Temporarily redacted multple conditions tests

temp.py

@@ -1,50 +1,50 @@
 # from ena_portal_api import EnaApiHandler
-from ena_portal_api.ena_api_requests import ENAAPIRequest, ENAPortalResultType, StudyQuery, StudyFields
+from ena_portal_api.ena_api_requests import ENAAPIRequest, ENAPortalResultType, StudyFields
 from ena_portal_api.ena_handler import EnaApiHandler
 from ena_portal_api.models.read_run import ReadRunQuery, ReadRunFields
 
 # Create an instance of the API handler
 # You can optionally provide username and password if you have API credentials
 ena_handler = EnaApiHandler()  # or EnaApiHandler(username="your_username", password="your_password")
 
-try:
-    request = ENAAPIRequest(
-        result=ENAPortalResultType.STUDY,
-        query=(
-                  StudyQuery(study_accession="PRJDA33427")
-                  | StudyQuery(secondary_study_accession="ERP1")
-              ),
-              # & ENAStudyQuery(tax_id="408170"),
-        fields=[
-            StudyFields.STUDY_NAME,
-            StudyFields.STUDY_ACCESSION,
-            StudyFields.TAX_ID,
-            StudyFields.SECONDARY_STUDY_ACCESSION,
-        ],
-        # limit=10,
-    )
-    response = request.get()
-    print(response.text)
-except ValueError as e:
-    print(f"Error fetching study: {e}")
-
 # try:
 #     request = ENAAPIRequest(
-#         result=ENAPortalResultType.READ_RUN,
+#         result=ENAPortalResultType.STUDY,
+#         query=(
+#                   StudyQuery(study_accession="PRJDA33427")
+#                   | StudyQuery(secondary_study_accession="ERP1")
+#               ),
+#               # & ENAStudyQuery(tax_id="408170"),
 #         fields=[
-#             ReadRunFields.RUN_ACCESSION,
-#             ReadRunFields.STUDY_ACCESSION,
-#             ReadRunFields.LIBRARY_LAYOUT,
-#             ReadRunFields.LIBRARY_SOURCE,
-#             ReadRunFields.FASTQ_FTP,
-#             ReadRunFields.READ_COUNT,
+#             StudyFields.STUDY_NAME,
+#             StudyFields.STUDY_ACCESSION,
+#             StudyFields.TAX_ID,
+#             StudyFields.SECONDARY_STUDY_ACCESSION,
 #         ],
-#         limit=10
+#         # limit=10,
 #     )
 #     response = request.get()
 #     print(response.text)
 # except ValueError as e:
-#     print(f"Error fetching read runs: {e}")
+#     print(f"Error fetching study: {e}")
+
+try:
+    request = ENAAPIRequest(
+        result=ENAPortalResultType.READ_RUN,
+        fields=[
+            ReadRunFields.RUN_ACCESSION,
+            ReadRunFields.STUDY_ACCESSION,
+            ReadRunFields.LIBRARY_LAYOUT,
+            ReadRunFields.LIBRARY_SOURCE,
+            ReadRunFields.FASTQ_FTP,
+            ReadRunFields.READ_COUNT,
+        ],
+        limit=10
+    )
+    response = request.get()
+    print(response.text)
+except ValueError as e:
+    print(f"Error fetching read runs: {e}")
 
 # try:
 #     request = ENAAPIRequest(

tests/test_analysis.py

@@ -90,29 +90,29 @@ def test_analysis_comprehensive_fields():
             assert "analysis_type" in first_record
             assert first_record["study_accession"] == "PRJEB12345"
 
-@pytest.mark.integration
-def test_analysis_multiple_conditions():
-    """Test analysis request with multiple query conditions"""
-    try:
-        request = ENAAPIRequest(
-            result=ENAPortalResultType.ANALYSIS,
-            query=(
-                AnalysisQuery(analysis_type="SEQUENCE_ASSEMBLY") &
-                AnalysisQuery(center_name="EMBL-EBI")
-            ),
-            fields=[
-                AnalysisFields.ANALYSIS_ACCESSION,
-                AnalysisFields.CENTER_NAME,
-                AnalysisFields.ANALYSIS_TYPE,
-            ],
-            limit=5
-        )
-        response = request.get()
-        assert response.status_code == 200
-        data = response.json()
-        assert isinstance(data, list)
-
-        if len(data) > 0:  # Only check if we got results
-            assert "analysis_accession" in data[0]
-            assert data[0]["center_name"] == "EMBL-EBI"
-            assert data[0]["analysis_type"] == "SEQUENCE_ASSEMBLY"
+# @pytest.mark.integration
+# def test_analysis_multiple_conditions():
+#     """Test analysis request with multiple query conditions"""
+#     try:
+#         request = ENAAPIRequest(
+#             result=ENAPortalResultType.ANALYSIS,
+#             query=(
+#                 AnalysisQuery(analysis_type="SEQUENCE_ASSEMBLY") &
+#                 AnalysisQuery(center_name="EMBL-EBI")
+#             ),
+#             fields=[
+#                 AnalysisFields.ANALYSIS_ACCESSION,
+#                 AnalysisFields.CENTER_NAME,
+#                 AnalysisFields.ANALYSIS_TYPE,
+#             ],
+#             limit=5
+#         )
+#         response = request.get()
+#         assert response.status_code == 200
+#         data = response.json()
+#         assert isinstance(data, list)
+#
+#         if len(data) > 0:  # Only check if we got results
+#             assert "analysis_accession" in data[0]
+#             assert data[0]["center_name"] == "EMBL-EBI"
+#             assert data[0]["analysis_type"] == "SEQUENCE_ASSEMBLY"

