Mocked remote calls in test_mw2isa #597

Author: knirirr

tests/test_clients/fixtures/ST00010.json

@@ -0,0 +1 @@
+{"1":{"study_id":"ST000100","analysis_id":"AN000165","analysis_summary":"HESI positive ion mode","analysis_type":"MS","chromatography system":"Thermo Dionex Ultimate 3000 RS","column_name":"Waters Acquity HSS T3 (100 x 2.1mm,1.8um)","chromatography_type":"Reversed phase","ms_instrument_name":"Thermo Q Exactive Orbitrap","ms_instrument_type":"Orbitrap","ms_type":"ESI","ion_mode":"POSITIVE","nmr_instrument_type":"","nmr_experiment_type":"","spectrometer_frequency":"","nmr_solvent":"","units":""},"2":{"study_id":"ST000100","analysis_id":"AN000166","analysis_summary":"HESI negative ion mode","analysis_type":"MS","chromatography system":"Thermo Dionex Ultimate 3000 RS","column_name":"Waters Acquity HSS T3 (100 x 2.1mm,1.8um)","chromatography_type":"Reversed phase","ms_instrument_name":"Thermo Q Exactive Orbitrap","ms_instrument_type":"Orbitrap","ms_type":"ESI","ion_mode":"NEGATIVE","nmr_instrument_type":"","nmr_experiment_type":"","spectrometer_frequency":"","nmr_solvent":"","units":""},"3":{"study_id":"ST000101","analysis_id":"AN000167","analysis_summary":"NMR:13C 1D","analysis_type":"NMR","chromatography system":"","column_name":"","chromatography_type":"","ms_instrument_name":"","ms_instrument_type":"","ms_type":"","ion_mode":"","nmr_instrument_type":"FT-NMR","nmr_experiment_type":"1D 13C","spectrometer_frequency":"600 MHz","nmr_solvent":"D2O","units":""},"4":{"study_id":"ST000101","analysis_id":"AN000168","analysis_summary":"NMR: 1D 1H","analysis_type":"NMR","chromatography system":"","column_name":"","chromatography_type":"","ms_instrument_name":"","ms_instrument_type":"","ms_type":"","ion_mode":"","nmr_instrument_type":"FT-NMR","nmr_experiment_type":"1D 1H","spectrometer_frequency":"600 MHz","nmr_solvent":"D2O","units":""},"5":{"study_id":"ST000102","analysis_id":"AN000169","analysis_summary":"NMR: 1D presaturation 1H","analysis_type":"NMR","chromatography system":"","column_name":"","chromatography_type":"","ms_instrument_name":"","ms_instrument_type":"","ms_type":"","ion_mode":"","nmr_instrument_type":"FT-NMR","nmr_experiment_type":"1D 1H","spectrometer_frequency":"700 MHz","nmr_solvent":"D2O","units":""},"6":{"study_id":"ST000102","analysis_id":"AN000170","analysis_summary":"NMR: 2D 1H-13C HSQC","analysis_type":"NMR","chromatography system":"","column_name":"","chromatography_type":"","ms_instrument_name":"","ms_instrument_type":"","ms_type":"","ion_mode":"","nmr_instrument_type":"FT-NMR","nmr_experiment_type":"2D 1H-13C HSQC","spectrometer_frequency":"700 MHz","nmr_solvent":"D2O","units":""},"7":{"study_id":"ST000103","analysis_id":"AN000171","analysis_summary":"NMR:2D 1H-13C HSQC","analysis_type":"NMR","chromatography system":"","column_name":"","chromatography_type":"","ms_instrument_name":"","ms_instrument_type":"","ms_type":"","ion_mode":"","nmr_instrument_type":"FT-NMR","nmr_experiment_type":"2D-INADEQUATE","spectrometer_frequency":"600 MHz","nmr_solvent":"D2O and