Merge branch '3699-arv-copy'

[arvados.git] / crunch_scripts / run-command

diff --git a/crunch_scripts/run-command b/crunch_scripts/run-command
index 840b4b6248fc763eb66a2475dc0ddca62169b304..c1e747506091863a11b028656b662e50f484ef5b 100755 (executable)
--- a/crunch_scripts/run-command
+++ b/crunch_scripts/run-command
@@ -1,49 +1,75 @@
 #!/usr/bin/env python
 
 #!/usr/bin/env python
 

+import logging
+
+logger = logging.getLogger('run-command')
+log_handler = logging.StreamHandler()
+log_handler.setFormatter(logging.Formatter("run-command: %(message)s"))
+logger.addHandler(log_handler)
+logger.setLevel(logging.INFO)
+

 import arvados
 import re
 import os
 import subprocess
 import sys
 import shutil
 import arvados
 import re
 import os
 import subprocess
 import sys
 import shutil

-import subst
+import crunchutil.subst as subst

 import time
 import arvados.commands.put as put
 import signal
 import stat
 import copy
 import traceback
 import time
 import arvados.commands.put as put
 import signal
 import stat
 import copy
 import traceback

+import pprint
+import multiprocessing
+import crunchutil.robust_put as robust_put
+import crunchutil.vwd as vwd
+import argparse
+import json
+import tempfile
+
+parser = argparse.ArgumentParser()
+parser.add_argument('--dry-run', action='store_true')
+parser.add_argument('--script-parameters', type=str, default="{}")
+args = parser.parse_args()

 
 os.umask(0077)
 
 
 os.umask(0077)
 

-t = arvados.current_task().tmpdir
-
-api = arvados.api('v1')
+if not args.dry_run:
+    api = arvados.api('v1')
+    t = arvados.current_task().tmpdir
+    os.chdir(arvados.current_task().tmpdir)
+    os.mkdir("tmpdir")
+    os.mkdir("output")

 
 

-os.chdir(arvados.current_task().tmpdir)
-os.mkdir("tmpdir")
-os.mkdir("output")
+    os.chdir("output")

 
 

-os.chdir("output")
+    outdir = os.getcwd()

 
 

-taskp = None
-jobp = arvados.current_job()['script_parameters']
-if len(arvados.current_task()['parameters']) > 0:
-    p = arvados.current_task()['parameters']
+    taskp = None
+    jobp = arvados.current_job()['script_parameters']
+    if len(arvados.current_task()['parameters']) > 0:
+        taskp = arvados.current_task()['parameters']
+else:
+    outdir = "/tmp"
+    jobp = json.loads(args.job_parameters)
+    os.environ['JOB_UUID'] = 'zzzzz-8i9sb-1234567890abcde'
+    os.environ['TASK_UUID'] = 'zzzzz-ot0gb-1234567890abcde'
+    os.environ['CRUNCH_SRC'] = '/tmp/crunche-src'
+    if 'TASK_KEEPMOUNT' not in os.environ:
+        os.environ['TASK_KEEPMOUNT'] = '/keep'

 
 links = []
 
 
 links = []
 

-def sub_link(v):
-    r = os.path.basename(v)
-    os.symlink(os.path.join(os.environ['TASK_KEEPMOUNT'], v) , r)
-    links.append(r)
-    return r
-

 def sub_tmpdir(v):
     return os.path.join(arvados.current_task().tmpdir, 'tmpdir')
 
 def sub_tmpdir(v):
     return os.path.join(arvados.current_task().tmpdir, 'tmpdir')
 

+def sub_outdir(v):
+    return outdir
+

 def sub_cores(v):
 def sub_cores(v):

-     return os.environ['CRUNCH_NODE_SLOTS']
+     return str(multiprocessing.cpu_count())

 
 def sub_jobid(v):
      return os.environ['JOB_UUID']
 
 def sub_jobid(v):
      return os.environ['JOB_UUID']


@@ -51,17 +77,15 @@ def sub_jobid(v):
 def sub_taskid(v):
      return os.environ['TASK_UUID']
 
 def sub_taskid(v):
      return os.environ['TASK_UUID']
 

-subst.default_subs["link "] = sub_link
+def sub_jobsrc(v):
+     return os.environ['CRUNCH_SRC']
+

 subst.default_subs["task.tmpdir"] = sub_tmpdir
 subst.default_subs["task.tmpdir"] = sub_tmpdir

+subst.default_subs["task.outdir"] = sub_outdir
+subst.default_subs["job.srcdir"] = sub_jobsrc

 subst.default_subs["node.cores"] = sub_cores
 subst.default_subs["node.cores"] = sub_cores

-subst.default_subs["job.id"] = sub_jobid
-subst.default_subs["task.id"] = sub_taskid
-
-rcode = 1
-
-def machine_progress(bytes_written, bytes_expected):
-    return "run-command: wrote {} total {}\n".format(
-        bytes_written, -1 if (bytes_expected is None) else bytes_expected)
+subst.default_subs["job.uuid"] = sub_jobid
+subst.default_subs["task.uuid"] = sub_taskid

 
 class SigHandler(object):
     def __init__(self):
 
 class SigHandler(object):
     def __init__(self):