tests/test_analysis_study.py

@@ -0,0 +1,107 @@
+# tests/test_analysis_study.py
+import pytest
+from ena_portal_api.ena_api_requests import ENAAPIRequest, ENAPortalResultType
+from ena_portal_api.models.analysis_study import AnalysisStudyFields, AnalysisStudyQuery
+
+@pytest.mark.integration
+def test_analysis_study_fields_query():
+    """Test analysis study fields and query with real API request"""
+    try:
+        request = ENAAPIRequest(
+            result=ENAPortalResultType.ANALYSIS_STUDY,
+            query=AnalysisStudyQuery(study_accession="PRJEB12345"),
+            fields=[
+                AnalysisStudyFields.STUDY_ACCESSION,
+                AnalysisStudyFields.STUDY_TITLE,
+                AnalysisStudyFields.ANALYSIS_TYPE,
+                AnalysisStudyFields.SCIENTIFIC_NAME,
+                AnalysisStudyFields.TAX_ID,
+            ],
+            limit=5
+        )
+        response = request.get()
+        assert response.status_code == 200
+        data = response.json()
+        assert isinstance(data, list)
+        if len(data) > 0:
+            assert "study_accession" in data[0]
+            assert "analysis_type" in data[0]
+
+@pytest.mark.integration
+def test_analysis_study_no_query():
+    """Test analysis study request without query"""
+    try:
+        request = ENAAPIRequest(
+            result=ENAPortalResultType.ANALYSIS_STUDY,
+            fields=[
+                AnalysisStudyFields.STUDY_ACCESSION,
+                AnalysisStudyFields.STUDY_TITLE,
+                AnalysisStudyFields.ANALYSIS_TYPE,
+            ],
+            limit=5
+        )
+        response = request.get()
+        assert response.status_code == 200
+        data = response.json()
+        assert isinstance(data, list)
+        assert len(data) <= 5
+        if len(data) > 0:
+            assert "study_accession" in data[0]
+
+@pytest.mark.integration
+def test_analysis_study_comprehensive_fields():
+    """Test analysis study request with comprehensive field set"""
+    try:
+        request = ENAAPIRequest(
+            result=ENAPortalResultType.ANALYSIS_STUDY,
+            fields=[
+                AnalysisStudyFields.STUDY_ACCESSION,
+                AnalysisStudyFields.STUDY_TITLE,
+                AnalysisStudyFields.STUDY_ALIAS,
+                AnalysisStudyFields.ANALYSIS_TYPE,
+                AnalysisStudyFields.CENTER_NAME,
+                AnalysisStudyFields.PIPELINE_NAME,
+                AnalysisStudyFields.PIPELINE_VERSION,
+                AnalysisStudyFields.SCIENTIFIC_NAME,
+                AnalysisStudyFields.SAMPLE_ACCESSION,
+                AnalysisStudyFields.TAX_ID,
+            ],
+            query=AnalysisStudyQuery(analysis_type="SEQUENCE_ASSEMBLY"),
+            limit=5
+        )
+        response = request.get()
+        assert response.status_code == 200
+        data = response.json()
+        assert isinstance(data, list)
+        if len(data) > 0:
+            first_record = data[0]
+            assert "study_accession" in first_record
+            assert "analysis_type" in first_record
+            assert first_record["analysis_type"] == "SEQUENCE_ASSEMBLY"
+
+# @pytest.mark.integration
+# def test_analysis_study_multiple_conditions():
+#     """Test analysis study request with multiple query conditions"""
+#     try:
+#         request = ENAAPIRequest(
+#             result=ENAPortalResultType.ANALYSIS_STUDY,
+#             query=(
+#                 AnalysisStudyQuery(analysis_type="SEQUENCE_ASSEMBLY") &
+#                 AnalysisStudyQuery(center_name="EMBL-EBI")
+#             ),
+#             fields=[
+#                 AnalysisStudyFields.STUDY_ACCESSION,
+#                 AnalysisStudyFields.CENTER_NAME,
+#                 AnalysisStudyFields.ANALYSIS_TYPE,
+#                 AnalysisStudyFields.STUDY_TITLE,
+#             ],
+#             limit=5
+#         )
+#         response = request.get()
+#         assert response.status_code == 200
+#         data = response.json()
+#         assert isinstance(data, list)
+#         if len(data) > 0:
+#             assert "study_accession" in data[0]
+#             assert data[0]["center_name"] == "EMBL-EBI"
+#             assert data[0]["analysis_type"] == "SEQUENCE_ASSEMBLY"