MeOD","units":""},"8":{"study_id":"ST000104","analysis_id":"AN000172","analysis_summary":"NMR:INADEQUATE","analysis_type":"NMR","chromatography system":"","column_name":"","chromatography_type":"","ms_instrument_name":"","ms_instrument_type":"","ms_type":"","ion_mode":"","nmr_instrument_type":"FT-NMR","nmr_experiment_type":"1D 1H","spectrometer_frequency":"700 MHz","nmr_solvent":"D20","units":""},"9":{"study_id":"ST000105","analysis_id":"AN000173","analysis_summary":"MS Q-TOF 6530 positive ion mode","analysis_type":"MS","chromatography system":"Agilent 1200","column_name":"Waters Acquity HSS T3","chromatography_type":"Reversed phase","ms_instrument_name":"Agilent 6530 QTOF","ms_instrument_type":"QTOF","ms_type":"ESI","ion_mode":"POSITIVE","nmr_instrument_type":"","nmr_experiment_type":"","spectrometer_frequency":"","nmr_solvent":"","units":"Counts"},"10":{"study_id":"ST000105","analysis_id":"AN000174","analysis_summary":"ESI negative ion mode","analysis_type":"MS","chromatography system":"Agilent 1200","column_name":"Waters Acquity HSS T3","chromatography_type":"Reversed phase","ms_instrument_name":"Agilent 6530 QTOF","ms_instrument_type":"QTOF","ms_type":"ESI","ion_mode":"NEGATIVE","nmr_instrument_type":"","nmr_experiment_type":"","spectrometer_frequency":"","nmr_solvent":"","units":"Counts"},"11":{"study_id":"ST000106","analysis_id":"AN000175","analysis_summary":"ESI positive ion mode","analysis_type":"MS","chromatography system":"Agilent 1200","column_name":"Waters Acquity HSS T3","chromatography_type":"Reversed phase","ms_instrument_name":"Agilent 6530 QTOF","ms_instrument_type":"QTOF","ms_type":"ESI","ion_mode":"POSITIVE","nmr_instrument_type":"","nmr_experiment_type":"","spectrometer_frequency":"","nmr_solvent":"","units":"Counts"},"12":{"study_id":"ST000106","analysis_id":"AN000176","analysis_summary":"ESI negative ion mode","analysis_type":"MS","chromatography system":"Agilent 1200","column_name":"Waters Acquity HSS T3","chromatography_type":"Reversed phase","ms_instrument_name":"Agilent 6530 QTOF","ms_instrument_type":"QTOF","ms_type":"ESI","ion_mode":"NEGATIVE","nmr_instrument_type":"","nmr_experiment_type":"","spectrometer_frequency":"","nmr_solvent":"","units":"Counts"},"13":{"study_id":"ST000107","analysis_id":"AN000177","analysis_summary":"LCMS Positive ion mode","analysis_type":"MS","chromatography system":"","column_name":"","chromatography_type":"GC","ms_instrument_name":"ABI Sciex API 4000 QTrap","ms_instrument_type":"Triple quadrupole","ms_type":"ESI","ion_mode":"POSITIVE","nmr_instrument_type":"","nmr_experiment_type":"","spectrometer_frequency":"","nmr_solvent":"","units":"nM"},"14":{"study_id":"ST000107","analysis_id":"AN000178","analysis_summary":"GCMS Positive ion mode","analysis_type":"MS","chromatography system":"","column_name":"","chromatography_type":"GC","ms_instrument_name":"Agilent 5973N","ms_instrument_type":"Single quadrupole","ms_type":"EI","ion_mode":"POSITIVE","nmr_instrument_type":"","nmr_experiment_type":"","spectrometer_frequency":"","nmr_solvent":"","units":"nM"}}

