Extend Gemini to include getting file content and logging out of the Archive.

Author: davner

astroquery/gemini/core.py

@@ -1,20 +1,21 @@
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
 """
-Search functionality for the Gemini archive of observations.
+==================================================
+Gemini Observatory Archive (GOA) Astroquery Module
+==================================================
 
-For questions, contact [email protected]
+Query public and proprietary data from GOA.
 """
-
 import os
-
 from datetime import date
 
 from astroquery import log
+import astropy
 from astropy import units
 from astropy.table import Table, MaskedColumn
-
-from astroquery.gemini.urlhelper import URLHelper
 import numpy as np
 
+from .urlhelper import URLHelper
 from ..query import QueryWithLogin
 from ..utils.class_or_instance import class_or_instance
 from . import conf
@@ -433,6 +434,97 @@ def get_file(self, filename, *, download_dir='.', timeout=None):
         local_filepath = os.path.join(download_dir, filename)
         self._download_file(url=url, local_filepath=local_filepath, timeout=timeout)
 
+    def _download_file_content(self, url, timeout=None, auth=None, method="GET", **kwargs):
+        """Download content from a URL and return it. Resembles
+        `_download_file` but returns the content instead of saving it to a
+        local file.
+
+        Parameters
+        ----------
+        url : str
+            The URL from where to download the file.
+        timeout : int, optional
+            Time in seconds to wait for the server response, by default
+            `None`.
+        auth : dict[str, Any], optional
+            Authentication details, by default `None`.
+        method : str, optional
+            The HTTP method to use, by default "GET".
+
+        Returns
+        -------
+        bytes
+            The downloaded content.
+        """
+
+        response = self._session.request(method, url, timeout=timeout, auth=auth, **kwargs)
+        response.raise_for_status()
+
+        if 'content-length' in response.headers:
+            length = int(response.headers['content-length'])
+            if length == 0:
+                log.warn(f'URL {url} has length=0')
+
+        blocksize = astropy.utils.data.conf.download_block_size
+        content = b""
+
+        for block in response.iter_content(blocksize):
+            content += block
+
+        response.close()
+
+        return content
+
+    def logout(self):
+        """Logout from the GOA service by deleting the specific session cookie
+        and updating the authentication state.
+        """
+        # Delete specific cookie.
+        cookie_name = "gemini_archive_session"
+        if cookie_name in self._session.cookies:
+            del self._session.cookies[cookie_name]
+
+        # Update authentication state.
+        self._authenticated = False
+
+    def get_file_content(self, filename, timeout=None, auth=None, method="GET", **kwargs):
+        """Wrapper around `_download_file_content`.
+
+        Parameters
+        ----------
+        filename : str
+            Name of the file to download content.
+        timeout : int, optional
+            Time in seconds to wait for the server response, by default
+            `None`.
+        auth : dict[str, Any], optional
+            Authentication details, by default `None`.
+        method : str, optional
+            The HTTP method to use, by default "GET".
+
+        Returns
+        -------
+        bytes
+            The downloaded content.
+        """
+        url = self.get_file_url(filename)
+        return self._download_file_content(url, timeout=timeout, auth=auth, method=method, **kwargs)
+
+    def get_file_url(self, filename):
+        """Generate the file URL based on the filename.
+
+        Parameters
+        ----------
+        filename : str
+            The name of the file.
+
+        Returns
+        -------
+        str
+            The URL where the file can be downloaded.
+        """
+        return f"https://archive.gemini.edu/file/{filename}"
+
 
 def _gemini_json_to_table(json):
     """

astroquery/gemini/tests/test_gemini.py

@@ -24,18 +24,37 @@ class MockResponse:
 
     def __init__(self, text):
         self.text = text
+        self.headers = {'content-length': str(len(text))}
+        self.status_code = 200
 
     def json(self):
         return json.loads(self.text)
 
+    def raise_for_status(self):
+        pass
+
+    def iter_content(self, blocksize):
+        yield self.text
+
+    def close(self):
+        pass
+
 
 @pytest.fixture
 def patch_get(request):
     """ mock get requests so they return our canned JSON to mimic Gemini's archive website """
     mp = request.getfixturevalue("monkeypatch")
 
     mp.setattr(requests.Session, 'request', get_mockreturn)
-    return mp
+
+
+@pytest.fixture
+def patch_content(monkeypatch):
+    """Mock requests with encoded content."""
+    def mock_request(*args, **kwargs):
+        return MockResponse(b"mock_content")
+
+    monkeypatch.setattr(requests.Session, 'request', mock_request)
 
