From f2131f161410cfe8605f1dd74db5d96f79b1f8c3 Mon Sep 17 00:00:00 2001
From: Matej Trojak <trojak@mail.muni.cz>
Date: Fri, 25 Jun 2021 13:32:59 +0200
Subject: [PATCH 1/9] Renamed MSP class to more general Spectra class

---
 README.md                   | 14 +++++++-------
 libs/{MSP.py => Spectra.py} |  2 +-
 2 files changed, 8 insertions(+), 8 deletions(-)
 rename libs/{MSP.py => Spectra.py} (99%)

diff --git a/README.md b/README.md
index 02d8929..2e5bdbc 100644
--- a/README.md
+++ b/README.md
@@ -7,23 +7,23 @@ Repository for tool that adds more annotations (e.g. SMILES, InChI, CAS number)
 
 ```python
 # import MSP class
-from libs.MSP import MSP
+from libs.Spectra import Spectra
 
 # create MSP object and import your .msp file
-msp = MSP()
-msp.load_msp_file('path_to_my_file.msp')
+spectra = Spectra()
+spectra.load_msp_file('path_to_my_file.msp')
 
 # main function to annotate the MSP file using all available approaches
-msp.annotate_spectrums_all_attributes()
+spectra.annotate_spectrums_all_attributes()
 
 # alternatively, it is possible to specify just particular jobs to do
 jobs = [('name', 'inchi', 'PubChem'),
         ('casno', 'inchikey', 'CTS')]
-msp.annotate_spectrums(jobs)
+spectra.annotate_spectrums(jobs)
 
 # to get available jobs
-available_jobs = msp.get_available_jobs()
+available_jobs = spectra.get_available_jobs()
 
 # export file 
-msp.save_msp_file('path_to_a_new_file.msp')
+spectra.save_msp_file('path_to_a_new_file.msp')
 ```
diff --git a/libs/MSP.py b/libs/Spectra.py
similarity index 99%
rename from libs/MSP.py
rename to libs/Spectra.py
index 496aea4..58f5f6f 100644
--- a/libs/MSP.py
+++ b/libs/Spectra.py
@@ -5,7 +5,7 @@
 from libs.Annotator import Annotator
 
 
-class MSP:
+class Spectra:
     def __init__(self):
         self.annotator = Annotator()
         self.spectrums = []

From 425cc35be6458a0139e4bd334a67cc873ea20252 Mon Sep 17 00:00:00 2001
From: Matej Trojak <trojak@mail.muni.cz>
Date: Fri, 25 Jun 2021 14:58:21 +0200
Subject: [PATCH 2/9] Changed code to asynchronous using aiohttp requests

---
 libs/Annotator.py          | 11 +++++---
 libs/Spectra.py            | 34 +++++++++++++++++++------
 libs/services/CIR.py       | 48 +++++++++++++++++------------------
 libs/services/CTS.py       | 51 ++++++++++++++++++++++----------------
 libs/services/Converter.py | 46 ++++++++++++++++++++--------------
 libs/services/NLM.py       | 21 ++++++++--------
 libs/services/PubChem.py   | 36 +++++++++++++++------------
 requirements.txt           |  3 ++-
 8 files changed, 146 insertions(+), 104 deletions(-)

diff --git a/libs/Annotator.py b/libs/Annotator.py
index d493579..952ce1f 100644
--- a/libs/Annotator.py
+++ b/libs/Annotator.py
@@ -10,7 +10,7 @@ class Annotator:
     def __init__(self):
         self.services = {'CTS': CTS(), 'CIR': CIR(), 'NLM': NLM(), 'PubChem': PubChem()}
 
-    def annotate(self, metadata, jobs, repeat=False):
+    async def annotate(self, spectra, jobs, session, repeat=False):
         """
         Runs all jobs to add annotations to given dictionary containing metadata
 
@@ -18,12 +18,14 @@ def annotate(self, metadata, jobs, repeat=False):
         and tries to obtain 'Target' attribute based on 'Source' attribute using
         'Service' service.
 
-        :param metadata: given spectra metadata
+        :param spectra: given spectra metadata
         :param jobs: specified list of jobs to be executed
         :param repeat: if some metadata was added, all jobs are executed again
+        :param session: current aiohttp session
         :return: annotated dictionary
         """
         jobs = convert_to_jobs(jobs)
+        metadata = spectra.metadata
 
         added_metadata = True
         while added_metadata:
@@ -40,7 +42,7 @@ def annotate(self, metadata, jobs, repeat=False):
                     pass  # TODO: log - source data not available for conversion
                 else:
                     try:
-                        result = service.convert(job.source, job.target, data)
+                        result = await service.convert(job.source, job.target, data, session)
                         metadata[job.target] = result
                         if repeat:
                             added_metadata = True
@@ -48,7 +50,8 @@ def annotate(self, metadata, jobs, repeat=False):
                         pass  # TODO log this type of conversion is not supported by the service
                     except DataNotRetrieved:
                         pass  # TODO log no data were retrieved
-        return metadata
+        spectra.metadata = metadata
+        return spectra
 
     def get_all_conversions(self):
         """
diff --git a/libs/Spectra.py b/libs/Spectra.py
index 58f5f6f..ddd442e 100644
--- a/libs/Spectra.py
+++ b/libs/Spectra.py
@@ -1,3 +1,5 @@
+import asyncio
+import aiohttp
 from matchms.importing import load_from_msp
 from matchms.exporting import save_as_msp
 
@@ -36,7 +38,23 @@ def get_available_jobs(self):
         """
         return self.annotator.get_all_conversions()
 
-    def annotate_spectrums(self, jobs):
+    async def annotate(self, jobs, batch_size, repeat):
+        """
+        Annotate data using specified jobs in asynchronous mode.
+        Spectrums are executed in batches to avoid flooding web services.
+
+        :param jobs: given list of jobs to do
+        :param batch_size: size of single batch
+        :param repeat: if some metadata was added, all jobs are executed again
+        """
+        async with aiohttp.ClientSession() as session:
+            results = []
+            for size in range(len(self.spectrums) // batch_size + 1):
+                results += await asyncio.gather(*[self.annotator.annotate(spectra, jobs, session, repeat) for spectra in
+                                                  self.spectrums[size * batch_size:(size + 1) * batch_size]])
+        self.spectrums = results
+
+    def annotate_spectrums(self, jobs, batch_size=10, repeat=False):
         """
         Adds additional metadata to all Spectra objects.
 
@@ -44,16 +62,16 @@ def annotate_spectrums(self, jobs):
         have to be defined in and add_ method of Annotator class (otherwise ignored).
 
         :param jobs: target annotation jobs
+        :param batch_size: number of spectrums annotated at once (to avoid flooding web services)
+        :param repeat: if some metadata was added, all jobs are executed again
         """
-        for i, spectrum in enumerate(self.spectrums):
-            metadata = curator.curate_metadata(spectrum.metadata)
-            spectrum.metadata = self.annotator.annotate(metadata, jobs)
+        for spectrum in self.spectrums:
+            spectrum.metadata = curator.curate_metadata(spectrum.metadata)
+        asyncio.run(self.annotate(jobs, batch_size, repeat))
 
-    def annotate_spectrums_all_attributes(self):
+    def annotate_spectrums_all_attributes(self, batch_size=10):
         """
         Adds all implemented metadata to all Spectra objects.
         """
         jobs = self.get_available_jobs()
-        for i, spectrum in enumerate(self.spectrums):
-            metadata = curator.curate_metadata(spectrum.metadata)
-            spectrum.metadata = self.annotator.annotate(metadata, jobs)
+        self.annotate_spectrums(jobs, batch_size, True)
diff --git a/libs/services/CIR.py b/libs/services/CIR.py
index ffb4294..f56b074 100644
--- a/libs/services/CIR.py
+++ b/libs/services/CIR.py
@@ -7,7 +7,7 @@ def __init__(self):
         # service URLs
         self.services = {'CIR': 'https://cactus.nci.nih.gov/chemical/structure/'}
 
-    def cas_to_smiles(self, cas_number):
+    async def cas_to_smiles(self, cas_number, session):
         """
         Convert CAS number to SMILES using CIR web service
         More info: https://cactus.nci.nih.gov/chemical/structure_documentation
@@ -16,11 +16,11 @@ def cas_to_smiles(self, cas_number):
         :return: obtained SMILES
         """
         args = f"{cas_number}/smiles?resolver=cas_number"
-        response = self.query_the_service('CIR', args)
-        if response.status_code == 200:
-            return response.text
+        response = await self.query_the_service('CIR', args, session)
+        if response:
+            return response
 
-    def inchikey_to_smiles(self, inchikey):
+    async def inchikey_to_smiles(self, inchikey, session):
         """
         Convert InChiKey to SMILES using CIR web service
         More info: https://cactus.nci.nih.gov/chemical/structure_documentation
@@ -29,11 +29,11 @@ def inchikey_to_smiles(self, inchikey):
         :return: obtained SMILES
         """
         args = f'{inchikey}/smiles'
-        response = self.query_the_service('CIR', args)
-        if response.status_code == 200:
-            return response.text.split('\n')[0]
+        response = await self.query_the_service('CIR', args, session)
+        if response:
+            return response.split('\n')[0]
 
-    def inchikey_to_inchi(self, inchikey):
+    async def inchikey_to_inchi(self, inchikey, session):
         """
         Convert InChiKey to InCHi using CIR web service
         More info: https://cactus.nci.nih.gov/chemical/structure_documentation
@@ -42,11 +42,11 @@ def inchikey_to_inchi(self, inchikey):
         :return: obtained InCHi
         """
         args = f'{inchikey}/stdinchi'
-        response = self.query_the_service('CIR', args)
-        if response.status_code == 200:
-            return response.text
+        response = await self.query_the_service('CIR', args, session)
+        if response:
+            return response
 
-    def inchikey_to_cas(self, inchikey):
+    async def inchikey_to_cas(self, inchikey, session):
         """
         Convert InChiKey to CAS number using CIR web service
         More info: https://cactus.nci.nih.gov/chemical/structure_documentation
@@ -55,11 +55,11 @@ def inchikey_to_cas(self, inchikey):
         :return: obtained CAS number
         """
         args = f'{inchikey}/cas'
-        response = self.query_the_service('CIR', args)
-        if response.status_code == 200:
-            return response.text
+        response = await self.query_the_service('CIR', args, session)
+        if response:
+            return response
 
-    def inchikey_to_formula(self, inchikey):
+    async def inchikey_to_formula(self, inchikey, session):
         """
         Convert InChiKey to chemical formula using CIR web service
         More info: https://cactus.nci.nih.gov/chemical/structure_documentation
@@ -68,11 +68,11 @@ def inchikey_to_formula(self, inchikey):
         :return: obtained chemical formula
         """
         args = f'{inchikey}/formula'
-        response = self.query_the_service('CIR', args)
-        if response.status_code == 200:
-            return response.text
+        response = await self.query_the_service('CIR', args, session)
+        if response:
+            return response
 
-    def smiles_to_inchikey(self, smiles):
+    async def smiles_to_inchikey(self, smiles, session):
         """
         Convert SMILES to InChiKey using CIR web service
         More info: https://cactus.nci.nih.gov/chemical/structure_documentation
@@ -81,6 +81,6 @@ def smiles_to_inchikey(self, smiles):
         :return: obtained InChiKey
         """
         args = f'{smiles}/stdinchikey'
-        response = self.query_the_service('CIR', args)
-        if response.status_code == 200:
-            return response.text[9:]
+        response = await self.query_the_service('CIR', args, session)
+        if response:
+            return response[9:]
diff --git a/libs/services/CTS.py b/libs/services/CTS.py
index bd0dfc8..b6ae7cf 100644
--- a/libs/services/CTS.py
+++ b/libs/services/CTS.py
@@ -1,3 +1,5 @@
+import json
+
 from libs.services.Converter import Converter
 
 
@@ -9,7 +11,7 @@ def __init__(self):
                          'CTS_compound': 'http://cts.fiehnlab.ucdavis.edu/service/compound/'
                          }
 
