updated docs

Author: hechth

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 +1,35 @@
+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 = [('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)