 
 # to inspect behavior, updated when the mock get call is made
@@ -171,3 +190,25 @@ def test_url_helper_eng_fail(test_arg):
     urlsplit = url.split('/')
     assert (('notengineering' in urlsplit) == should_have_noteng)
     assert (('NotFail' in urlsplit) == should_have_notfail)
+
+
+def test_logout():
+    """Test logout functionality."""
+    gemini.Observations._session.cookies = {"gemini_archive_session": "some_value"}
+    gemini.Observations._authenticated = True
+    gemini.Observations.logout()
+    assert "gemini_archive_session" not in gemini.Observations._session.cookies
+    assert gemini.Observations._authenticated is False
+
+
+def test_get_file_content(patch_content):
+    """Test wrapper around _download_file_content."""
+    content = gemini.Observations.get_file_content("filename", timeout=5)
+    assert content == b"mock_content"
+
+
+def test_get_file_url():
+    """Test generating file URL based on filename."""
+    url = gemini.Observations.get_file_url("filename")
+    assert url == "https://archive.gemini.edu/file/filename"
+

astroquery/gemini/tests/test_remote.py

@@ -8,6 +8,7 @@
 https://astroquery.readthedocs.io/en/latest/testing.html
 """
 import pytest
+import requests
 
 import os
 import shutil
@@ -23,6 +24,10 @@
 """ Coordinates to use for testing """
 coords = SkyCoord(210.80242917, 54.34875, unit="deg")
 
+# Filename and url
+filename = "S20231016S0018.fits.bz2"  # Small file
+file_url = f"https://archive.gemini.edu/file{filename}"
+
 
 @pytest.mark.remote_data
 class TestGemini:
@@ -78,3 +83,14 @@ def test_get_file(self):
             os.unlink(filepath)
         if os.path.exists(tempdir):
             shutil.rmtree(tempdir)
+
+    def test_get_file_content(self):
+        """Test the `get_file_content` function."""
+        content = gemini.Observations.get_file_content(filename)
+        assert isinstance(content, bytes)
+        assert len(content) > 0
+
+    def test_get_file_content_with_timeout(self):
+        """Test `get_file_content` with a timeout."""
+        with pytest.raises(requests.exceptions.Timeout):
+            gemini.Observations.get_file_content(filename, timeout=0.001)

docs/gemini/gemini.rst

@@ -132,19 +132,21 @@ the *NotFail* or *notengineering* terms respectively.
 Authenticated Sessions
 ----------------------
 
-The Gemini module allows for authenticated sessions using your GOA account.  This is the same account you login
-with on the GOA homepage at `<https://archive.gemini.edu/>`__.  The `astroquery.gemini.ObservationsClass.login`
-method returns `True` if successful.
+The Gemini module allows for authenticated sessions using your GOA account.  This is the same account you
+login with on the GOA homepage at `<https://archive.gemini.edu/>`__.  The
+`astroquery.gemini.ObservationsClass.login` method returns `True` if successful. To logout, use the
+`astroquery.gemini.ObservationsClass.logout` method to remove the Gemini Observatory Archive session cookie.
 
 .. doctest-skip::
 
                 >>> from astroquery.gemini import Observations
                 >>> Observations.login(username, password)
                 >>> # do something with your elevated access
+                >>> Observations.logout()
 
 
-File Downloading
-----------------
+File Downloading and File Content Getting
+-----------------------------------------
 
 As a convenience, you can request file downloads directly from the Gemini module.  This constructs the appropriate
 URL and fetches the file.  It will use any authenticated session you may have, so it will retrieve any
@@ -156,6 +158,15 @@ proprietary data you may be permissioned for.
                 >>> Observations.get_file("GS2020AQ319-10.fits", download_dir="/tmp")  # doctest: +IGNORE_OUTPUT
 
 
+To get the file content without writing to disk, you can use the method
+`astroquery.gemini.ObservationsClass.get_file_content`. This constructs the appropriate url and fetches the
+file contents. This will use any authenticated session you have for proprietary data.
+
+.. doctest-remote-data::
+                >>> from astroquery.gemini import Observations
+                >>> Observations.get_file_content("GS2020AQ319-10.fits")  # doctest: +IGNORE_OUTPUT
+
+
 Reference/API
 =============