adding more testing from Metabolights

Author: mwang87

Dockerfile

@@ -33,6 +33,12 @@ RUN conda install -c conda-forge openjdk=11.0.9.1
 COPY requirements.txt .
 RUN pip install -r requirements.txt
 
+# Install Aspera
+# RUN wget -qO- https://ak-delivery04-mul.dhe.ibm.com/sar/CMA/OSA/0a07f/0/ibm-aspera-connect_4.1.0.46-linux_x86_64.tar.gz | tar xvz
+# RUN chmod +x ibm-aspera-connect_4.1.0.46-linux_x86_64.sh
+# RUN ./ibm-aspera-connect_4.1.0.46-linux_x86_64.sh
+
+
 COPY . /app
 WORKDIR /app
 

test/Makefile

@@ -3,7 +3,9 @@ all:
 	pytest --durations=0 test_2d.py test_usi_resolution.py test_xic.py -n 8
 
 resolve:
+	pytest test_usi_resolution.py::test_resolve_remote_url -v --capture=tee-sys
 	pytest test_usi_resolution.py -v
+	
 
 benchmark:
 	pytest --durations=0 -n 4 speed_test.py -v --profile-svg

test/test_usi_resolution.py

@@ -13,6 +13,7 @@ def test_resolve_remote_url():
     for record in df.to_dict(orient="records"):
         print(record["usi"])
         remote_link, resource_name = download._resolve_usi_remotelink(record["usi"])
+        print("RESOLVED URL", remote_link, resource_name)
         assert(len(remote_link) > 0)
 
 # Testing conversion

test/usi_list.tsv

@@ -31,4 +31,7 @@ mzspec:PXD002854:20150414_QEp1_LC7_GaPI_SA_Serum_DT_03_150416181741:scan:2308:[+
 mzspec:ST001709:Sample_01___neg.mzXML
 mzspec:MSV000084754:ccms_peak/raw/Toronamide_MS3_DDA_2.mzML
 mzspec:MSV000086834:raw/20210210 GNPS LMCS/PA1MeOH1.aia.CDF
-mzspec:MSV000084169:raw/FractA1/0205045.CDF
+mzspec:MSV000084169:raw/FractA1/0205045.CDF
+mzspec:PXD002854:20150414_QEp1_LC7_GaPI_SA_Serum_DT_03_150416181741.mzXML
+mzspec:PXD028694:QEp21-1189_Song_SYDE2_Rep_aniso+inhib_FT.raw
+mzspec:MTBLS338:0307_63.CDF