-    def cas_to_inchikey(self, cas_number):
+    async def cas_to_inchikey(self, cas_number, session):
         """
         Convert CAS number to InChiKey using CTS web service
         More info: http://cts.fiehnlab.ucdavis.edu/services
@@ -20,12 +22,13 @@ def cas_to_inchikey(self, cas_number):
         :return: obtained InChiKey
         """
         args = f'CAS/InChIKey/{cas_number}'
-        response = self.query_the_service('CTS', args)
-        if response.status_code == 200:
-            if len(response.json()[0]['results']) != 0:
-                return response.json()[0]['results'][0]
+        response = await self.query_the_service('CTS', args, session)
+        if response:
+            response_json = json.loads(response)
+            if len(response_json[0]['results']) != 0:
+                return response_json[0]['results'][0]
 
-    def inchikey_to_inchi(self, inchikey):
+    async def inchikey_to_inchi(self, inchikey, session):
         """
         Convert InChiKey to InChi using CTS compound service
         More info: http://cts.fiehnlab.ucdavis.edu/services
@@ -34,11 +37,12 @@ def inchikey_to_inchi(self, inchikey):
         :return: obtained InChi
         """
         args = inchikey
-        response = self.query_the_service('CTS_compound', args)
-        if response.status_code == 200:
-            return response.json()["inchicode"]
+        response = await self.query_the_service('CTS_compound', args, session)
+        if response:
+            response_json = json.loads(response)
+            return response_json["inchicode"]
 
-    def name_to_inchikey(self, name):
+    async def name_to_inchikey(self, name, session):
         """
         Convert Chemical name to InChiKey using CTS service
         More info: http://cts.fiehnlab.ucdavis.edu/services
@@ -47,12 +51,13 @@ def name_to_inchikey(self, name):
         :return: obtained InChiKey
         """
         args = f'Chemical%20Name/InChIKey/{name}'
-        response = self.query_the_service('CTS', args)
-        if response.status_code == 200:
-            if len(response.json()[0]['results']) != 0:
-                return response.json()[0]['results'][0]
+        response = await self.query_the_service('CTS', args, session)
+        if response:
+            response_json = json.loads(response)
+            if len(response_json[0]['results']) != 0:
+                return response_json[0]['results'][0]
 
-    def inchikey_to_name(self, inchikey):
+    async def inchikey_to_name(self, inchikey, session):
         """
         Convert InChiKey to Chemical name using CTS compound service
         More info: http://cts.fiehnlab.ucdavis.edu/services
@@ -61,14 +66,15 @@ def inchikey_to_name(self, inchikey):
         :return: obtained Chemical name
         """
         args = inchikey
-        response = self.query_the_service('CTS_compound', args)
-        if response.status_code == 200:
-            synonyms = response.json()['synonyms']
+        response = await self.query_the_service('CTS_compound', args, session)
+        if response:
+            response_json = json.loads(response)
+            synonyms = response_json['synonyms']
             names = [item['name'] for item in synonyms if item['type'] == 'Synonym']
             if names:
                 return names[0]
 
-    def inchikey_to_iupac_name(self, inchikey):
+    async def inchikey_to_iupac_name(self, inchikey, session):
         """
         Convert InChiKey to IUPAC name using CTS compound service
         More info: http://cts.fiehnlab.ucdavis.edu/services
@@ -77,9 +83,10 @@ def inchikey_to_iupac_name(self, inchikey):
         :return: obtained IUPAC name
         """
         args = inchikey
-        response = self.query_the_service('CTS_compound', args)
-        if response.status_code == 200:
-            synonyms = response.json()['synonyms']
+        response = await self.query_the_service('CTS_compound', args, session)
+        if response:
+            response_json = json.loads(response)
+            synonyms = response_json['synonyms']
             names = [item['name'] for item in synonyms if item['type'] == 'IUPAC Name (Preferred)']
             if names:
                 return names[0]
diff --git a/libs/services/Converter.py b/libs/services/Converter.py
index c246068..50564f9 100644
--- a/libs/services/Converter.py
+++ b/libs/services/Converter.py
@@ -1,14 +1,10 @@
+from aiohttp.client_exceptions import ServerDisconnectedError
 import requests
 from libs.utils.Errors import DataNotRetrieved, ConversionNotSupported
 
 
 class Converter:
-    def __init__(self):
-        # used to store individual API calls to avoid executing
-        # the same query multiple times in single session
-        self.cache = dict()
-
-    def query_the_service(self, service, args, method='GET', data=None):
+    async def query_the_service(self, service, args, session, method='GET', data=None):
         """
         Make get request to given service with arguments.
         Raises ConnectionError if service is not available.
@@ -20,17 +16,12 @@ def query_the_service(self, service, args, method='GET', data=None):
         :return: obtained response
         """
         try:
-            identification = f'{service}:{args}'
-            cached_result = self.cache.get(identification, None)
-            if cached_result:
-                return cached_result
-            result = self.execute_request(self.services[service] + args, method, data)
-            self.cache[identification] = result
+            result = await self.execute_request(self.services[service] + args, method, data, session)
             return result
         except requests.exceptions.ConnectionError:
             raise ConnectionError(f'Service {service} is not available')
 
-    def execute_request(self, url, method, data=None):
+    async def execute_request(self, url, method, data, session, depth=10):
         """
         Execute request with type depending on specified method.
 
@@ -39,22 +30,39 @@ def execute_request(self, url, method, data=None):
         :param data: given arguments for POST request
         :return: obtained response
         """
-        if method == 'GET':
-            return requests.get(url)
-        else:
-            return requests.post(url, data=data)
+        try:
+            if method == 'GET':
+                async with session.get(url=url) as response:
+                    result = await response.text()
+                    if response.ok:
+                        return result
+                    elif response.status == 503:
+                        if depth > 0:
+                            return await self.execute_request(url, method, data, session, depth - 1)
+            else:
+                async with session.post(url=url, data=data) as response:
+                    result = await response.text()
+                    if response.ok:
+                        return result
+                    elif response.status == 503:
+                        if depth > 0:
+                            return await self.execute_request(url, method, data, session, depth - 1)
+        except ServerDisconnectedError:
+            if depth > 0:
+                return await self.execute_request(url, method, data, session, depth - 1)
 
-    def convert(self, source, target, data):
+    async def convert(self, source, target, data, session):
         """
         Converts specified {source} attribute (provided in {data}) to {target} attribute.
 
         :param source: given attribute name
         :param target: required attribute name
         :param data: given attribute value
+        :param session: current aiohttp session
         :return: obtained value of target attribute
         """
         try:
-            result = getattr(self, f'{source}_to_{target}')(data)
+            result = await getattr(self, f'{source}_to_{target}')(data, session)
             if result:
                 return result
             raise DataNotRetrieved(f'Target attribute {target} not available.')
diff --git a/libs/services/NLM.py b/libs/services/NLM.py
index 1bd33e1..87604c3 100644
--- a/libs/services/NLM.py
+++ b/libs/services/NLM.py
@@ -10,7 +10,7 @@ def __init__(self):
         # service URLs
         self.services = {'NLM': 'https://chem.nlm.nih.gov/api/data/'}
 
-    def inchikey_to_name(self, inchikey):
+    async def inchikey_to_name(self, inchikey, session):
         """
         Convert InChiKey to Chemical name using NLM service
         More info: https://chem.nlm.nih.gov/chemidplus/inchikey
@@ -19,13 +19,14 @@ def inchikey_to_name(self, inchikey):
         :return: obtained Chemical name
         """
         args = f'inchikey/equals/{inchikey}?data=summary&format=tsv'
-        response = self.query_the_service('NLM', args)
-        if response.status_code == 200 and response.text != 'EXPRESSION_INVALID':
-            table = pd.read_csv(StringIO(response.text), sep='\t')
-            if not table.empty:
-                return table['Name'][0]
+        response = await self.query_the_service('NLM', args, session)
+        if response:
+            if response != 'EXPRESSION_INVALID':
+                table = pd.read_csv(StringIO(response), sep='\t')
+                if not table.empty:
+                    return table['Name'][0]
 
-    def name_to_inchikey(self, name):
+    async def name_to_inchikey(self, name, session):
         """
         Convert Chemical name to InChiKey using NLM service
         More info: https://chem.nlm.nih.gov/chemidplus/inchikey
@@ -34,8 +35,8 @@ def name_to_inchikey(self, name):
         :return: obtained InChiKey
         """
         args = f'name/equals/{name}?data=summary&format=tsv'
-        response = self.query_the_service('NLM', args)
-        if response.status_code == 200:
-            table = pd.read_csv(StringIO(response.text), sep='\t')
+        response = await self.query_the_service('NLM', args, session)
+        if response:
+            table = pd.read_csv(StringIO(response), sep='\t')
             if not table.empty:
                 return table['InChIKey'][0]
diff --git a/libs/services/PubChem.py b/libs/services/PubChem.py
index e5b3613..cff40a9 100644
--- a/libs/services/PubChem.py
+++ b/libs/services/PubChem.py
@@ -1,3 +1,5 @@
+import json
+
 from libs.services.Converter import Converter
 
 
@@ -7,7 +9,7 @@ def __init__(self):
         # service URLs
         self.services = {'PubChem': 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/'}
 
-    def name_to_inchi(self, name):
+    async def name_to_inchi(self, name, session):
         """
         Convert Chemical name to InChi using PubChem service
         More info: https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest
@@ -16,13 +18,14 @@ def name_to_inchi(self, name):
         :return: found InChi
         """
         args = f'name/{name}/JSON'
-        response = self.query_the_service('PubChem', args)
-        if response.status_code == 200:
-            for prop in response.json()['PC_Compounds'][0]['props']:
+        response = await self.query_the_service('PubChem', args, session)
+        if response:
+            response_json = json.loads(response)
+            for prop in response_json['PC_Compounds'][0]['props']:
                 if prop['urn']['label'] == 'InChI':
                     return prop['value']['sval']
 
-    def inchi_to_inchikey(self, inchi):
+    async def inchi_to_inchikey(self, inchi, session):
         """
         Convert InChi to InChiKey using PubChem service
         More info: https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest
@@ -30,13 +33,13 @@ def inchi_to_inchikey(self, inchi):
         :param inchi: given InChi
         :return: found InChiKey
         """
-        props = self.get_props_from_inchi(inchi)
+        props = await self.get_props_from_inchi(inchi, session)
         if props:
             for prop in props:
                 if prop['urn']['label'] == 'InChIKey':
                     return prop['value']['sval']
 
-    def inchi_to_iupac_name(self, inchi):
+    async def inchi_to_iupac_name(self, inchi, session):
         """
         Convert InChi to IUPAC name using PubChem service
         More info: https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest
@@ -44,13 +47,13 @@ def inchi_to_iupac_name(self, inchi):
         :param inchi: given InChi
         :return: found IUPAC name
         """
-        props = self.get_props_from_inchi(inchi)
+        props = await self.get_props_from_inchi(inchi, session)
         if props:
             for prop in props:
                 if prop['urn']['label'] == 'IUPAC Name' and prop['urn']['name'] == 'Preferred':
                     return prop['value']['sval']
 
-    def inchi_to_formula(self, inchi):
+    async def inchi_to_formula(self, inchi, session):
         """
         Convert InChi to chemical formula using PubChem service
         More info: https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest
@@ -58,13 +61,13 @@ def inchi_to_formula(self, inchi):
         :param inchi: given InChi
         :return: found chemical formula
         """
-        props = self.get_props_from_inchi(inchi)
+        props = await self.get_props_from_inchi(inchi, session)
         if props:
             for prop in props:
                 if prop['urn']['label'] == 'Molecular Formula':
                     return prop['value']['sval']
 
-    def inchi_to_smiles(self, inchi):
+    async def inchi_to_smiles(self, inchi, session):
         """
         Convert InChi to SMILES using PubChem service
         More info: https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest
@@ -72,13 +75,13 @@ def inchi_to_smiles(self, inchi):
         :param inchi: given InChi
         :return: found SMILES
         """
-        props = self.get_props_from_inchi(inchi)
+        props = await self.get_props_from_inchi(inchi, session)
         if props:
             for prop in props:
                 if prop['urn']['label'] == 'SMILES' and prop['urn']['name'] == 'Canonical':
                     return prop['value']['sval']
 
-    def get_props_from_inchi(self, inchi):
+    async def get_props_from_inchi(self, inchi, session):
         """
         General methods to obtain all possible data based on InChi.
 
