPException(status_code=500,
-                            detail=f"Could not find object with file_name {offset_file_name} {offsets_records}")
-    offsets_record = offsets_records[0]
-    if "did" not in offsets_record:
-        raise HTTPException(status_code=500, detail=f"Could not find did within {offsets_record}")
-    offsets_object_id = offsets_record["did"]
+    redirect_url = None
+    match RegexEqual(source_record['file_name']):
+        case "\\.ome.tif?":
+            redirect_url = aviator_url(source_record, base_url, file_service, index_service)
+        case "\\.vcf":
+            redirect_url = genome_browser_url(source_record, request.base_url, access_token, file_service, index_service)
 
-    # get the signed url for the source object
-    source_signed_url = get_signed_url(object_id, file_service)
-    offsets_signed_url = get_signed_url(offsets_object_id, file_service)
+    if not redirect_url:
+        raise HTTPException(status_code=500, detail=f"Could not match a viewer for {source_record['file_name']}")
 
-    # Use the configurable base_url from settings
-    # we encode the signed url because it will contain special characters
-    redirect_url = f"{base_url}{urllib.parse.quote_plus(source_signed_url)}&offsets_url={urllib.parse.quote_plus(offsets_signed_url)}"
     return redirect_url

pyproject.toml

@@ -7,15 +7,16 @@ name = "image_viewer"
 version = "0.1.0"
 description = "A FastAPI project for viewing images"
 authors = [
-    { name = "Your Name", email = "your.email@example.com" }
+    { name = "Brian Walsh", email = "walsbr@ohsu.edu" }
 ]
 dependencies = [
     "fastapi",
     "uvicorn",
     "requests",
     "pydantic-settings",
     "python-dotenv",
-    "gen3"
+    "gen3",
+    "cacheout"
 ]
 
 [project.optional-dependencies]

tests/unit/app/conftest.py

@@ -1,6 +1,6 @@
 import urllib.parse
 from importlib import reload
-
+from fastapi import Request
 from fastapi.testclient import TestClient
 import pytest
 import image_viewer.app
@@ -41,17 +41,19 @@ def monkey_patch_aviator(monkeypatch):
     """Monkey patch the Aviator URL response."""
     import image_viewer.indexd_searcher
 
-    def mock_aviator_url(object_id, access_token, base_url):
+    def mock_aviator_url(object_id, access_token, base_url, request: Request):
         """Mock the Aviator URL response"""
+        print("In mock_aviator_url")
         image_url = urllib.parse.quote_plus(f'https://image-{object_id}')
         offsets_url = urllib.parse.quote_plus(f'https://offsets-{object_id}')
         parms = f'image_url={image_url}&offsets_url={offsets_url}'
         _ = f"https://env-file-url.com/objects/?{parms}"
-        print(f"Mocked aviator_url: {object_id} {access_token} {base_url} -> {_}")
+        print(f"Mocked redirection_url: {object_id} {access_token} {base_url} -> {_}")
         return _
 
-    monkeypatch.setattr(image_viewer.indexd_searcher, "aviator_url", mock_aviator_url)
-    print("Monkey patched aviator_url")
+    monkeypatch.setattr(image_viewer.indexd_searcher, "redirection_url", mock_aviator_url)
+    print("Monkey patched redirection_url")
+    # print(image_viewer.indexd_searcher.redirection_url("123", "456", "789", None))
 
 
 def monkey_patch_signed_url(monkeypatch):

tests/unit/app/test_auth_needed_env_variable.py

@@ -16,11 +16,13 @@ def client_with_cookie_base_url(monkeypatch, base_url, valid_token):
     client_ = TestClient(image_viewer.app.app)
 
     client_.cookies.update({"access_token": valid_token})
+    print(client_)
     yield client_
 
 
 # Test setting base_url via environment variable
 def test_base_url_from_env_variable(monkeypatch, client_with_cookie_base_url, base_url):
+    print(client_with_cookie_base_url)
 
     object_id = "123"
     response = client_with_cookie_base_url.get(f"/view/{object_id}", follow_redirects=False)

tests/unit/app/test_file_type.py

@@ -0,0 +1,32 @@
+from image_viewer.indexd_searcher import RegexEqual
+
+
+def test_simple_match():
+    match RegexEqual("Something to match"):
+        case "^...match":
+            print("Nope...")
+        case "^S.*ing$":
+            print("Closer...")
+        case "^S.*match$":
+            print("Yep!")
+        case _:
+            assert False, "Should not match anything else"
+
+
+def test_extension_match():
+
+    match RegexEqual("/a/b/c/d.txt"):
+        case "\\.txt":
+            print("ok")
+        case _:
+            assert False, "Should not match anything else"
+
+    for file_name in ["/a/b/c/d.ome.tif", "/a/b/c/d.ome.tiff", "/a/b/c/d.vcf.gz", "/a/b/c/d.vcf"]:
+        match RegexEqual(file_name):
+            case "\\.ome.tif?":
+                continue
+            case "\\.vcf":
+                continue
+            case _:
+                assert False, "Should not match anything else"
+        assert False, "Should not match anything else"