Merge pull request #172 from RECETOX/hechth/issue163

updated docs

Author: hechth

MSMetaEnhancer/app.py

@@ -83,7 +83,8 @@ async def annotate_spectra(
 
             # start converters status checker and wait for first status
             try:
-                monitor.start()
+                if not monitor.is_alive():
+                    monitor.start()
                 monitor.first_check.wait()
 
                 # create all possible jobs if not given

MSMetaEnhancer/libs/utils/Monitor.py

@@ -55,7 +55,7 @@ def run(self):
         Such a converter is considered available.
         This is checked periodically to always have up-to-date information.
         """
-        while not self.stop_request.isSet():
+        while not self.stop_request.is_set():
             for converter in self.converters.values():
                 url = self.get_base_url(converter)
                 converter.is_available = self.check_service(url)

README.md

@@ -20,6 +20,11 @@ Troják et al., (2022). MSMetaEnhancer: A Python package for mass spectra metada
 import asyncio
 
 from MSMetaEnhancer import Application
+from MSMetaEnhancer.libs.converters.web import CTS, CIR, IDSM, PubChem, BridgeDb
+from MSMetaEnhancer.libs.converters.compute import RDKit
+from MSMetaEnhancer.libs.utils.ConverterBuilder import ConverterBuilder
+
+ConverterBuilder.register([CTS, CIR, IDSM, PubChem, BridgeDb, RDKit])
 
 app = Application()
 

tests/test_integration.py

@@ -0,0 +1,41 @@
+import asyncio
+import os
+
+from MSMetaEnhancer import Application
+from MSMetaEnhancer.libs.converters.web import CTS, CIR, IDSM, PubChem, BridgeDb
+from MSMetaEnhancer.libs.converters.compute import RDKit
+from MSMetaEnhancer.libs.utils.ConverterBuilder import ConverterBuilder
+
+ConverterBuilder.register([CTS, CIR, IDSM, PubChem, BridgeDb, RDKit])
+
+
+def test_integration(tmp_path):
+    app = Application()
+
+    # import your .msp file
+    app.load_data("tests/test_data/sample.msp", file_format="msp")
+
+    # curate given metadata (e.g. fix CAS numbers)
+    app.curate_metadata()
+
+    # specify requested services (these are supported)
+    services = ["CTS", "CIR", "IDSM", "PubChem", "BridgeDb", "RDKit"]
+
+    # specify requested jobs
+    jobs = [
+        ("compound_name", "inchi", "IDSM"),
+        ("inchi", "formula", "IDSM"),
+        ("inchi", "inchikey", "IDSM"),
+        ("inchi", "iupac_name", "IDSM"),
+        ("inchi", "canonical_smiles", "IDSM"),
+    ]
+
+    # run asynchronous annotations of spectra data
+    asyncio.run(app.annotate_spectra(services, jobs))
+
+    # export .msp file
+    outpath = os.path.join(tmp_path, "sample_out.msp")
+    app.save_data(outpath, file_format="msp")
+    assert os.path.isfile(outpath)
+
+    os.remove(outpath)