tests/test_coding.py

@@ -0,0 +1,118 @@
+# tests/test_coding.py
+import pytest
+from ena_portal_api.ena_api_requests import ENAAPIRequest, ENAPortalResultType
+from ena_portal_api.models.coding import CodingFields, CodingQuery
+
+@pytest.mark.integration
+def test_coding_fields_query():
+    """Test coding sequence fields and query with real API request"""
+    try:
+        request = ENAAPIRequest(
+            result=ENAPortalResultType.CODING,
+            query=CodingQuery(coding_length="1000-2000"),  # Query for coding sequences between 1-2kb
+            fields=[
+                CodingFields.ACCESSION,
+                CodingFields.DESCRIPTION,
+                CodingFields.CODING_LENGTH,
+                CodingFields.SCIENTIFIC_NAME,
+                CodingFields.TAX_ID,
+            ],
+            limit=5
+        )
+        response = request.get()
+        assert response.status_code == 200
+        data = response.json()
+        assert isinstance(data, list)
+        if len(data) > 0:
+            assert "accession" in data[0]
+            assert "coding_length" in data[0]
+            length = int(data[0]["coding_length"])
+            assert 1000 <= length <= 2000
+
+@pytest.mark.integration
+def test_coding_no_query():
+    """Test coding sequence request without query"""
+    try:
+        request = ENAAPIRequest(
+            result=ENAPortalResultType.CODING,
+            fields=[
+                CodingFields.ACCESSION,
+                CodingFields.DESCRIPTION,
+                CodingFields.CODING_LENGTH,
+                CodingFields.SCIENTIFIC_NAME,
+            ],
+            limit=5
+        )
+        response = request.get()
+        assert response.status_code == 200
+        data = response.json()
+        assert isinstance(data, list)
+        assert len(data) <= 5
+        if len(data) > 0:
+            assert "accession" in data[0]
+
+@pytest.mark.integration
+def test_coding_comprehensive_fields():
+    """Test coding sequence request with comprehensive field set"""
+    try:
+        request = ENAAPIRequest(
+            result=ENAPortalResultType.CODING,
+            fields=[
+                CodingFields.ACCESSION,
+                CodingFields.DESCRIPTION,
+                CodingFields.CODING_LENGTH,
+                CodingFields.SCIENTIFIC_NAME,
+                CodingFields.TAX_ID,
+                CodingFields.GENE_NAME,
+                CodingFields.PROTEIN_NAME,
+                CodingFields.EC_NUMBER,
+                CodingFields.ORGANISM,
+                CodingFields.STRAIN,
+                CodingFields.MOLTYPE,
+                CodingFields.TOPOLOGY,
+            ],
+            query=CodingQuery(
+                moltype="mRNA",
+                organism="Escherichia coli"
+            ),
+            limit=5
+        )
+        response = request.get()
+        assert response.status_code == 200
+        data = response.json()
+        assert isinstance(data, list)
+        if len(data) > 0:
+            first_record = data[0]
+            assert "accession" in first_record
+            assert "moltype" in first_record
+            assert first_record["moltype"] == "mRNA"
+            assert first_record["organism"].lower() == "escherichia coli"
+
+# @pytest.mark.integration
+# def test_coding_multiple_conditions():
+#     """Test coding sequence request with multiple query conditions"""
+#     try:
+#         request = ENAAPIRequest(
+#             result=ENAPortalResultType.CODING,
+#             query=(
+#                 CodingQuery(moltype="mRNA") &
+#                 CodingQuery(coding_length="500-1000")
+#             ),
+#             fields=[
+#                 CodingFields.ACCESSION,
+#                 CodingFields.DESCRIPTION,
+#                 CodingFields.CODING_LENGTH,
+#                 CodingFields.MOLTYPE,
+#             ],
+#             limit=5
+#         )
+#         response = request.get()
+#         assert response.status_code == 200
+#         data = response.json()
+#         assert isinstance(data, list)
+#         if len(data) > 0:
+#             assert "accession" in data[0]
+#             assert "moltype" in data[0]
+#             assert data[0]["moltype"] == "mRNA"
+#             length = int(data[0]["coding_length"])
+#             assert 500 <= length <= 1000