@@ -86,6 +89,7 @@ def get_props_from_inchi(self, inchi):
         :return: obtained properties associated to the given InChi
         """
         args = "inchi/JSON"
-        response = self.query_the_service('PubChem', args, method='POST', data={'inchi': inchi})
-        if response.status_code == 200:
-            return response.json()['PC_Compounds'][0]['props']
+        response = await self.query_the_service('PubChem', args, session, method='POST', data={'inchi': inchi})
+        if response:
+            response_json = json.loads(response)
+            return response_json['PC_Compounds'][0]['props']
diff --git a/requirements.txt b/requirements.txt
index 517fd57..adc3d5b 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,5 @@
 matchms~=0.9.0
 pandas~=1.2.4
 requests~=2.25.1
-mock~=4.0.3
\ No newline at end of file
+mock~=4.0.3
+aiohttp~=3.7.4.post0
\ No newline at end of file

From 7730e64afbc2fc210c8fc6f3f32d6061edfaf1f5 Mon Sep 17 00:00:00 2001
From: Matej Trojak <trojak@mail.muni.cz>
Date: Fri, 25 Jun 2021 15:56:12 +0200
Subject: [PATCH 3/9] Covered some special cases in aiohttp requests

---
 libs/services/Converter.py | 8 +++++---
 libs/services/NLM.py       | 6 +++++-
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/libs/services/Converter.py b/libs/services/Converter.py
index 50564f9..e4eb7d3 100644
--- a/libs/services/Converter.py
+++ b/libs/services/Converter.py
@@ -1,5 +1,4 @@
 from aiohttp.client_exceptions import ServerDisconnectedError
-import requests
 from libs.utils.Errors import DataNotRetrieved, ConversionNotSupported
 
 
@@ -11,6 +10,7 @@ async def query_the_service(self, service, args, session, method='GET', data=Non
 
         :param service: requested service to be queried
         :param args: additional query arguments
+        :param session: current aiohttp session
         :param method: GET (default) or POST
         :param data: data for POST request
         :return: obtained response
@@ -18,8 +18,8 @@ async def query_the_service(self, service, args, session, method='GET', data=Non
         try:
             result = await self.execute_request(self.services[service] + args, method, data, session)
             return result
-        except requests.exceptions.ConnectionError:
-            raise ConnectionError(f'Service {service} is not available')
+        except TypeError:
+            pass  # TODO: log - probably given argument is incorrect
 
     async def execute_request(self, url, method, data, session, depth=10):
         """
@@ -28,6 +28,8 @@ async def execute_request(self, url, method, data, session, depth=10):
         :param url: service URL
         :param method: GET/POST
         :param data: given arguments for POST request
+        :param session: current aiohttp session
+        :param depth: allowed recursion depth for unsuccessful requests
         :return: obtained response
         """
         try:
diff --git a/libs/services/NLM.py b/libs/services/NLM.py
index 87604c3..a7deb5f 100644
--- a/libs/services/NLM.py
+++ b/libs/services/NLM.py
@@ -1,4 +1,6 @@
 from io import StringIO
+
+import math
 import pandas as pd
 
 from libs.services.Converter import Converter
@@ -39,4 +41,6 @@ async def name_to_inchikey(self, name, session):
         if response:
             table = pd.read_csv(StringIO(response), sep='\t')
             if not table.empty:
-                return table['InChIKey'][0]
+                inchikey = table['InChIKey'][0]
+                if not math.isnan(inchikey):
+                    return inchikey

From b162b1c48df584817798c669abbb921cd3c983c2 Mon Sep 17 00:00:00 2001
From: Matej Trojak <trojak@mail.muni.cz>
Date: Fri, 25 Jun 2021 17:06:14 +0200
Subject: [PATCH 4/9] Fixed minor issues with NLM service

---
 libs/services/NLM.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/libs/services/NLM.py b/libs/services/NLM.py
index a7deb5f..2565aad 100644
--- a/libs/services/NLM.py
+++ b/libs/services/NLM.py
@@ -1,6 +1,5 @@
 from io import StringIO
 
-import math
 import pandas as pd
 
 from libs.services.Converter import Converter
@@ -42,5 +41,5 @@ async def name_to_inchikey(self, name, session):
             table = pd.read_csv(StringIO(response), sep='\t')
             if not table.empty:
                 inchikey = table['InChIKey'][0]
-                if not math.isnan(inchikey):
+                if type(inchikey) == str:
                     return inchikey

From d06cfaef0547e6204237c197eb5d4630b28cf9d8 Mon Sep 17 00:00:00 2001
From: xtrojak <trojak@mail.muni.cz>
Date: Mon, 28 Jun 2021 09:20:35 +0200
Subject: [PATCH 5/9] Improved code structure in Converter

---
 libs/services/Converter.py | 41 ++++++++++++++++++++++++--------------
 1 file changed, 26 insertions(+), 15 deletions(-)

diff --git a/libs/services/Converter.py b/libs/services/Converter.py
index e4eb7d3..d9bfc99 100644
--- a/libs/services/Converter.py
+++ b/libs/services/Converter.py
@@ -16,12 +16,12 @@ async def query_the_service(self, service, args, session, method='GET', data=Non
         :return: obtained response
         """
         try:
-            result = await self.execute_request(self.services[service] + args, method, data, session)
+            result = await self.loop_request(self.services[service] + args, method, data, session)
             return result
         except TypeError:
             pass  # TODO: log - probably given argument is incorrect
 
-    async def execute_request(self, url, method, data, session, depth=10):
+    async def loop_request(self, url, method, data, session, depth=10):
         """
         Execute request with type depending on specified method.
 
@@ -35,23 +35,34 @@ async def execute_request(self, url, method, data, session, depth=10):
         try:
             if method == 'GET':
                 async with session.get(url=url) as response:
-                    result = await response.text()
-                    if response.ok:
-                        return result
-                    elif response.status == 503:
-                        if depth > 0:
-                            return await self.execute_request(url, method, data, session, depth - 1)
+                    return await self.process_request(response, url, method, data, session, depth)
             else:
                 async with session.post(url=url, data=data) as response:
-                    result = await response.text()
-                    if response.ok:
-                        return result
-                    elif response.status == 503:
-                        if depth > 0:
-                            return await self.execute_request(url, method, data, session, depth - 1)
+                    return await self.process_request(response, url, method, data, session, depth)
         except ServerDisconnectedError:
             if depth > 0:
-                return await self.execute_request(url, method, data, session, depth - 1)
+                return await self.loop_request(url, method, data, session, depth - 1)
+
+    async def process_request(self, response, url, method, data, session, depth):
+        """
+        Method to wrap response handling (same for POST and GET requests).
+
+        :param response: given async response
+        :param url: service URL
+        :param method: GET/POST
+        :param data: given arguments for POST request
+        :param session: current aiohttp session
+        :param depth: allowed recursion depth for unsuccessful requests
+        :return: processed response
+        """
+        result = await response.text()
+        if response.ok:
+            return result
+        elif response.status == 503:
+            if depth > 0:
+                return await self.loop_request(url, method, data, session, depth - 1)
+        else:
+            pass  # TODO: log - other error responses
 
     async def convert(self, source, target, data, session):
         """

From 22550abe021106aff282a1ea33d432cec526f213 Mon Sep 17 00:00:00 2001
From: xtrojak <trojak@mail.muni.cz>
Date: Mon, 28 Jun 2021 13:24:23 +0200
Subject: [PATCH 6/9] Changed aiohttp session to property of Converter

---
 libs/Annotator.py          | 10 +++++++---
 libs/Spectra.py            |  3 ++-
 libs/services/CIR.py       | 24 ++++++++++++------------
 libs/services/CTS.py       | 20 ++++++++++----------
 libs/services/Converter.py | 31 +++++++++++++++----------------
 libs/services/NLM.py       |  8 ++++----
 libs/services/PubChem.py   | 24 ++++++++++++------------
 7 files changed, 62 insertions(+), 58 deletions(-)

diff --git a/libs/Annotator.py b/libs/Annotator.py
index 952ce1f..b093177 100644
--- a/libs/Annotator.py
+++ b/libs/Annotator.py
@@ -9,8 +9,9 @@
 class Annotator:
     def __init__(self):
         self.services = {'CTS': CTS(), 'CIR': CIR(), 'NLM': NLM(), 'PubChem': PubChem()}
+        self.session = None
 
-    async def annotate(self, spectra, jobs, session, repeat=False):
+    async def annotate(self, spectra, jobs, repeat=False):
         """
         Runs all jobs to add annotations to given dictionary containing metadata
 
@@ -21,9 +22,12 @@ async def annotate(self, spectra, jobs, session, repeat=False):
         :param spectra: given spectra metadata
         :param jobs: specified list of jobs to be executed
         :param repeat: if some metadata was added, all jobs are executed again
-        :param session: current aiohttp session
         :return: annotated dictionary
         """
+        # set session to every service
+        for service in self.services.values():
+            service.session = self.session
+
         jobs = convert_to_jobs(jobs)
         metadata = spectra.metadata
 
@@ -42,7 +46,7 @@ async def annotate(self, spectra, jobs, session, repeat=False):
                     pass  # TODO: log - source data not available for conversion
                 else:
                     try:
-                        result = await service.convert(job.source, job.target, data, session)
+                        result = await service.convert(job.source, job.target, data)
                         metadata[job.target] = result
                         if repeat:
                             added_metadata = True
diff --git a/libs/Spectra.py b/libs/Spectra.py
index ddd442e..bae508e 100644
--- a/libs/Spectra.py
+++ b/libs/Spectra.py
@@ -48,9 +48,10 @@ async def annotate(self, jobs, batch_size, repeat):
         :param repeat: if some metadata was added, all jobs are executed again
         """
         async with aiohttp.ClientSession() as session:
+            self.annotator.session = session
             results = []
             for size in range(len(self.spectrums) // batch_size + 1):
-                results += await asyncio.gather(*[self.annotator.annotate(spectra, jobs, session, repeat) for spectra in
+                results += await asyncio.gather(*[self.annotator.annotate(spectra, jobs, repeat) for spectra in
                                                   self.spectrums[size * batch_size:(size + 1) * batch_size]])
         self.spectrums = results
 
diff --git a/libs/services/CIR.py b/libs/services/CIR.py
index f56b074..a82cead 100644
--- a/libs/services/CIR.py
+++ b/libs/services/CIR.py
@@ -7,7 +7,7 @@ def __init__(self):
         # service URLs
         self.services = {'CIR': 'https://cactus.nci.nih.gov/chemical/structure/'}
 
-    async def cas_to_smiles(self, cas_number, session):
+    async def cas_to_smiles(self, cas_number):
         """
         Convert CAS number to SMILES using CIR web service
         More info: https://cactus.nci.nih.gov/chemical/structure_documentation
@@ -16,11 +16,11 @@ async def cas_to_smiles(self, cas_number, session):
         :return: obtained SMILES
         """
         args = f"{cas_number}/smiles?resolver=cas_number"
-        response = await self.query_the_service('CIR', args, session)
+        response = await self.query_the_service('CIR', args)
         if response:
             return response
 
-    async def inchikey_to_smiles(self, inchikey, session):
+    async def inchikey_to_smiles(self, inchikey):
         """
         Convert InChiKey to SMILES using CIR web service
         More info: https://cactus.nci.nih.gov/chemical/structure_documentation
@@ -29,11 +29,11 @@ async def inchikey_to_smiles(self, inchikey, session):
         :return: obtained SMILES
         """
         args = f'{inchikey}/smiles'
-        response = await self.query_the_service('CIR', args, session)
+        response = await self.query_the_service('CIR', args)
         if response:
             return response.split('\n')[0]
 
-    async def inchikey_to_inchi(self, inchikey, session):
+    async def inchikey_to_inchi(self, inchikey):
         """
         Convert InChiKey to InCHi using CIR web service
         More info: https://cactus.nci.nih.gov/chemical/structure_documentation
@@ -42,11 +42,11 @@ async def inchikey_to_inchi(self, inchikey, session):
         :return: obtained InCHi
         """
         args = f'{inchikey}/stdinchi'
-        response = await self.query_the_service('CIR', args, session)
+        response = await self.query_the_service('CIR', args)
         if response:
             return response
 
-    async def inchikey_to_cas(self, inchikey, session):
+    async def inchikey_to_cas(self, inchikey):
         """
         Convert InChiKey to CAS number using CIR web service
         More info: https://cactus.nci.nih.gov/chemical/structure_documentation
@@ -55,11 +55,11 @@ async def inchikey_to_cas(self, inchikey, session):
         :return: obtained CAS number
         """
         args = f'{inchikey}/cas'
-        response = await self.query_the_service('CIR', args, session)
+        response = await self.query_the_service('CIR', args)
         if response:
             return response
 
