From 75741bffe89b92cde9b84f3f3c2426dc3e0e3954 Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Wed, 29 May 2024 13:05:15 -0700
Subject: [PATCH] Wrapper to upload a reference and fix bugs in search (#6)

---
 src/celldex/__init__.py          |  1 +
 src/celldex/search_references.py | 12 ++---
 src/celldex/upload_reference.py  | 88 ++++++++++++++++++++++++++++++++
 tests/test_search_refs.py        |  6 +--
 4 files changed, 95 insertions(+), 12 deletions(-)
 create mode 100644 src/celldex/upload_reference.py

diff --git a/src/celldex/__init__.py b/src/celldex/__init__.py
index 2ac565f..8cf719e 100644
--- a/src/celldex/__init__.py
+++ b/src/celldex/__init__.py
@@ -20,3 +20,4 @@
 from .list_versions import fetch_latest_version, list_versions
 from .save_reference import save_reference
 from .search_references import search_references
+from .upload_reference import upload_reference
diff --git a/src/celldex/search_references.py b/src/celldex/search_references.py
index c87634b..5e4ca90 100644
--- a/src/celldex/search_references.py
+++ b/src/celldex/search_references.py
@@ -48,18 +48,12 @@ def search_references(
 
     .. code-block:: python
 
-        res = search_references("brain")
+        res = search_references("human")
 
-        res = search_references(define_text_query("Neuro%", partial=True")
+        res = search_references(define_text_query("Immun%", partial=True")
 
         res = search_references(define_text_query("10090", field="taxonomy_id")
 
-        res = search_references(
-            define_text_query("GRCm38", field="genome") &
-            (define_text_query("neuro%", partial=True) |
-                define_text_query("pancrea%", partial=True))
-        )
-
     Args:
         query:
             The search query string or a
@@ -97,7 +91,7 @@ def search_references(
         stmt += ", versions.latest AS latest"
         key_names.append("latest")
 
-    stmt += " FROM paths LEFT JOIN versions ON paths.vid = versions.vid WHERE versions.project = 'scRNAseq'"
+    stmt += " FROM paths LEFT JOIN versions ON paths.vid = versions.vid WHERE versions.project = 'celldex'"
 
     if latest:
         stmt += " AND versions.latest = 1"
diff --git a/src/celldex/upload_reference.py b/src/celldex/upload_reference.py
new file mode 100644
index 0000000..5fd676e
--- /dev/null
+++ b/src/celldex/upload_reference.py
@@ -0,0 +1,88 @@
+from gypsum_client import cache_directory, rest_url, upload_directory
+
+__author__ = "Jayaram Kancherla"
+__copyright__ = "Jayaram Kancherla"
+__license__ = "MIT"
+
+
+def upload_reference(
+    directory: str,
+    name: str,
+    version: str,
+    package: str = "celldex",
+    cache_dir: str = cache_directory(),
+    deduplicate: bool = True,
+    probation: bool = False,
+    url: str = rest_url(),
+    token: str = None,
+    concurrent: int = 1,
+    abort_failed: bool = True,
+):
+    """Upload the reference dataset to the gypsum bucket.
+
+    This is a wrapper around
+    :py:func:`~gypsum_client.upload_file_actions.upload_directory`
+    specific to the `celldex` package.
+
+    See Also:
+        :py:func:`~gypsum_client.upload_file_actions.upload_directory`,
+        to upload a directory to the gypsum backend.
+
+    Args:
+        Name:
+            Reference dataset name.
+
+        version:
+            Version name for the reference.
+
+        directory:
+            Path to a directory containing the ``files`` to be uploaded.
+            This directory is assumed to correspond to a version of an asset.
+
+        cache_dir:
+            Path to the cache for saving files, e.g., in
+            :py:func:`~gypsum_client.save_operations.save_version`.
+
+            Used to convert symbolic links to upload links,see
+            :py:func:`~gypsum_client.prepare_directory_for_upload.prepare_directory_upload`.
+
+        deduplicate:
+            Whether the backend should attempt deduplication of ``files``
+            in the immediately previous version.
+            Defaults to True.
+
+        probation:
+            Whether to perform a probational upload.
+            Defaults to False.
+
+        url:
+            URL of the gypsum REST API.
+
+        token:
+            GitHub access token to authenticate to the gypsum REST API.
+
+        concurrent:
+            Number of concurrent downloads.
+            Defaults to 1.
+
+        abort_failed:
+            Whether to abort the upload on any failure.
+
+            Setting this to `False` can be helpful for diagnosing upload problems.
+
+    Returns:
+        `True` if successfull, otherwise `False`.
+    """
+    return upload_directory(
+        directory,
+        package,
+        name,
+        version,
+        cache_dir=cache_dir,
+        deduplicate=deduplicate,
+        probation=probation,
+        url=url,
+        token=token,
+        concurrent=concurrent,
+        abort_failed=abort_failed,
+    )
diff --git a/tests/test_search_refs.py b/tests/test_search_refs.py
index 9eac96d..e824d07 100644
--- a/tests/test_search_refs.py
+++ b/tests/test_search_refs.py
@@ -8,11 +8,11 @@
 
 
 def test_search_references():
-    res = search_references("brain")
-    assert len(res) > 10
+    res = search_references("human")
+    assert len(res) > 3
     assert isinstance(res, pd.DataFrame)
 
-    res = search_references(define_text_query("Neuro%", partial=True))
+    res = search_references(define_text_query("Immun%", partial=True))
     assert isinstance(res, pd.DataFrame)
     assert len(res) > 0