Add working placeholder for lipid pipeline

Dockerfile

@@ -4,7 +4,14 @@ WORKDIR /metams
 COPY metaMS/ /metams/metaMS/
 COPY README.md disclaimer.txt Makefile requirements.txt setup.py /metams/
 COPY db/ /metams/db/
-RUN pip3 install --editable .
 
+# Install the specific version of corems
+RUN pip3 install corems==2.2.1
+
+# Install other dependencies from requirements.txt
+RUN pip3 install -r requirements.txt
+
+# Install the MetaMS package in editable mode
+RUN pip3 install --editable .
 
 

metaMS/cli.py

@@ -198,3 +198,6 @@ def run_lipidomics_workflow(paramaters_file, directory, output_directory, token_
             directory=directory, output_directory=output_directory, cores=cores
         )
     click.echo("Running lipidomics workflow")
+    # test call:
+    # MetaMS run-lipidomics-workflow -p configuration/lipidomics_metams.toml
+    # miniwdl run wdl/metaMS_lipidomics.wdl -i wdl/metams_input_lipidomics.json

metaMS/lcms_lipidomics_workflow.py

@@ -4,8 +4,8 @@
 import datetime
 from multiprocessing import Pool
 
-from corems.mass_spectra.input.mzml import MZMLSpectraParser
-from corems.mass_spectra.input.rawFileReader import ImportMassSpectraThermoMSFileReader
+#from corems.mass_spectra.input.mzml import MZMLSpectraParser
+#from corems.mass_spectra.input.rawFileReader import ImportMassSpectraThermoMSFileReader
 
 @dataclass
 class LipidomicsWorkflowParameters:
@@ -58,10 +58,12 @@ def instantiate_lcms_obj(file_in):
         #parser = ImportMassSpectraThermoMSFileReader(file_in)
 
     if ".mzML" in str(file_in):
-        parser = MZMLSpectraParser(file_in)
+        #parser = MZMLSpectraParser(file_in)
+        pass
 
     # Instantiate lc-ms data object using parser and pull in ms1 spectra into dataframe (without storing as MassSpectrum objects to save memory)
-    myLCMSobj = parser.get_lcms_obj(spectra="ms1")
+    #myLCMSobj = parser.get_lcms_obj(spectra="ms1")
+    myLCMSobj = None
 
     return myLCMSobj
 
@@ -129,5 +131,6 @@ def run_lcms_lipidomics_workflow(
         mz_dicts = pool.starmap(run_lipid_sp_ms1, args)
         pool.close()
         pool.join()
+    print("Finished processing all files")
 
     # TODO KRH: Add full lipidomics workflow here

requirements.txt

@@ -1,4 +1,4 @@
-corems>=2.0.0
+corems==2.2.1
 Click>=7.1.1
 requests
 nmdc-schema>=7.0.0

wdl/metaMS_lipidomics.wdl

@@ -17,5 +17,4 @@ task runLipidomicsMetaMS {
         docker: "local-metams:latest"
         #TODO KRH: Change to dockerhub version after we've pushed the updated image
     }
-}
-
+}

wdl/metams_input_lipidomics.json

@@ -1,3 +1,3 @@
 {
-    "lcmsLipidomics.runLipidomicsMetaMS.config_file": "lipidomics_metams.toml"
+    "lcmsLipidomics.runLipidomicsMetaMS.config_file": "./configuration/lipidomics_metams.toml"
 }