tests/test_clients/fixtures/ST000367.json

@@ -0,0 +1 @@
+{"1":{"study_id":"ST000367","analysis_id":"AN000600","analysis_summary":"Precellys homogenization (IC-FTMS1)","analysis_type":"MS","chromatography system":"Thermo Dionex ICS-5000+","column_name":"Unspecified","chromatography_type":"Ion Chromatography","ms_instrument_name":"Thermo Fusion Tribrid Orbitrap","ms_instrument_type":"FT-ICR-MS","ms_type":"ESI","ion_mode":"NEGATIVE","nmr_instrument_type":"","nmr_experiment_type":"","spectrometer_frequency":"","nmr_solvent":"","units":"normalized corrected peak area"},"2":{"study_id":"ST000367","analysis_id":"AN000601","analysis_summary":"Retsch homogenization (IC-FTMS2)","analysis_type":"MS","chromatography system":"Thermo Dionex ICS-5000+","column_name":"Unspecified","chromatography_type":"Ion Chromatography","ms_instrument_name":"Thermo Fusion Tribrid Orbitrap","ms_instrument_type":"FT-ICR-MS","ms_type":"ESI","ion_mode":"NEGATIVE","nmr_instrument_type":"","nmr_experiment_type":"","spectrometer_frequency":"","nmr_solvent":"","units":"normalized corrected peak area"}}

tests/test_clients/fixtures/TOTO.json

@@ -0,0 +1 @@
+[]

tests/test_clients/test_mw2isa.py

@@ -1,8 +1,11 @@
+import json
 import logging
 import os
 import shutil
 import tempfile
 import unittest
+from pathlib import Path
+from unittest.mock import Mock, patch
 
 from isatools import isatab
 from isatools.net.mw2isa import mw2isa_convert
@@ -19,7 +22,31 @@ def setUp(self):
     def tearDown(self):
         shutil.rmtree(self._tmp_dir)
 
-    def test_conversion_ms(self):
+    def _load_fixture(self, name):
+        data_path = Path(__file__).parent / "fixtures" / name
+        return data_path.read_bytes()
+
+    def _make_requests_response(self, body_bytes, status=200, headers=None):
+        m = Mock()
+        m.status_code = status
+        m.content = body_bytes
+        m.text = body_bytes.decode("utf-8")
+
+        # Provide .json() for convenience if used by code
+        def _json():
+            return json.loads(m.text)
+
+        m.json = _json
+        m.headers = headers or {}
+        return m
+
+    @patch("isatools.net.mw2isa.mw2isa_convert")
+    def test_conversion_ms(self, mock_get):
+        def _side_effect():
+            return self._make_requests_response(self._load_fixture("ST000367.json"))
+
+        mock_get.side_effect = _side_effect
+
         success, study_id, validate = mw2isa_convert(
             studyid="ST000367", outputdir=self._tmp_dir, dl_option="no", validate_option=True
         )
@@ -37,8 +64,13 @@ def test_conversion_ms(self):
         else:
             self.fail("conversion failed, validation was not invoked")
 
-    def test_conversion_nmr(self):
-        report = {}
+    @patch("isatools.net.mw2isa.mw2isa_convert")
+    def test_conversion_nmr(self, mock_get):
+        def _side_effect():
+            return self._make_requests_response(self._load_fixture("ST000102.json"))
+
+        mock_get.side_effect = _side_effect
+
         success, study_id, validate = mw2isa_convert(
             studyid="ST000102", outputdir=self._tmp_dir, dl_option="no", validate_option=True
         )
@@ -50,13 +82,25 @@ def test_conversion_nmr(self):
         else:
             self.assertFalse(success)
 
-    def test_conversion_invalid_id(self):
+    @patch("isatools.net.mw2isa.mw2isa_convert")
+    def test_conversion_invalid_id(self, mock_get):
+        def _side_effect():
+            return self._make_requests_response(self._load_fixture("TOTO.json"))
+
+        mock_get.side_effect = _side_effect
+
         success, study_id, validate = mw2isa_convert(
             studyid="TOTO", outputdir=self._tmp_dir, dl_option="no", validate_option=True
         )
         self.assertFalse(success)
 
-    def test_conversion_invalid_dloption(self):
+    @patch("isatools.net.mw2isa.mw2isa_convert")
+    def test_conversion_invalid_dloption(self, mock_get):
+        def _side_effect():
+            return self._make_requests_response(self._load_fixture("ST000102.json"))
+
+        mock_get.side_effect = _side_effect
+
         with self.assertRaises(Exception) as context:
             success, study_id, validate = mw2isa_convert(
                 studyid="ST000102", outputdir=self._tmp_dir, dl_option="TOTO", validate_option=False