diff gmql_rest_queries.py @ 0:c74a1c7121ec draft default tip

planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gmql_rest_queries.py	Tue Jun 26 08:59:49 2018 -0400
@@ -0,0 +1,247 @@
+# Galaxy plugin to REST access to the GMQL services
+# (Queries)
+# ----------------------------------------------------------------------------
+# Luana Brancato, [e-mail]
+# ----------------------------------------------------------------------------
+
+import argparse
+from time import sleep
+
+from gmql_rest_datasets import list_datasets, import_samples
+from utilities import *
+
+module_execution = 'query_exec'
+module_monitor = 'query_monitor'
+
+
+def check_input(query):
+
+    # Clean the input from Galaxy escape characters.
+
+    query = query.replace('__dq__', '"')
+    query = query.replace('__sq__', "'")
+    query = query.replace('__gt__', ">")
+    query = query.replace('__lt__', "<")
+    query = query.replace('__cn__', '\n')
+
+
+    return query
+
+
+def compile_query(user, filename, query, log_file):
+    """Compile the given query"""
+
+    call = 'compile'
+
+    #Read query from file
+    with open(query, 'r') as f_in:
+        query_text = f_in.read()
+
+    #Check the input
+    query_cl = check_input(query_text)
+
+
+    # Then ask it to be compiled
+    url = compose_url(module_execution, call)
+
+    outcome = post(url, query_cl, user=user, content_type='text')
+
+    status = outcome['status']
+    message = outcome['message']
+    target_ds = outcome['id']
+
+    if status == 'COMPILE_SUCCESS':
+        with open(log_file, 'w') as f:
+            f.write("{status}\n{dataset}".format(status=status, dataset=target_ds))
+        f.close()
+    if status == 'COMPILE_FAILED':
+        with open(log_file, 'w') as f:
+            f.write("{status}\n{message}".format(status=status, message=message))
+        f.close()
+        stop_err("Compilation failed.\nSee log for details.")
+
+
+def run_query(user, filename, query, log_file, rs_format, importResult=True):
+    """Run the given query. It returns an execution log and the resulting dataset."""
+
+
+    call = 'run'
+
+    # Read query from file
+    with open(query, 'r') as f_in:
+        query_text = f_in.read()
+
+    # Check the input
+    query_cl = check_input(query_text)
+
+    # Then ask it to be executed
+
+    status = "NEW"
+
+    url = compose_url(module_execution, call)
+    url = url.format(name=filename,output=rs_format)
+
+    outcome = post(url, query_cl, user=user, content_type='text')
+
+    jobid = outcome['id']
+
+    while status != "SUCCESS" and status != "EXEC_FAILED" and status != "DS_CREATION_FAILED":
+        log = read_status(user, jobid)
+        status = log['status']
+        sleep(5)
+
+    message = log['message']
+    time = log['executionTime']
+
+    if status == "EXEC_FAILED" or status == "DS_CREATION_FAILED":
+        with open(log_file, 'w') as f:
+            f.write("{status}\n{message}\n{execTime}".format(status=status, message=message, execTime=time))
+        f.close()
+        stop_err("Execution failed.\nSee log for details")
+
+    if status == "SUCCESS":
+        ext_log = read_complete_log(user, jobid)
+        job_list = ext_log['log']
+        jobs = ""
+        for j in job_list:
+            jobs = "{j_list}{j}\n".format(j_list=jobs, j=j)
+
+        with open(log_file, 'w') as f:
+            f.write("{status}\n"
+                    "{message}\n"
+                    "{execTime}\n"
+                    "\n"
+                    "{jobs}\n".format(status=status, message=message, execTime=time, jobs=jobs))
+        f.close()
+
+        importResult = bool(importResult)
+
+        if importResult:
+            # For now, it gets only the final result (it's easier to deal later with simple collections
+            # than a nested ones)
+
+            ds = log['datasets'][-1]
+            ds_name = ds.get('name')
+            import_samples(user, ds_name)
+
+
+def read_status(user, jobid):
+    """Given the job id, it retrieves the status of the current operation
+    (as a JSON file)"""
+
+    call = 'status'
+
+    url = compose_url(module_monitor, call)
+    url = url.format(jobid=jobid)
+
+    status = get(url, user=user, response_type='json')
+
+    return status
+
+
+
+def read_complete_log(user, jobid):
+    """Given the jobid, it retrieves the complete log of the latest operation
+    (as a JSON file)"""
+
+    call = 'log'
+
+    url = compose_url(module_monitor, call)
+    url = url.format(jobid=jobid)
+
+    log = get(url, user=user, response_type='json')
+
+    return log
+
+
+def show_jobs(user, output):
+    """Retrieve the list of the user's jobs"""
+
+    call = 'jobs'
+
+    url = compose_url(module_monitor, call)
+
+    jobs = get(url, user=user, response_type='json')
+
+    jobs_list = jobs['jobs']
+    jobs_out = list()
+
+    # For each job in the list retrieve the relative status info
+    for j in jobs_list:
+        job = dict()
+        j_id = j['id']
+        job.update(id=j_id)
+        trace = read_status(user, j_id)
+
+        status = trace['status']
+        if status == 'SUCCESS' :
+            job.update(message=trace['message'],
+                       status=status,
+                       ds=trace['datasets'][0]['name'],
+                       time=trace['executionTime'])
+        else :
+            job.update(message=trace['message'],
+                       status=status,
+                       ds=trace['datasets'][0]['name'])
+
+        jobs_out.append(job)
+
+    with open(output, 'w') as f:
+        for j in jobs_out:
+            f.write("{jobid}\t"
+                    "{status}\t"
+                    "{message}\t"
+                    "{ds}\t"
+                    "{time}\n".format(jobid=j.get('id'), status=j.get('status'), message=j.get('message'),
+                                      ds=j.get('ds'),time=j.get('time')))
+    f.close()
+
+def stop_query(user,jobid,output) :
+    """Stop the execution of the given job"""
+
+    call = 'stop'
+
+    url = compose_url(module_monitor, call)
+    url = url.format(jobid=jobid)
+
+    outcome = get(url, user=user, response_type='json')
+
+    with open(output,'w') as f_out :
+        json.dump(outcome, f_out)
+
+
+
+def stop_err(msg):
+    sys.stderr.write("%s\n" % msg)
+
+
+def __main__():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-user")
+    parser.add_argument("-cmd")
+    parser.add_argument("-name")
+    parser.add_argument("-query")
+    parser.add_argument("-queryNew")
+    parser.add_argument("-queryLocal")
+    parser.add_argument("-log")
+    parser.add_argument("-job")
+    parser.add_argument("-format")
+    parser.add_argument("-importFlag")
+    parser.add_argument("-add_output")
+
+
+    args = parser.parse_args()
+
+    if args.cmd == 'compile':
+        compile_query(args.user, args.name, args.query, args.log)
+    if args.cmd == 'execute':
+        run_query(args.user, args.name, args.query, args.log, args.format, args.importFlag)
+        list_datasets(args.user,args.add_output)
+    if args.cmd == 'jobs':
+        show_jobs(args.user, args.log)
+    if args.cmd == 'stop' :
+        stop_query(args.user, args.job, args.log)
+
+
+if __name__ == "__main__":
+    __main__()