-    async def inchikey_to_formula(self, inchikey, session):
+    async def inchikey_to_formula(self, inchikey):
         """
         Convert InChiKey to chemical formula using CIR web service
         More info: https://cactus.nci.nih.gov/chemical/structure_documentation
@@ -68,11 +68,11 @@ async def inchikey_to_formula(self, inchikey, session):
         :return: obtained chemical formula
         """
         args = f'{inchikey}/formula'
-        response = await self.query_the_service('CIR', args, session)
+        response = await self.query_the_service('CIR', args)
         if response:
             return response
 
-    async def smiles_to_inchikey(self, smiles, session):
+    async def smiles_to_inchikey(self, smiles):
         """
         Convert SMILES to InChiKey using CIR web service
         More info: https://cactus.nci.nih.gov/chemical/structure_documentation
@@ -81,6 +81,6 @@ async def smiles_to_inchikey(self, smiles, session):
         :return: obtained InChiKey
         """
         args = f'{smiles}/stdinchikey'
-        response = await self.query_the_service('CIR', args, session)
+        response = await self.query_the_service('CIR', args)
         if response:
             return response[9:]
diff --git a/libs/services/CTS.py b/libs/services/CTS.py
index b6ae7cf..5f52da6 100644
--- a/libs/services/CTS.py
+++ b/libs/services/CTS.py
@@ -11,7 +11,7 @@ def __init__(self):
                          'CTS_compound': 'http://cts.fiehnlab.ucdavis.edu/service/compound/'
                          }
 
-    async def cas_to_inchikey(self, cas_number, session):
+    async def cas_to_inchikey(self, cas_number):
         """
         Convert CAS number to InChiKey using CTS web service
         More info: http://cts.fiehnlab.ucdavis.edu/services
@@ -22,13 +22,13 @@ async def cas_to_inchikey(self, cas_number, session):
         :return: obtained InChiKey
         """
         args = f'CAS/InChIKey/{cas_number}'
-        response = await self.query_the_service('CTS', args, session)
+        response = await self.query_the_service('CTS', args)
         if response:
             response_json = json.loads(response)
             if len(response_json[0]['results']) != 0:
                 return response_json[0]['results'][0]
 
-    async def inchikey_to_inchi(self, inchikey, session):
+    async def inchikey_to_inchi(self, inchikey):
         """
         Convert InChiKey to InChi using CTS compound service
         More info: http://cts.fiehnlab.ucdavis.edu/services
@@ -37,12 +37,12 @@ async def inchikey_to_inchi(self, inchikey, session):
         :return: obtained InChi
         """
         args = inchikey
-        response = await self.query_the_service('CTS_compound', args, session)
+        response = await self.query_the_service('CTS_compound', args)
         if response:
             response_json = json.loads(response)
             return response_json["inchicode"]
 
-    async def name_to_inchikey(self, name, session):
+    async def name_to_inchikey(self, name):
         """
         Convert Chemical name to InChiKey using CTS service
         More info: http://cts.fiehnlab.ucdavis.edu/services
@@ -51,13 +51,13 @@ async def name_to_inchikey(self, name, session):
         :return: obtained InChiKey
         """
         args = f'Chemical%20Name/InChIKey/{name}'
-        response = await self.query_the_service('CTS', args, session)
+        response = await self.query_the_service('CTS', args)
         if response:
             response_json = json.loads(response)
             if len(response_json[0]['results']) != 0:
                 return response_json[0]['results'][0]
 
-    async def inchikey_to_name(self, inchikey, session):
+    async def inchikey_to_name(self, inchikey):
         """
         Convert InChiKey to Chemical name using CTS compound service
         More info: http://cts.fiehnlab.ucdavis.edu/services
@@ -66,7 +66,7 @@ async def inchikey_to_name(self, inchikey, session):
         :return: obtained Chemical name
         """
         args = inchikey
-        response = await self.query_the_service('CTS_compound', args, session)
+        response = await self.query_the_service('CTS_compound', args)
         if response:
             response_json = json.loads(response)
             synonyms = response_json['synonyms']
@@ -74,7 +74,7 @@ async def inchikey_to_name(self, inchikey, session):
             if names:
                 return names[0]
 
-    async def inchikey_to_iupac_name(self, inchikey, session):
+    async def inchikey_to_iupac_name(self, inchikey):
         """
         Convert InChiKey to IUPAC name using CTS compound service
         More info: http://cts.fiehnlab.ucdavis.edu/services
@@ -83,7 +83,7 @@ async def inchikey_to_iupac_name(self, inchikey, session):
         :return: obtained IUPAC name
         """
         args = inchikey
-        response = await self.query_the_service('CTS_compound', args, session)
+        response = await self.query_the_service('CTS_compound', args)
         if response:
             response_json = json.loads(response)
             synonyms = response_json['synonyms']
diff --git a/libs/services/Converter.py b/libs/services/Converter.py
index d9bfc99..28d8bae 100644
--- a/libs/services/Converter.py
+++ b/libs/services/Converter.py
@@ -3,47 +3,48 @@
 
 
 class Converter:
-    async def query_the_service(self, service, args, session, method='GET', data=None):
+    def __init__(self):
+        self.session = None
+
+    async def query_the_service(self, service, args, method='GET', data=None):
         """
         Make get request to given service with arguments.
         Raises ConnectionError if service is not available.
 
         :param service: requested service to be queried
         :param args: additional query arguments
-        :param session: current aiohttp session
         :param method: GET (default) or POST
         :param data: data for POST request
         :return: obtained response
         """
         try:
-            result = await self.loop_request(self.services[service] + args, method, data, session)
+            result = await self.loop_request(self.services[service] + args, method, data)
             return result
         except TypeError:
             pass  # TODO: log - probably given argument is incorrect
 
-    async def loop_request(self, url, method, data, session, depth=10):
+    async def loop_request(self, url, method, data, depth=10):
         """
         Execute request with type depending on specified method.
 
         :param url: service URL
         :param method: GET/POST
         :param data: given arguments for POST request
-        :param session: current aiohttp session
         :param depth: allowed recursion depth for unsuccessful requests
         :return: obtained response
         """
         try:
             if method == 'GET':
-                async with session.get(url=url) as response:
-                    return await self.process_request(response, url, method, data, session, depth)
+                async with self.session.get(url=url) as response:
+                    return await self.process_request(response, url, method, data, depth)
             else:
-                async with session.post(url=url, data=data) as response:
-                    return await self.process_request(response, url, method, data, session, depth)
+                async with self.session.post(url=url, data=data) as response:
+                    return await self.process_request(response, url, method, data, depth)
         except ServerDisconnectedError:
             if depth > 0:
-                return await self.loop_request(url, method, data, session, depth - 1)
+                return await self.loop_request(url, method, data, depth - 1)
 
-    async def process_request(self, response, url, method, data, session, depth):
+    async def process_request(self, response, url, method, data, depth):
         """
         Method to wrap response handling (same for POST and GET requests).
 
@@ -51,7 +52,6 @@ async def process_request(self, response, url, method, data, session, depth):
         :param url: service URL
         :param method: GET/POST
         :param data: given arguments for POST request
-        :param session: current aiohttp session
         :param depth: allowed recursion depth for unsuccessful requests
         :return: processed response
         """
@@ -60,22 +60,21 @@ async def process_request(self, response, url, method, data, session, depth):
             return result
         elif response.status == 503:
             if depth > 0:
-                return await self.loop_request(url, method, data, session, depth - 1)
+                return await self.loop_request(url, method, data, depth - 1)
         else:
             pass  # TODO: log - other error responses
 
-    async def convert(self, source, target, data, session):
+    async def convert(self, source, target, data):
         """
         Converts specified {source} attribute (provided in {data}) to {target} attribute.
 
         :param source: given attribute name
         :param target: required attribute name
         :param data: given attribute value
-        :param session: current aiohttp session
         :return: obtained value of target attribute
         """
         try:
-            result = await getattr(self, f'{source}_to_{target}')(data, session)
+            result = await getattr(self, f'{source}_to_{target}')(data)
             if result:
                 return result
             raise DataNotRetrieved(f'Target attribute {target} not available.')
diff --git a/libs/services/NLM.py b/libs/services/NLM.py
index 2565aad..ce2a813 100644
--- a/libs/services/NLM.py
+++ b/libs/services/NLM.py
@@ -11,7 +11,7 @@ def __init__(self):
         # service URLs
         self.services = {'NLM': 'https://chem.nlm.nih.gov/api/data/'}
 
-    async def inchikey_to_name(self, inchikey, session):
+    async def inchikey_to_name(self, inchikey):
         """
         Convert InChiKey to Chemical name using NLM service
         More info: https://chem.nlm.nih.gov/chemidplus/inchikey
@@ -20,14 +20,14 @@ async def inchikey_to_name(self, inchikey, session):
         :return: obtained Chemical name
         """
         args = f'inchikey/equals/{inchikey}?data=summary&format=tsv'
-        response = await self.query_the_service('NLM', args, session)
+        response = await self.query_the_service('NLM', args)
         if response:
             if response != 'EXPRESSION_INVALID':
                 table = pd.read_csv(StringIO(response), sep='\t')
                 if not table.empty:
                     return table['Name'][0]
 
-    async def name_to_inchikey(self, name, session):
+    async def name_to_inchikey(self, name):
         """
         Convert Chemical name to InChiKey using NLM service
         More info: https://chem.nlm.nih.gov/chemidplus/inchikey
@@ -36,7 +36,7 @@ async def name_to_inchikey(self, name, session):
         :return: obtained InChiKey
         """
         args = f'name/equals/{name}?data=summary&format=tsv'
-        response = await self.query_the_service('NLM', args, session)
+        response = await self.query_the_service('NLM', args)
         if response:
             table = pd.read_csv(StringIO(response), sep='\t')
             if not table.empty:
diff --git a/libs/services/PubChem.py b/libs/services/PubChem.py
index cff40a9..0308f18 100644
--- a/libs/services/PubChem.py
+++ b/libs/services/PubChem.py
@@ -9,7 +9,7 @@ def __init__(self):
         # service URLs
         self.services = {'PubChem': 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/'}
 
-    async def name_to_inchi(self, name, session):
+    async def name_to_inchi(self, name):
         """
         Convert Chemical name to InChi using PubChem service
         More info: https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest
@@ -18,14 +18,14 @@ async def name_to_inchi(self, name, session):
         :return: found InChi
         """
         args = f'name/{name}/JSON'
-        response = await self.query_the_service('PubChem', args, session)
+        response = await self.query_the_service('PubChem', args)
         if response:
             response_json = json.loads(response)
             for prop in response_json['PC_Compounds'][0]['props']:
                 if prop['urn']['label'] == 'InChI':
                     return prop['value']['sval']
 
-    async def inchi_to_inchikey(self, inchi, session):
+    async def inchi_to_inchikey(self, inchi):
         """
         Convert InChi to InChiKey using PubChem service
         More info: https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest
@@ -33,13 +33,13 @@ async def inchi_to_inchikey(self, inchi, session):
         :param inchi: given InChi
         :return: found InChiKey
         """
-        props = await self.get_props_from_inchi(inchi, session)
+        props = await self.get_props_from_inchi(inchi)
         if props:
             for prop in props:
                 if prop['urn']['label'] == 'InChIKey':
                     return prop['value']['sval']
 
-    async def inchi_to_iupac_name(self, inchi, session):
+    async def inchi_to_iupac_name(self, inchi):
         """
         Convert InChi to IUPAC name using PubChem service
         More info: https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest
@@ -47,13 +47,13 @@ async def inchi_to_iupac_name(self, inchi, session):
         :param inchi: given InChi
         :return: found IUPAC name
         """
-        props = await self.get_props_from_inchi(inchi, session)
+        props = await self.get_props_from_inchi(inchi)
         if props:
             for prop in props:
                 if prop['urn']['label'] == 'IUPAC Name' and prop['urn']['name'] == 'Preferred':
                     return prop['value']['sval']
 
-    async def inchi_to_formula(self, inchi, session):
+    async def inchi_to_formula(self, inchi):
         """
         Convert InChi to chemical formula using PubChem service
         More info: https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest
@@ -61,13 +61,13 @@ async def inchi_to_formula(self, inchi, session):
         :param inchi: given InChi
         :return: found chemical formula
         """
-        props = await self.get_props_from_inchi(inchi, session)
+        props = await self.get_props_from_inchi(inchi)
         if props:
             for prop in props:
                 if prop['urn']['label'] == 'Molecular Formula':
                     return prop['value']['sval']
 
-    async def inchi_to_smiles(self, inchi, session):
+    async def inchi_to_smiles(self, inchi):
         """
         Convert InChi to SMILES using PubChem service
         More info: https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest
@@ -75,13 +75,13 @@ async def inchi_to_smiles(self, inchi, session):
         :param inchi: given InChi
         :return: found SMILES
         """
-        props = await self.get_props_from_inchi(inchi, session)
+        props = await self.get_props_from_inchi(inchi)
         if props:
             for prop in props:
                 if prop['urn']['label'] == 'SMILES' and prop['urn']['name'] == 'Canonical':
                     return prop['value']['sval']
 
-    async def get_props_from_inchi(self, inchi, session):
+    async def get_props_from_inchi(self, inchi):
         """
         General methods to obtain all possible data based on InChi.
 
