Handle missing VALUE in value_x dict (#223)

* pysradb/sraweb.py: adding a default None value when VALUE is not a key in the value_x dict; this works for the test case in issue #222 * Drop Python 3.7, 3.8 * Update release notes * Update release notes * Suppress ena search test --------- Co-authored-by: Saket Choudhary <[email protected]>
saketkc · Oct 25, 2024 · 85abf88 · 85abf88
1 parent 35dbf24
commit 85abf88
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diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9, '3.10', '3.11']
+        python-version: [3.9, '3.10', '3.11']
 
     steps:
     - uses: actions/checkout@v2

diff --git a/.github/workflows/push.yml b/.github/workflows/push.yml
@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9, '3.10', '3.11']
+        python-version: [3.9, '3.10', '3.11']
 
     steps:
     - uses: actions/checkout@v2

diff --git a/HISTORY.md b/HISTORY.md
@@ -1,5 +1,8 @@
 # History
 
+# UNRELEASED
+- Fix for handling missing metadata keys [#223](https://github.com/saketkc/pysradb/pull/223). Thanks [@andrewdavidsmith](https://github.com/andrewdavidsmith)
+
 # 2.2.2 (2024-10-03)
 - Fix for handling ENA urls for paired end data
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -8,7 +8,7 @@ dynamic = ["version"]
 description = "A Python package for interacting with SRAdb and downloading datasets from SRA/ENA/GEO"
 readme = "README.md"
 license = {file = "LICENSE"}
-requires-python = ">=3.7"
+requires-python = ">=3.9"
 authors = [
     { name = "Saket Choudhary", email = "[email protected]" },
 ]
@@ -22,8 +22,6 @@ classifiers = [
     "License :: OSI Approved :: BSD License",
     "Natural Language :: English",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.7",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",

diff --git a/pysradb/sraweb.py b/pysradb/sraweb.py
@@ -593,7 +593,7 @@ def sra_metadata(
                         if not isinstance(value_x, dict):
                             continue
                         tag = value_x["TAG"].lower()
-                        value = value_x["VALUE"]
+                        value = value_x["VALUE"] if "VALUE" in value_x else None
                         detailed_record[tag] = value
                 lib_record = exp_record["DESIGN"]["LIBRARY_DESCRIPTOR"]
                 for key, value in lib_record.items():

diff --git a/tests/test_search.py b/tests/test_search.py
@@ -1074,7 +1074,7 @@ def _test_ena_search_3(capsys):
     )
 
 
-def test_valid_search_query_1_ena(valid_search_inputs_1):
+def _test_valid_search_query_1_ena(valid_search_inputs_1):
     expected_query = [
         '(experiment_title="*covid-19*" OR study_accession="COVID-19" OR secondary_study_accession="COVID-19" OR'
         ' sample_accession="COVID-19" OR secondary_sample_accession="COVID-19" OR experiment_accession="COVID-19" OR'
@@ -1102,7 +1102,7 @@ def test_valid_search_query_1_ena(valid_search_inputs_1):
         )
 
 
-def test_valid_search_query_2_ena(valid_search_inputs_2):
+def _test_valid_search_query_2_ena(valid_search_inputs_2):
     expected_query = [
         'library_layout="TRIPLE"',
         '(experiment_title="*Escherichia coli*") AND (study_accession="SRS6898222" OR '