Improved handling of user query for higlass items

CHANGELOG.rst

@@ -7,6 +7,12 @@ foursight
 Change Log
 ----------
 
+4.4.3
+=====
+* Add helper to convert user input str to list for select queries in higlass_checks.py
+
+`PR 564: Improved handling of user query for higlass items <https://github.com/4dn-dcic/foursight/pull/564>`_
+
 4.4.2
 =====
 * Added 'input_bed' to attr_keys in wfr_utils.py's start_missing_run for ATAC-seq pipeline

chalicelib_fourfront/checks/higlass_checks.py

@@ -354,12 +354,7 @@ def find_files_requiring_higlass_items(connection, check_name, action_name, sear
     check.queries = []
     check.action = action_name
 
-    # If no search query was provided, fail
-    if not search_queries:
-        check.summary = check.description = "No search query provided, nothing to update."
-        check.status = 'PASS'
-        check.allow_action = False
-        return check
+    check, search_queries = verify_queries(check, search_queries, False)
 
     # Add the fields we want to return.
     fields_to_include = '&field=' + '&field='.join((
@@ -827,12 +822,7 @@ def find_expsets_processedfiles_requiring_higlass_items(connection, check_name,
         "static_content",
     ])
 
-    # If no search query was provided, fail
-    if not search_queries:
-        check.summary = check.description = "No search query provided, nothing to update."
-        check.status = 'PASS'
-        check.allow_action = False
-        return check
+    check, search_queries = verify_queries(check, search_queries, False)
 
     expsets_by_accession = {}
     # Use all of the search queries to make a list of the ExpSets we will work on.
@@ -1177,12 +1167,7 @@ def find_expsets_otherprocessedfiles_requiring_higlass_items(connection, check_n
     check.queries = []
     check.action = action_name
 
-    # If no search query was provided and find_opfs_missing_higlass is False, pass with no results
-    if not (search_queries or find_opfs_missing_higlass):
-        check.summary = check.description = "No search query provided, nothing to update."
-        check.status = 'PASS'
-        check.allow_action = False
-        return check
+    check, search_queries = verify_queries(check, search_queries, find_opfs_missing_higlass)
 
     if find_opfs_missing_higlass:
         search_queries = [
@@ -2287,3 +2272,31 @@ def convert_es_timestamp_to_datetime(raw):
         "%Y-%m-%dT%H:%M:%S"
     )
     return converted_date
+
+def verify_queries(check, search_queries, ignore_queries):
+    """
+    Helper to check that a search query if properly formatted and reformat if necessary
+
+    Args:
+        check(CheckResult): Result of check, to be passed from check.
+        search_queries(list or string): A list of search queries. All Files found in at least one of the queries will be modified.
+        ignore_queries(Boolean): If True, ignore search queries (used for other processed files default query)
+
+    Returns:
+        Check results object
+        Formatted search_queries (list)
+    """
+    # If no search query was provided (and ignore_queries is False), pass with no results
+    if not (search_queries or ignore_queries):
+        check.summary = check.description = "No search query provided, nothing to update."
+        check.status = 'PASS'
+        check.allow_action = False
+
+    if isinstance(search_queries, str):
+        # for case where (possibly multiple) query is passed in via kwargs
+        queries = search_queries.split(',')
+        search_queries = [q.strip() for q in queries]
+        check.brief_output = {
+            "corrected_query": "The query was not formatted as a list, please double check results"
+        }
+    return check, search_queries

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "foursight"
-version = "4.4.2"
+version = "4.4.3"
 description = "Serverless Chalice Application for Monitoring"
 authors = ["4DN-DCIC Team <[email protected]>"]
 license = "MIT"