@@ -89,7 +89,7 @@ async def get_props_from_inchi(self, inchi, session):
         :return: obtained properties associated to the given InChi
         """
         args = "inchi/JSON"
-        response = await self.query_the_service('PubChem', args, session, method='POST', data={'inchi': inchi})
+        response = await self.query_the_service('PubChem', args, method='POST', data={'inchi': inchi})
         if response:
             response_json = json.loads(response)
             return response_json['PC_Compounds'][0]['props']

From 46021b384f2a6b6f64933e14dedae8c6580a8f47 Mon Sep 17 00:00:00 2001
From: xtrojak <trojak@mail.muni.cz>
Date: Mon, 28 Jun 2021 14:12:50 +0200
Subject: [PATCH 7/9] Updated tests to asynchronous version

---
 tests/test_CIR.py       | 36 +++++++++++----------
 tests/test_CTS.py       | 72 ++++++++++++++++++++---------------------
 tests/test_NLM.py       | 19 ++++++-----
 tests/test_annotator.py | 29 ++++++++++-------
 tests/test_pubchem.py   | 54 ++++++++++++++-----------------
 5 files changed, 108 insertions(+), 102 deletions(-)

diff --git a/tests/test_CIR.py b/tests/test_CIR.py
index c3c7d2b..25d2531 100644
--- a/tests/test_CIR.py
+++ b/tests/test_CIR.py
@@ -1,6 +1,8 @@
+import asyncio
 import unittest
 
 from libs.services.CIR import CIR
+from tests.utils import run_in_session
 
 
 class TestCIR(unittest.TestCase):
@@ -11,63 +13,63 @@ def test_connect_to_service(self):
         # test basic CIR service
         cas_number = '7783-89-3'
         args = '{}/smiles?resolver=cas_number'.format(cas_number)
-        response = self.converter.query_the_service('CIR', args)
-        self.assertEqual(response.status_code, 200)
-        self.assertTrue(type(response.text) == str)
+        response = asyncio.run(run_in_session(self.converter, 'query_the_service', ['CIR', args]))
+        self.assertTrue(type(response) == str)
 
         # incorrect CAS number
         cas_number = '7783893'
         args = '{}/smiles?resolver=cas_number'.format(cas_number)
-        response = self.converter.query_the_service('CIR', args)
-        self.assertEqual(response.status_code, 500)
+        response = asyncio.run(run_in_session(self.converter, 'query_the_service', ['CIR', args]))
+        self.assertIsNone(response)
 
     def test_cas_to_smiles(self):
         smiles = '[Ag+].[O-][Br](=O)=O'
         cas_number = '7783-89-3'
-        self.assertEqual(self.converter.cas_to_smiles(cas_number), smiles)
+        self.assertEqual(asyncio.run(run_in_session(self.converter, 'cas_to_smiles', [cas_number])), smiles)
 
         cas_number = '7783893'
-        self.assertIsNone(self.converter.cas_to_smiles(cas_number))
+        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'cas_to_smiles', [cas_number])))
 
     def test_inchikey_to_smiles(self):
         inchikey = 'XQLMNMQWVCXIKR-UHFFFAOYSA-M'
         smiles = '[Ag+].[O-][Br](=O)=O'
-        self.assertEqual(self.converter.inchikey_to_smiles(inchikey), smiles)
+        self.assertEqual(asyncio.run(run_in_session(self.converter, 'inchikey_to_smiles', [inchikey])), smiles)
 
         inchikey = 'XQLMNVCXIKR-UHFFFAOYSA-M'
-        self.assertIsNone(self.converter.inchikey_to_smiles(inchikey))
+        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchikey_to_smiles', [inchikey])))
 
     def test_inchikey_to_inchi(self):
         inchikey = 'XQLMNMQWVCXIKR-UHFFFAOYSA-M'
         inchi = 'InChI=1S/Ag.BrHO3/c;2-1(3)4/h;(H,2,3,4)/q+1;/p-1'
-        self.assertEqual(self.converter.inchikey_to_inchi(inchikey), inchi)
+
+        self.assertEqual(asyncio.run(run_in_session(self.converter, 'inchikey_to_inchi', [inchikey])), inchi)
 
         inchikey = 'XQLMNVCXIKR-UHFFFAOYSA-M'
-        self.assertIsNone(self.converter.inchikey_to_inchi(inchikey))
+        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchikey_to_inchi', [inchikey])))
 
     def test_inchikey_to_cas(self):
         inchikey = 'XQLMNMQWVCXIKR-UHFFFAOYSA-M'
         cas_number = '7783-89-3'
 
-        self.assertEqual(self.converter.inchikey_to_cas(inchikey), cas_number)
+        self.assertEqual(asyncio.run(run_in_session(self.converter, 'inchikey_to_cas', [inchikey])), cas_number)
 
         inchikey = 'XQLMNVCXIKR-UHFFFAOYSA-M'
-        self.assertIsNone(self.converter.inchikey_to_cas(inchikey))
+        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchikey_to_cas', [inchikey])))
 
     def test_inchikey_to_formula(self):
         inchikey = 'XQLMNMQWVCXIKR-UHFFFAOYSA-M'
         formula = 'AgBrO3'
 
-        self.assertEqual(self.converter.inchikey_to_formula(inchikey), formula)
+        self.assertEqual(asyncio.run(run_in_session(self.converter, 'inchikey_to_formula', [inchikey])), formula)
 
         inchikey = 'XQLMNVCXIKR-UHFFFAOYSA-M'
-        self.assertIsNone(self.converter.inchikey_to_formula(inchikey))
+        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchikey_to_formula', [inchikey])))
 
     def test_smiles_to_inchikey(self):
         inchikey = 'XQLMNMQWVCXIKR-UHFFFAOYSA-M'
         smiles = '[Ag+].[O-][Br](=O)=O'
 
-        self.assertEqual(self.converter.smiles_to_inchikey(smiles), inchikey)
+        self.assertEqual(asyncio.run(run_in_session(self.converter, 'smiles_to_inchikey', [smiles])), inchikey)
 
         smiles = '[Ag+].O-][Br](=O)=O'
-        self.assertIsNone(self.converter.smiles_to_inchikey(smiles))
+        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'smiles_to_inchikey', [smiles])))
diff --git a/tests/test_CTS.py b/tests/test_CTS.py
index fde639a..b85ace2 100644
--- a/tests/test_CTS.py
+++ b/tests/test_CTS.py
@@ -1,6 +1,10 @@
+import asyncio
 import unittest
+import json
+from aiohttp.client_exceptions import ClientConnectorError
 
 from libs.services.CTS import CTS
+from tests.utils import run_in_session
 
 
 class TestCTS(unittest.TestCase):
@@ -11,77 +15,71 @@ def test_connect_to_service(self):
         # test basic CTS service
         cas_number = '7783-89-3'
         args = 'CAS/InChIKey/{}'.format(cas_number)
-        response = self.converter.query_the_service('CTS', args)
-        self.assertEqual(response.status_code, 200)
-        json = response.json()
-        self.assertTrue(type(json == list))
-        self.assertEqual(len(json), 1)
-        self.assertIn('results', json[0])
-        self.assertEqual(len(json[0]['results']), 1)
+        response = asyncio.run(run_in_session(self.converter, 'query_the_service', ['CTS', args]))
+        response_json = json.loads(response)
+        self.assertTrue(type(response_json == list))
+        self.assertEqual(len(response_json), 1)
+        self.assertIn('results', response_json[0])
+        self.assertEqual(len(response_json[0]['results']), 1)
 
         # incorrect CAS number
         cas_number = '7783893'
         args = 'CAS/InChIKey/{}'.format(cas_number)
-        response = self.converter.query_the_service('CTS', args)
-        self.assertEqual(response.status_code, 200)
-        json = response.json()
-        self.assertTrue(type(json == list))
-        self.assertEqual(len(json), 1)
-        self.assertIn('results', json[0])
-        self.assertEqual(len(json[0]['results']), 0)
+        response = asyncio.run(run_in_session(self.converter, 'query_the_service', ['CTS', args]))
+        response_json = json.loads(response)
+        self.assertTrue(type(response_json == list))
+        self.assertEqual(len(response_json), 1)
+        self.assertIn('results', response_json[0])
+        self.assertEqual(len(response_json[0]['results']), 0)
 
         # test incorrect service (simulates unavailable service)
         self.converter.services['random'] = 'https://random_strange_url.com'
-        self.assertRaises(ConnectionError, self.converter.query_the_service, 'random', '')
+        try:
+            asyncio.run(run_in_session(self.converter, 'query_the_service', ['random', '']))
+        except ClientConnectorError:
+            pass
+        else:
+            self.fail('ConnectionError not raised')
 
     def test_cas_to_inchikey(self):
         inchikey = 'XQLMNMQWVCXIKR-UHFFFAOYSA-M'
         cas_number = '7783-89-3'
-        self.assertEqual(self.converter.cas_to_inchikey(cas_number), inchikey)
+        self.assertEqual(asyncio.run(run_in_session(self.converter, 'cas_to_inchikey', [cas_number])), inchikey)
 
         cas_number = '7783893'
-        self.assertIsNone(self.converter.cas_to_inchikey(cas_number))
+        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'cas_to_inchikey', [cas_number])))
 
     def test_inchikey_to_inchi(self):
         inchikey = 'XQLMNMQWVCXIKR-UHFFFAOYSA-M'
         inchi = 'InChI=1S/Ag.BrHO3/c;2-1(3)4/h;(H,2,3,4)/q+1;/p-1'
-        self.assertEqual(self.converter.inchikey_to_inchi(inchikey), inchi)
+
+        self.assertEqual(asyncio.run(run_in_session(self.converter, 'inchikey_to_inchi', [inchikey])), inchi)
 
         inchikey = 'XQLMNMQIKR-UHFFFAOYSA-M'
-        self.assertIsNone(self.converter.inchikey_to_inchi(inchikey))
+        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchikey_to_inchi', [inchikey])))
 
     def test_name_to_inchikey(self):
         name = 'L-Alanine'
         inchikey = 'QNAYBMKLOCPYGJ-REOHCLBHSA-N'
-        self.assertEqual(self.converter.name_to_inchikey(name), inchikey)
+        self.assertEqual(asyncio.run(run_in_session(self.converter, 'name_to_inchikey', [name])), inchikey)
 
         name = 'L-Alalalalanine'
-        self.assertIsNone(self.converter.name_to_inchikey(name))
+        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'name_to_inchikey', [name])))
 
     def test_inchikey_to_name(self):
         inchikey = 'QNAYBMKLOCPYGJ-REOHCLBHSA-N'
         name = 'L-2-Aminopropanoic acid'
-        self.assertEqual(self.converter.inchikey_to_name(inchikey), name)
+
+        self.assertEqual(asyncio.run(run_in_session(self.converter, 'inchikey_to_name', [inchikey])), name)
 
         inchikey = 'XQLMNMQIKR-UHFFFAOYSA-M'
-        self.assertIsNone(self.converter.inchikey_to_name(inchikey))
+        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchikey_to_name', [inchikey])))
 
