diff options
Diffstat (limited to 'app/dock_docker.py')
| -rw-r--r-- | app/dock_docker.py | 36 |
1 files changed, 27 insertions, 9 deletions
diff --git a/app/dock_docker.py b/app/dock_docker.py index 712e725..e2da478 100644 --- a/app/dock_docker.py +++ b/app/dock_docker.py @@ -68,6 +68,23 @@ def get3DModel(protein,ligand): cmd.save("model.dae") session.stop() +def CopyContentOfFolder(sauce,destination): + src_files = os.listdir(sauce) + for file_name in src_files: + full_file_name = os.path.join(sauce, file_name) + if os.path.isfile(full_file_name): + copy(full_file_name, destination) + +def RemoveAllFilesMatching(directory,pattern): + print(directory+"/*"+pattern) + FileList = glob.glob(directory+"/*"+pattern) + for FilePath in FileList: + try: + print(FilePath) + os.remove(FilePath) + except: + print("Error in removing misc file") + receptor_name = "protein.pdbqt" ligand_name = "ligand.pdbqt" description = "Curie Web Task" @@ -87,41 +104,43 @@ date = r[8] if r[9] is not None: description = r[9] -import os +import os,glob cd = os.getcwd() f = os.path.join(cd,"static/uploads") reportDirectory = os.path.join(f,"reports") +scripts = os.path.join(cd,"scripts") modelDirectory = os.path.join(f,"3DModels") #t = os.path.join(f,"receptor",target) #r = os.path.join(f,"ligands",ligand) #c = os.path.join(f,"configs",config) print(f) import tempfile -from shutil import make_archive, copyfile +from shutil import make_archive, copyfile,copy with tempfile.TemporaryDirectory() as directory: print('The created temporary directory is %s' % directory) os.chdir(directory) -# copy(t,os.getcwd()) -# copy(r,os.getcwd()) -# copy(c, os.getcwd()) with open(receptor_name,"wb") as file: file.write(targetB) with open(ligand_name,"wb") as file: file.write(ligandB) with open("config.txt","wb") as file: file.write(configB) - os.system("docker run --rm -v ${PWD}:/results -w /results -u $(id -u ${USER}):$(id -g ${USER}) navanchauhan/curie-cli -r %s -l %s -c config.txt -dpi" % (receptor_name,ligand_name)) - #copy("report.pdf",f) + # Legacy Docker Curie-Cli Run + #os.system("docker run --rm -v ${PWD}:/results -w /results -u $(id -u ${USER}):$(id -g ${USER}) navanchauhan/curie-cli -r %s -l %s -c config.txt -dpi" % (receptor_name,ligand_name)) + CopyContentOfFolder(scripts,directory) + os.system("./main.sh -r %s -l %s -c config.txt -dpi" % (receptor_name,ligand_name)) + RemoveAllFilesMatching(directory,".py") + RemoveAllFilesMatching(directory,".sh") z = "Curie_Web_Result_"+str(jobID) zi = os.path.join(f,z) make_archive(zi, 'zip', directory) - #copy(("Curie_Web_Result_"+str(jobID)),f) copyfile("report.pdf",os.path.join(reportDirectory,(str(jobID)+".pdf"))) get3DModel(receptor_name,ligand_name.replace(".pdbqt","_out.pdbqt")) os.system("collada2gltf -i model.dae -o model.gltf") copyfile("model.gltf",os.path.join(modelDirectory,(str(jobID)+".gltf"))) arch = os.popen("uname -m").read() + print("Generating 3D Model") if "x86" in arch: os.system("docker run -it --rm -v $(pwd):/usr/app leon/usd-from-gltf:latest model.gltf model.usdz") elif "aarch64" in arch: @@ -131,6 +150,5 @@ with tempfile.TemporaryDirectory() as directory: except: print("Could not generate USDZ file") email(zi) - #print((str(zi) + ".zip")) mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID)) mycon.commit() |