     def test_inchikey_to_IUPAC_name(self):
         inchikey = 'QNAYBMKLOCPYGJ-REOHCLBHSA-N'
         uipac_name = '(2S)-2-aminopropanoic acid'
-        self.assertEqual(self.converter.inchikey_to_iupac_name(inchikey), uipac_name)
+        asyncio.run(run_in_session(self.converter, 'inchikey_to_iupac_name', [inchikey]))
+        self.assertEqual(asyncio.run(run_in_session(self.converter, 'inchikey_to_iupac_name', [inchikey])), uipac_name)
 
         inchikey = 'XQLMNMQIKR-UHFFFAOYSA-M'
-        self.assertIsNone(self.converter.inchikey_to_iupac_name(inchikey))
-
-    def test_cache(self):
-        inchikey = 'XQLMNMQWVCXIKR-UHFFFAOYSA-M'
-        identification = 'CTS_compound:' + inchikey
-        _ = self.converter.inchikey_to_inchi(inchikey)
-
-        self.assertIn(identification, self.converter.cache)
-
-        _ = self.converter.inchikey_to_name(inchikey)
-        _ = self.converter.inchikey_to_iupac_name(inchikey)
-
-        self.assertIn(identification, self.converter.cache)
+        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchikey_to_iupac_name', [inchikey])))
diff --git a/tests/test_NLM.py b/tests/test_NLM.py
index 7080f5c..eaf10f2 100644
--- a/tests/test_NLM.py
+++ b/tests/test_NLM.py
@@ -1,8 +1,10 @@
+import asyncio
 import unittest
 from io import StringIO
 import pandas as pd
 
 from libs.services.NLM import NLM
+from tests.utils import run_in_session
 
 
 class TestNLM(unittest.TestCase):
@@ -13,27 +15,28 @@ def test_connect_to_service(self):
         # test basic NLM service
         inchikey = 'QNAYBMKLOCPYGJ-REOHCLBHSA-N'
         args = 'inchikey/equals/{}?data=summary&format=tsv'.format(inchikey)
-        response = self.converter.query_the_service('NLM', args)
-        self.assertEqual(response.status_code, 200)
+        response = asyncio.run(run_in_session(self.converter, 'query_the_service', ['NLM', args]))
 
-        table = pd.read_csv(StringIO(response.text), sep='\t')
+        table = pd.read_csv(StringIO(response), sep='\t')
         self.assertFalse(table.empty)
 
     def test_inchikey_to_name(self):
         inchikey = 'QNAYBMKLOCPYGJ-REOHCLBHSA-N'
         name = 'Alanine [USAN:INN]'
-        self.assertEqual(self.converter.inchikey_to_name(inchikey), name)
+
+        self.assertEqual(asyncio.run(run_in_session(self.converter, 'inchikey_to_name', [inchikey])), name)
 
         inchikey = 'QNAYBMLOXXXXGJ-REOHCLBHSA-N'
-        self.assertIsNone(self.converter.inchikey_to_name(inchikey))
+        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchikey_to_name', [inchikey])))
 
         inchikey = 'QNAYMLGJ-REOLBHSA-N'
-        self.assertIsNone(self.converter.inchikey_to_name(inchikey))
+        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchikey_to_name', [inchikey])))
 
     def test_name_to_inchikey(self):
         name = 'L-Alanine'
         inchikey = 'QNAYBMKLOCPYGJ-REOHCLBHSA-N'
-        self.assertEqual(self.converter.name_to_inchikey(name), inchikey)
+
+        self.assertEqual(asyncio.run(run_in_session(self.converter, 'name_to_inchikey', [name])), inchikey)
 
         name = 'L-Alanne'
-        self.assertIsNone(self.converter.name_to_inchikey(name))
+        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'name_to_inchikey', [name])))
diff --git a/tests/test_annotator.py b/tests/test_annotator.py
index 7e6cbc2..8ff2352 100644
--- a/tests/test_annotator.py
+++ b/tests/test_annotator.py
@@ -1,7 +1,9 @@
+import asyncio
 import unittest
 import mock
 
 from libs.Annotator import Annotator
+from tests.utils import run_in_session
 
 
 class TestAnnotator(unittest.TestCase):
@@ -10,29 +12,34 @@ def setUp(self):
 
     def test_annotate(self):
         jobs = [('name', 'inchi', 'PubChem')]
-
         pubchem = self.annotator.services['PubChem']
-        pubchem.name_to_inchi = mock.Mock(return_value='a InChi value')
+        pubchem.name_to_inchi = mock.AsyncMock(return_value='a InChi value')
         self.annotator.services['PubChem'] = pubchem
 
-        metadata = {'name': 'a good name'}
-        expected_metadata = {'name': 'a good name', 'inchi': 'a InChi value'}
-        self.assertEqual(self.annotator.annotate(metadata, jobs), expected_metadata)
+        spectra = mock.Mock()
+        spectra.metadata = {'name': 'a good name'}
+        expected_spectra = mock.AsyncMock()
+        expected_spectra.metadata = {'name': 'a good name', 'inchi': 'a InChi value'}
+        self.assertEqual(asyncio.run(run_in_session(self.annotator, 'annotate', [spectra, jobs])).metadata,
+                         expected_spectra.metadata)
 
     def test_service_unknown(self):
         jobs = [('name', 'inchi', 'Jumbo')]
-        metadata = {'name': 'a good name'}
-        self.assertEqual(self.annotator.annotate(metadata, jobs), metadata)
+        spectra = mock.Mock()
+        spectra.metadata = {'name': 'a good name'}
+        self.assertEqual(asyncio.run(run_in_session(self.annotator, 'annotate', [spectra, jobs])), spectra)
 
     def test_source_unknown(self):
         jobs = [('random_name', 'inchi', 'Jumbo')]
-        metadata = {'name': 'a good name'}
-        self.assertEqual(self.annotator.annotate(metadata, jobs), metadata)
+        spectra = mock.Mock()
+        spectra.metadata = {'name': 'a good name'}
+        self.assertEqual(asyncio.run(run_in_session(self.annotator, 'annotate', [spectra, jobs])), spectra)
 
     def test_target_unknown(self):
         jobs = [('name', 'random_name', 'CTS')]
-        metadata = {'name': 'a good name'}
-        self.assertEqual(self.annotator.annotate(metadata, jobs), metadata)
+        spectra = mock.Mock()
+        spectra.metadata = {'name': 'a good name'}
+        self.assertEqual(asyncio.run(run_in_session(self.annotator, 'annotate', [spectra, jobs])), spectra)
 
     def test_get_all_conversions(self):
         expected_result = [('cas', 'inchikey', 'CTS'), ('inchikey', 'inchi', 'CTS'), ('inchikey', 'iupac_name', 'CTS'),
diff --git a/tests/test_pubchem.py b/tests/test_pubchem.py
index 8c81a08..d317633 100644
--- a/tests/test_pubchem.py
+++ b/tests/test_pubchem.py
@@ -1,6 +1,9 @@
+import asyncio
 import unittest
+import json
 
 from libs.services.PubChem import PubChem
+from tests.utils import run_in_session
 
 
 class TestPubChem(unittest.TestCase):
@@ -10,62 +13,55 @@ def setUp(self):
     def test_connect_to_service(self):
         inchi = 'InChI=1S/C9H10O4/c10-7-3-1-6(2-4-7)5-8(11)9(12)13/h1-4,8,10-11H,5H2,(H,12,13)'
         args = "inchi/JSON"
-        response = self.converter.query_the_service('PubChem', args, method='POST', data={'inchi': inchi})
-        self.assertEqual(response.status_code, 200)
-        json = response.json()
-        self.assertIn('PC_Compounds', json)
-        self.assertTrue(len(json['PC_Compounds']) == 1)
-        self.assertIn('props', json['PC_Compounds'][0])
-        self.assertTrue(type(json['PC_Compounds'][0]['props']) == list)
+        response = asyncio.run(run_in_session(self.converter, 'query_the_service',
+                                              ['PubChem', args, 'POST', {'inchi': inchi}]))
+        response_json = json.loads(response)
+        self.assertIn('PC_Compounds', response_json)
+        self.assertTrue(len(response_json['PC_Compounds']) == 1)
+        self.assertIn('props', response_json['PC_Compounds'][0])
+        self.assertTrue(type(response_json['PC_Compounds'][0]['props']) == list)
 
     def test_inchi_to_inchikey(self):
         inchi = 'InChI=1S/C9H10O4/c10-7-3-1-6(2-4-7)5-8(11)9(12)13/h1-4,8,10-11H,5H2,(H,12,13)'
         inchikey = 'JVGVDSSUAVXRDY-UHFFFAOYSA-N'
-        self.assertEqual(self.converter.inchi_to_inchikey(inchi), inchikey)
 
-        # clear the cache
-        self.converter.cache = dict()
+        self.assertEqual(asyncio.run(run_in_session(self.converter, 'inchi_to_inchikey', [inchi])), inchikey)
 
-        wrong_inchi = 'InChI=1S/C9H10O4/c102-4-7)5-8(11)9(12)13/h1-4,8,10-11H,5H2,(H,12,13)'
-        self.assertIsNone(self.converter.inchi_to_inchikey(wrong_inchi))
+        inchi = 'InChI=1S/C9H10O4/c102-4-7)5-8(11)9(12)13/h1-4,8,10-11H,5H2,(H,12,13)'
+        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchi_to_inchikey', [inchi])))
 
     def test_name_to_inchi(self):
         name = '3-Methyl-5-[p-fluorophenyl]-2H-1,3-[3H]-oxazine-2,6-dione'
         inchi = 'InChI=1S/C11H8FNO3/c1-13-6-9(10(14)16-11(13)15)7-2-4-8(12)5-3-7/h2-6H,1H3'
-        self.assertEqual(self.converter.name_to_inchi(name), inchi)
+
+        self.assertEqual(asyncio.run(run_in_session(self.converter, 'name_to_inchi', [name])), inchi)
 
         name = 'HYDROXYPHENYLLACTATE M-H'
-        self.assertIsNone(self.converter.name_to_inchi(name))
+        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'name_to_inchi', [name])))
 
     def test_inchi_to_IUPAC_name(self):
         inchi = 'InChI=1S/C11H8FNO3/c1-13-6-9(10(14)16-11(13)15)7-2-4-8(12)5-3-7/h2-6H,1H3'
         IUPAC_name = '5-(4-fluorophenyl)-3-methyl-1,3-oxazine-2,6-dione'
-        self.assertEqual(self.converter.inchi_to_iupac_name(inchi), IUPAC_name)
 
-        # clear the cache
-        self.converter.cache = dict()
+        self.assertEqual(asyncio.run(run_in_session(self.converter, 'inchi_to_iupac_name', [inchi])), IUPAC_name)
 
-        wrong_inchi = 'InChI=1S/C9H10O4/c102-4-7)5-8(11)93/1-4,8,10-11H,5H2,(H,12,13)'
-        self.assertIsNone(self.converter.inchi_to_iupac_name(wrong_inchi))
+        inchi = 'InChI=1S/C9H10O4/c102-4-7)5-8(11)93/1-4,8,10-11H,5H2,(H,12,13)'
+        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchi_to_iupac_name', [inchi])))
 
     def test_inchi_to_formula(self):
         inchi = 'InChI=1S/C11H8FNO3/c1-13-6-9(10(14)16-11(13)15)7-2-4-8(12)5-3-7/h2-6H,1H3'
         formula = 'C11H8FNO3'
-        self.assertEqual(self.converter.inchi_to_formula(inchi), formula)
 
-        # clear the cache
-        self.converter.cache = dict()
+        self.assertEqual(asyncio.run(run_in_session(self.converter, 'inchi_to_formula', [inchi])), formula)
 
-        wrong_inchi = 'InChI=1S/C9H10O4/c102-4-7)5-8(11)93/1-4,8,10-11H,5H2,(H,12,13)'
-        self.assertIsNone(self.converter.inchi_to_formula(wrong_inchi))
+        inchi = 'InChI=1S/C9H10O4/c102-4-7)5-8(11)93/1-4,8,10-11H,5H2,(H,12,13)'
+        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchi_to_formula', [inchi])))
 
     def test_inchi_to_smiles(self):
         inchi = 'InChI=1S/C11H8FNO3/c1-13-6-9(10(14)16-11(13)15)7-2-4-8(12)5-3-7/h2-6H,1H3'
         smiles = 'CN1C=C(C(=O)OC1=O)C2=CC=C(C=C2)F'
-        self.assertEqual(self.converter.inchi_to_smiles(inchi), smiles)
 
-        # clear the cache
-        self.converter.cache = dict()
+        self.assertEqual(asyncio.run(run_in_session(self.converter, 'inchi_to_smiles', [inchi])), smiles)
 
-        wrong_inchi = 'InChI=1S/C9H10O4/c102-4-7)5-8(11)93/1-4,8,10-11H,5H2,(H,12,13)'
-        self.assertIsNone(self.converter.inchi_to_smiles(wrong_inchi))
+        inchi = 'InChI=1S/C9H10O4/c102-4-7)5-8(11)93/1-4,8,10-11H,5H2,(H,12,13)'
+        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchi_to_smiles', [inchi])))

From b16b8b2b923da1f557dd9f04a5c4d32691c29025 Mon Sep 17 00:00:00 2001
From: xtrojak <trojak@mail.muni.cz>
Date: Mon, 28 Jun 2021 14:13:31 +0200
Subject: [PATCH 8/9] Wrapper function to enable async calls with active
 aiohttp session

---
 tests/utils.py | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 tests/utils.py

diff --git a/tests/utils.py b/tests/utils.py
new file mode 100644
index 0000000..338ccb1
--- /dev/null
+++ b/tests/utils.py
@@ -0,0 +1,7 @@
+import aiohttp
+
+
+async def run_in_session(converter, method, args):
+    async with aiohttp.ClientSession() as session:
+        converter.session = session
+        return await getattr(converter, method)(*args)

From f7c6ac4acb2fbb8d5adff94ee731fd8f90dfc9c8 Mon Sep 17 00:00:00 2001
From: Matej Trojak <trojak@mail.muni.cz>
Date: Tue, 29 Jun 2021 14:26:56 +0200
Subject: [PATCH 9/9] Renamed session wrapper for tests

---
 tests/test_CIR.py       | 30 +++++++++++++++---------------
 tests/test_CTS.py       | 30 +++++++++++++++---------------
 tests/test_NLM.py       | 14 +++++++-------
 tests/test_annotator.py | 10 +++++-----
 tests/test_pubchem.py   | 26 +++++++++++++-------------
 tests/utils.py          |  2 +-
 6 files changed, 56 insertions(+), 56 deletions(-)

diff --git a/tests/test_CIR.py b/tests/test_CIR.py
index 25d2531..6a629ca 100644
--- a/tests/test_CIR.py
+++ b/tests/test_CIR.py
@@ -2,7 +2,7 @@
 import unittest
 
 from libs.services.CIR import CIR
-from tests.utils import run_in_session
+from tests.utils import wrap_with_session
 
 
 class TestCIR(unittest.TestCase):
@@ -13,63 +13,63 @@ def test_connect_to_service(self):
         # test basic CIR service
         cas_number = '7783-89-3'
         args = '{}/smiles?resolver=cas_number'.format(cas_number)
-        response = asyncio.run(run_in_session(self.converter, 'query_the_service', ['CIR', args]))
+        response = asyncio.run(wrap_with_session(self.converter, 'query_the_service', ['CIR', args]))
         self.assertTrue(type(response) == str)
 
         # incorrect CAS number
         cas_number = '7783893'
         args = '{}/smiles?resolver=cas_number'.format(cas_number)
-        response = asyncio.run(run_in_session(self.converter, 'query_the_service', ['CIR', args]))
+        response = asyncio.run(wrap_with_session(self.converter, 'query_the_service', ['CIR', args]))
         self.assertIsNone(response)
 
     def test_cas_to_smiles(self):
         smiles = '[Ag+].[O-][Br](=O)=O'
         cas_number = '7783-89-3'
-        self.assertEqual(asyncio.run(run_in_session(self.converter, 'cas_to_smiles', [cas_number])), smiles)
+        self.assertEqual(asyncio.run(wrap_with_session(self.converter, 'cas_to_smiles', [cas_number])), smiles)
 
         cas_number = '7783893'
-        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'cas_to_smiles', [cas_number])))
+        self.assertIsNone(asyncio.run(wrap_with_session(self.converter, 'cas_to_smiles', [cas_number])))
 
     def test_inchikey_to_smiles(self):
         inchikey = 'XQLMNMQWVCXIKR-UHFFFAOYSA-M'
         smiles = '[Ag+].[O-][Br](=O)=O'
-        self.assertEqual(asyncio.run(run_in_session(self.converter, 'inchikey_to_smiles', [inchikey])), smiles)
+        self.assertEqual(asyncio.run(wrap_with_session(self.converter, 'inchikey_to_smiles', [inchikey])), smiles)
 
         inchikey = 'XQLMNVCXIKR-UHFFFAOYSA-M'
-        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchikey_to_smiles', [inchikey])))
+        self.assertIsNone(asyncio.run(wrap_with_session(self.converter, 'inchikey_to_smiles', [inchikey])))
 
     def test_inchikey_to_inchi(self):
         inchikey = 'XQLMNMQWVCXIKR-UHFFFAOYSA-M'
         inchi = 'InChI=1S/Ag.BrHO3/c;2-1(3)4/h;(H,2,3,4)/q+1;/p-1'
 
-        self.assertEqual(asyncio.run(run_in_session(self.converter, 'inchikey_to_inchi', [inchikey])), inchi)
+        self.assertEqual(asyncio.run(wrap_with_session(self.converter, 'inchikey_to_inchi', [inchikey])), inchi)
 
         inchikey = 'XQLMNVCXIKR-UHFFFAOYSA-M'
-        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchikey_to_inchi', [inchikey])))
+        self.assertIsNone(asyncio.run(wrap_with_session(self.converter, 'inchikey_to_inchi', [inchikey])))
 
     def test_inchikey_to_cas(self):
         inchikey = 'XQLMNMQWVCXIKR-UHFFFAOYSA-M'
         cas_number = '7783-89-3'
 
-        self.assertEqual(asyncio.run(run_in_session(self.converter, 'inchikey_to_cas', [inchikey])), cas_number)
+        self.assertEqual(asyncio.run(wrap_with_session(self.converter, 'inchikey_to_cas', [inchikey])), cas_number)
 
         inchikey = 'XQLMNVCXIKR-UHFFFAOYSA-M'
-        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchikey_to_cas', [inchikey])))
+        self.assertIsNone(asyncio.run(wrap_with_session(self.converter, 'inchikey_to_cas', [inchikey])))
 
     def test_inchikey_to_formula(self):
         inchikey = 'XQLMNMQWVCXIKR-UHFFFAOYSA-M'
         formula = 'AgBrO3'
 
-        self.assertEqual(asyncio.run(run_in_session(self.converter, 'inchikey_to_formula', [inchikey])), formula)
+        self.assertEqual(asyncio.run(wrap_with_session(self.converter, 'inchikey_to_formula', [inchikey])), formula)
 
         inchikey = 'XQLMNVCXIKR-UHFFFAOYSA-M'
-        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchikey_to_formula', [inchikey])))
+        self.assertIsNone(asyncio.run(wrap_with_session(self.converter, 'inchikey_to_formula', [inchikey])))
 
     def test_smiles_to_inchikey(self):
         inchikey = 'XQLMNMQWVCXIKR-UHFFFAOYSA-M'
         smiles = '[Ag+].[O-][Br](=O)=O'
 
-        self.assertEqual(asyncio.run(run_in_session(self.converter, 'smiles_to_inchikey', [smiles])), inchikey)
+        self.assertEqual(asyncio.run(wrap_with_session(self.converter, 'smiles_to_inchikey', [smiles])), inchikey)
 
         smiles = '[Ag+].O-][Br](=O)=O'
-        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'smiles_to_inchikey', [smiles])))
+        self.assertIsNone(asyncio.run(wrap_with_session(self.converter, 'smiles_to_inchikey', [smiles])))
diff --git a/tests/test_CTS.py b/tests/test_CTS.py
index b85ace2..d269fd3 100644
--- a/tests/test_CTS.py
+++ b/tests/test_CTS.py
@@ -4,7 +4,7 @@
 from aiohttp.client_exceptions import ClientConnectorError
 
 from libs.services.CTS import CTS
-from tests.utils import run_in_session
+from tests.utils import wrap_with_session
 
 
 class TestCTS(unittest.TestCase):
@@ -15,7 +15,7 @@ def test_connect_to_service(self):
         # test basic CTS service
         cas_number = '7783-89-3'
         args = 'CAS/InChIKey/{}'.format(cas_number)
-        response = asyncio.run(run_in_session(self.converter, 'query_the_service', ['CTS', args]))
+        response = asyncio.run(wrap_with_session(self.converter, 'query_the_service', ['CTS', args]))
         response_json = json.loads(response)
         self.assertTrue(type(response_json == list))
         self.assertEqual(len(response_json), 1)
@@ -25,7 +25,7 @@ def test_connect_to_service(self):
         # incorrect CAS number
         cas_number = '7783893'
         args = 'CAS/InChIKey/{}'.format(cas_number)
-        response = asyncio.run(run_in_session(self.converter, 'query_the_service', ['CTS', args]))
+        response = asyncio.run(wrap_with_session(self.converter, 'query_the_service', ['CTS', args]))
         response_json = json.loads(response)
         self.assertTrue(type(response_json == list))
         self.assertEqual(len(response_json), 1)
@@ -35,7 +35,7 @@ def test_connect_to_service(self):
         # test incorrect service (simulates unavailable service)
         self.converter.services['random'] = 'https://random_strange_url.com'
         try:
-            asyncio.run(run_in_session(self.converter, 'query_the_service', ['random', '']))
+            asyncio.run(wrap_with_session(self.converter, 'query_the_service', ['random', '']))
         except ClientConnectorError:
             pass
         else:
@@ -44,42 +44,42 @@ def test_connect_to_service(self):
     def test_cas_to_inchikey(self):
         inchikey = 'XQLMNMQWVCXIKR-UHFFFAOYSA-M'
         cas_number = '7783-89-3'
-        self.assertEqual(asyncio.run(run_in_session(self.converter, 'cas_to_inchikey', [cas_number])), inchikey)
+        self.assertEqual(asyncio.run(wrap_with_session(self.converter, 'cas_to_inchikey', [cas_number])), inchikey)
 
         cas_number = '7783893'
-        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'cas_to_inchikey', [cas_number])))
+        self.assertIsNone(asyncio.run(wrap_with_session(self.converter, 'cas_to_inchikey', [cas_number])))
 
     def test_inchikey_to_inchi(self):
         inchikey = 'XQLMNMQWVCXIKR-UHFFFAOYSA-M'
         inchi = 'InChI=1S/Ag.BrHO3/c;2-1(3)4/h;(H,2,3,4)/q+1;/p-1'
 
-        self.assertEqual(asyncio.run(run_in_session(self.converter, 'inchikey_to_inchi', [inchikey])), inchi)
+        self.assertEqual(asyncio.run(wrap_with_session(self.converter, 'inchikey_to_inchi', [inchikey])), inchi)
 
         inchikey = 'XQLMNMQIKR-UHFFFAOYSA-M'
-        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchikey_to_inchi', [inchikey])))
+        self.assertIsNone(asyncio.run(wrap_with_session(self.converter, 'inchikey_to_inchi', [inchikey])))
 
     def test_name_to_inchikey(self):
         name = 'L-Alanine'
         inchikey = 'QNAYBMKLOCPYGJ-REOHCLBHSA-N'
-        self.assertEqual(asyncio.run(run_in_session(self.converter, 'name_to_inchikey', [name])), inchikey)
+        self.assertEqual(asyncio.run(wrap_with_session(self.converter, 'name_to_inchikey', [name])), inchikey)
 
         name = 'L-Alalalalanine'
-        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'name_to_inchikey', [name])))
+        self.assertIsNone(asyncio.run(wrap_with_session(self.converter, 'name_to_inchikey', [name])))
 
     def test_inchikey_to_name(self):
         inchikey = 'QNAYBMKLOCPYGJ-REOHCLBHSA-N'
         name = 'L-2-Aminopropanoic acid'
 
-        self.assertEqual(asyncio.run(run_in_session(self.converter, 'inchikey_to_name', [inchikey])), name)
+        self.assertEqual(asyncio.run(wrap_with_session(self.converter, 'inchikey_to_name', [inchikey])), name)
 
         inchikey = 'XQLMNMQIKR-UHFFFAOYSA-M'
-        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchikey_to_name', [inchikey])))
+        self.assertIsNone(asyncio.run(wrap_with_session(self.converter, 'inchikey_to_name', [inchikey])))
 
     def test_inchikey_to_IUPAC_name(self):
         inchikey = 'QNAYBMKLOCPYGJ-REOHCLBHSA-N'
         uipac_name = '(2S)-2-aminopropanoic acid'
-        asyncio.run(run_in_session(self.converter, 'inchikey_to_iupac_name', [inchikey]))
-        self.assertEqual(asyncio.run(run_in_session(self.converter, 'inchikey_to_iupac_name', [inchikey])), uipac_name)
+        asyncio.run(wrap_with_session(self.converter, 'inchikey_to_iupac_name', [inchikey]))
+        self.assertEqual(asyncio.run(wrap_with_session(self.converter, 'inchikey_to_iupac_name', [inchikey])), uipac_name)
 
         inchikey = 'XQLMNMQIKR-UHFFFAOYSA-M'
-        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchikey_to_iupac_name', [inchikey])))
+        self.assertIsNone(asyncio.run(wrap_with_session(self.converter, 'inchikey_to_iupac_name', [inchikey])))
diff --git a/tests/test_NLM.py b/tests/test_NLM.py
index eaf10f2..537962b 100644
--- a/tests/test_NLM.py
+++ b/tests/test_NLM.py
@@ -4,7 +4,7 @@
 import pandas as pd
 
 from libs.services.NLM import NLM
-from tests.utils import run_in_session
+from tests.utils import wrap_with_session
 
 
 class TestNLM(unittest.TestCase):
@@ -15,7 +15,7 @@ def test_connect_to_service(self):
         # test basic NLM service
         inchikey = 'QNAYBMKLOCPYGJ-REOHCLBHSA-N'
         args = 'inchikey/equals/{}?data=summary&format=tsv'.format(inchikey)
-        response = asyncio.run(run_in_session(self.converter, 'query_the_service', ['NLM', args]))
+        response = asyncio.run(wrap_with_session(self.converter, 'query_the_service', ['NLM', args]))
 
         table = pd.read_csv(StringIO(response), sep='\t')
         self.assertFalse(table.empty)
@@ -24,19 +24,19 @@ def test_inchikey_to_name(self):
         inchikey = 'QNAYBMKLOCPYGJ-REOHCLBHSA-N'
         name = 'Alanine [USAN:INN]'
 
-        self.assertEqual(asyncio.run(run_in_session(self.converter, 'inchikey_to_name', [inchikey])), name)
+        self.assertEqual(asyncio.run(wrap_with_session(self.converter, 'inchikey_to_name', [inchikey])), name)
 
         inchikey = 'QNAYBMLOXXXXGJ-REOHCLBHSA-N'
-        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchikey_to_name', [inchikey])))
+        self.assertIsNone(asyncio.run(wrap_with_session(self.converter, 'inchikey_to_name', [inchikey])))
 
         inchikey = 'QNAYMLGJ-REOLBHSA-N'
-        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchikey_to_name', [inchikey])))
+        self.assertIsNone(asyncio.run(wrap_with_session(self.converter, 'inchikey_to_name', [inchikey])))
 
     def test_name_to_inchikey(self):
         name = 'L-Alanine'
         inchikey = 'QNAYBMKLOCPYGJ-REOHCLBHSA-N'
 
-        self.assertEqual(asyncio.run(run_in_session(self.converter, 'name_to_inchikey', [name])), inchikey)
+        self.assertEqual(asyncio.run(wrap_with_session(self.converter, 'name_to_inchikey', [name])), inchikey)
 
         name = 'L-Alanne'
-        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'name_to_inchikey', [name])))
+        self.assertIsNone(asyncio.run(wrap_with_session(self.converter, 'name_to_inchikey', [name])))
diff --git a/tests/test_annotator.py b/tests/test_annotator.py
index 8ff2352..9f68cb9 100644
--- a/tests/test_annotator.py
+++ b/tests/test_annotator.py
@@ -3,7 +3,7 @@
 import mock
 
 from libs.Annotator import Annotator
-from tests.utils import run_in_session
+from tests.utils import wrap_with_session
 
 
 class TestAnnotator(unittest.TestCase):
@@ -20,26 +20,26 @@ def test_annotate(self):
         spectra.metadata = {'name': 'a good name'}
         expected_spectra = mock.AsyncMock()
         expected_spectra.metadata = {'name': 'a good name', 'inchi': 'a InChi value'}
-        self.assertEqual(asyncio.run(run_in_session(self.annotator, 'annotate', [spectra, jobs])).metadata,
+        self.assertEqual(asyncio.run(wrap_with_session(self.annotator, 'annotate', [spectra, jobs])).metadata,
                          expected_spectra.metadata)
 
     def test_service_unknown(self):
         jobs = [('name', 'inchi', 'Jumbo')]
         spectra = mock.Mock()
         spectra.metadata = {'name': 'a good name'}
-        self.assertEqual(asyncio.run(run_in_session(self.annotator, 'annotate', [spectra, jobs])), spectra)
+        self.assertEqual(asyncio.run(wrap_with_session(self.annotator, 'annotate', [spectra, jobs])), spectra)
 
     def test_source_unknown(self):
         jobs = [('random_name', 'inchi', 'Jumbo')]
         spectra = mock.Mock()
         spectra.metadata = {'name': 'a good name'}
-        self.assertEqual(asyncio.run(run_in_session(self.annotator, 'annotate', [spectra, jobs])), spectra)
+        self.assertEqual(asyncio.run(wrap_with_session(self.annotator, 'annotate', [spectra, jobs])), spectra)
 
     def test_target_unknown(self):
         jobs = [('name', 'random_name', 'CTS')]
         spectra = mock.Mock()
         spectra.metadata = {'name': 'a good name'}
-        self.assertEqual(asyncio.run(run_in_session(self.annotator, 'annotate', [spectra, jobs])), spectra)
+        self.assertEqual(asyncio.run(wrap_with_session(self.annotator, 'annotate', [spectra, jobs])), spectra)
 
     def test_get_all_conversions(self):
         expected_result = [('cas', 'inchikey', 'CTS'), ('inchikey', 'inchi', 'CTS'), ('inchikey', 'iupac_name', 'CTS'),
diff --git a/tests/test_pubchem.py b/tests/test_pubchem.py
index d317633..a304611 100644
--- a/tests/test_pubchem.py
+++ b/tests/test_pubchem.py
@@ -3,7 +3,7 @@
 import json
 
 from libs.services.PubChem import PubChem
-from tests.utils import run_in_session
+from tests.utils import wrap_with_session
 
 
 class TestPubChem(unittest.TestCase):
@@ -13,8 +13,8 @@ def setUp(self):
     def test_connect_to_service(self):
         inchi = 'InChI=1S/C9H10O4/c10-7-3-1-6(2-4-7)5-8(11)9(12)13/h1-4,8,10-11H,5H2,(H,12,13)'
         args = "inchi/JSON"
-        response = asyncio.run(run_in_session(self.converter, 'query_the_service',
-                                              ['PubChem', args, 'POST', {'inchi': inchi}]))
+        response = asyncio.run(wrap_with_session(self.converter, 'query_the_service',
+                                                 ['PubChem', args, 'POST', {'inchi': inchi}]))
         response_json = json.loads(response)
         self.assertIn('PC_Compounds', response_json)
         self.assertTrue(len(response_json['PC_Compounds']) == 1)
@@ -25,43 +25,43 @@ def test_inchi_to_inchikey(self):
         inchi = 'InChI=1S/C9H10O4/c10-7-3-1-6(2-4-7)5-8(11)9(12)13/h1-4,8,10-11H,5H2,(H,12,13)'
         inchikey = 'JVGVDSSUAVXRDY-UHFFFAOYSA-N'
 
-        self.assertEqual(asyncio.run(run_in_session(self.converter, 'inchi_to_inchikey', [inchi])), inchikey)
+        self.assertEqual(asyncio.run(wrap_with_session(self.converter, 'inchi_to_inchikey', [inchi])), inchikey)
 
         inchi = 'InChI=1S/C9H10O4/c102-4-7)5-8(11)9(12)13/h1-4,8,10-11H,5H2,(H,12,13)'
-        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchi_to_inchikey', [inchi])))
+        self.assertIsNone(asyncio.run(wrap_with_session(self.converter, 'inchi_to_inchikey', [inchi])))
 
     def test_name_to_inchi(self):
         name = '3-Methyl-5-[p-fluorophenyl]-2H-1,3-[3H]-oxazine-2,6-dione'
         inchi = 'InChI=1S/C11H8FNO3/c1-13-6-9(10(14)16-11(13)15)7-2-4-8(12)5-3-7/h2-6H,1H3'
 
-        self.assertEqual(asyncio.run(run_in_session(self.converter, 'name_to_inchi', [name])), inchi)
+        self.assertEqual(asyncio.run(wrap_with_session(self.converter, 'name_to_inchi', [name])), inchi)
 
         name = 'HYDROXYPHENYLLACTATE M-H'
-        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'name_to_inchi', [name])))
+        self.assertIsNone(asyncio.run(wrap_with_session(self.converter, 'name_to_inchi', [name])))
 
     def test_inchi_to_IUPAC_name(self):
         inchi = 'InChI=1S/C11H8FNO3/c1-13-6-9(10(14)16-11(13)15)7-2-4-8(12)5-3-7/h2-6H,1H3'
         IUPAC_name = '5-(4-fluorophenyl)-3-methyl-1,3-oxazine-2,6-dione'
 
-        self.assertEqual(asyncio.run(run_in_session(self.converter, 'inchi_to_iupac_name', [inchi])), IUPAC_name)
+        self.assertEqual(asyncio.run(wrap_with_session(self.converter, 'inchi_to_iupac_name', [inchi])), IUPAC_name)
 
         inchi = 'InChI=1S/C9H10O4/c102-4-7)5-8(11)93/1-4,8,10-11H,5H2,(H,12,13)'
-        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchi_to_iupac_name', [inchi])))
+        self.assertIsNone(asyncio.run(wrap_with_session(self.converter, 'inchi_to_iupac_name', [inchi])))
 
     def test_inchi_to_formula(self):
         inchi = 'InChI=1S/C11H8FNO3/c1-13-6-9(10(14)16-11(13)15)7-2-4-8(12)5-3-7/h2-6H,1H3'
         formula = 'C11H8FNO3'
 
-        self.assertEqual(asyncio.run(run_in_session(self.converter, 'inchi_to_formula', [inchi])), formula)
+        self.assertEqual(asyncio.run(wrap_with_session(self.converter, 'inchi_to_formula', [inchi])), formula)
 
         inchi = 'InChI=1S/C9H10O4/c102-4-7)5-8(11)93/1-4,8,10-11H,5H2,(H,12,13)'
-        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchi_to_formula', [inchi])))
+        self.assertIsNone(asyncio.run(wrap_with_session(self.converter, 'inchi_to_formula', [inchi])))
 
     def test_inchi_to_smiles(self):
         inchi = 'InChI=1S/C11H8FNO3/c1-13-6-9(10(14)16-11(13)15)7-2-4-8(12)5-3-7/h2-6H,1H3'
         smiles = 'CN1C=C(C(=O)OC1=O)C2=CC=C(C=C2)F'
 
-        self.assertEqual(asyncio.run(run_in_session(self.converter, 'inchi_to_smiles', [inchi])), smiles)
+        self.assertEqual(asyncio.run(wrap_with_session(self.converter, 'inchi_to_smiles', [inchi])), smiles)
 
         inchi = 'InChI=1S/C9H10O4/c102-4-7)5-8(11)93/1-4,8,10-11H,5H2,(H,12,13)'
-        self.assertIsNone(asyncio.run(run_in_session(self.converter, 'inchi_to_smiles', [inchi])))
+        self.assertIsNone(asyncio.run(wrap_with_session(self.converter, 'inchi_to_smiles', [inchi])))
diff --git a/tests/utils.py b/tests/utils.py
index 338ccb1..d663587 100644
--- a/tests/utils.py
+++ b/tests/utils.py
@@ -1,7 +1,7 @@
 import aiohttp
 
 
-async def run_in_session(converter, method, args):
+async def wrap_with_session(converter, method, args):
     async with aiohttp.ClientSession() as session:
         converter.session = session
         return await getattr(converter, method)(*args)