@@ -71,6 +95,12 @@ class SigHandler(object):
         sp.send_signal(signum)
         self.sig = signum
 
         sp.send_signal(signum)
         self.sig = signum
 

+def add_to_group(gr, match):
+    m = match.groups()
+    if m not in gr:
+        gr[m] = []
+    gr[m].append(match.group(0))
+

 def expand_item(p, c):
     if isinstance(c, dict):
         if "foreach" in c and "command" in c:
 def expand_item(p, c):
     if isinstance(c, dict):
         if "foreach" in c and "command" in c:


@@ -82,69 +112,157 @@ def expand_item(p, c):
                 params[var] = i
                 r.extend(expand_list(params, c["command"]))
             return r
                 params[var] = i
                 r.extend(expand_list(params, c["command"]))
             return r

+        if "list" in c and "index" in c and "command" in c:
+            var = c["list"]
+            items = get_items(p, p[var])
+            params = copy.copy(p)
+            params[var] = items[int(c["index"])]
+            return expand_list(params, c["command"])
+        if "regex" in c:
+            pattern = re.compile(c["regex"])
+            if "filter" in c:
+                items = get_items(p, p[c["filter"]])
+                return [i for i in items if pattern.match(i)]
+            elif "group" in c:
+                items = get_items(p, p[c["group"]])
+                groups = {}
+                for i in items:
+                    match = pattern.match(i)
+                    if match:
+                        add_to_group(groups, match)
+                return [groups[k] for k in groups]
+            elif "extract" in c:
+                items = get_items(p, p[c["extract"]])
+                r = []
+                for i in items:
+                    match = pattern.match(i)
+                    if match:
+                        r.append(list(match.groups()))
+                return r

     elif isinstance(c, list):
         return expand_list(p, c)
     elif isinstance(c, list):
         return expand_list(p, c)

-    elif isinstance(c, str):
+    elif isinstance(c, basestring):

         return [subst.do_substitution(p, c)]
 
     return []
 
 def expand_list(p, l):
         return [subst.do_substitution(p, c)]
 
     return []
 
 def expand_list(p, l):

-    return [exp for arg in l for exp in expand_item(p, arg)]
+    if isinstance(l, basestring):
+        return expand_item(p, l)
+    else:
+        return [exp for arg in l for exp in expand_item(p, arg)]

 
 def get_items(p, value):
 
 def get_items(p, value):

+    if isinstance(value, dict):
+        return expand_item(p, value)
+

     if isinstance(value, list):
         return expand_list(p, value)
 
     fn = subst.do_substitution(p, value)
     mode = os.stat(fn).st_mode
     prefix = fn[len(os.environ['TASK_KEEPMOUNT'])+1:]
     if isinstance(value, list):
         return expand_list(p, value)
 
     fn = subst.do_substitution(p, value)
     mode = os.stat(fn).st_mode
     prefix = fn[len(os.environ['TASK_KEEPMOUNT'])+1:]

-    if mode != None:
+    if mode is not None:

         if stat.S_ISDIR(mode):
         if stat.S_ISDIR(mode):

-            items = ["$(dir %s/%s)" % (prefix, l) for l in os.listdir(fn)]
+            items = [os.path.join(fn, l) for l in os.listdir(fn)]

         elif stat.S_ISREG(mode):
             with open(fn) as f:
         elif stat.S_ISREG(mode):
             with open(fn) as f:

-                items = [line for line in f]
+                items = [line.rstrip("\r\n") for line in f]

         return items
     else:
         return None
 
         return items
     else:
         return None
 

-if "task.foreach" in jobp:
-    if arvados.current_task()['sequence'] == 0:
-        var = jobp["task.foreach"]
-        items = get_items(jobp, jobp[var])
-        if items != None:
-            print("run-command: parallelizing on %s with items %s" % (var, items))
+stdoutname = None
+stdoutfile = None
+stdinname = None
+stdinfile = None
+rcode = 1

 
 

-            for i in items:
-                params = copy.copy(jobp)
-                params[var] = i
-                arvados.api().job_tasks().create(body={
-                    'job_uuid': arvados.current_job()['uuid'],
-                    'created_by_job_task_uuid': arvados.current_task()['uuid'],
-                    'sequence': 1,
-                    'parameters': params
-                    }
-                ).execute()
-            arvados.current_task().set_output(None)
-            sys.exit(0)
-        else:
-            sys.exit(1)
-else:
-    p = jobp
+def recursive_foreach(params, fvars):
+    var = fvars[0]
+    fvars = fvars[1:]
+    items = get_items(params, params[var])
+    logger.info("parallelizing on %s with items %s" % (var, items))
+    if items is not None:
+        for i in items:
+            params = copy.copy(params)
+            params[var] = i
+            if len(fvars) > 0:
+                recursive_foreach(params, fvars)
+            else:
+                if not args.dry_run:
+                    arvados.api().job_tasks().create(body={
+                        'job_uuid': arvados.current_job()['uuid'],
+                        'created_by_job_task_uuid': arvados.current_task()['uuid'],
+                        'sequence': 1,
+                        'parameters': params
+                    }).execute()
+                else:
+                    logger.info(expand_list(params, params["command"]))
+    else:
+        logger.error("parameter %s with value %s in task.foreach yielded no items" % (var, params[var]))
+        sys.exit(1)

 
 try:
 
 try:

-    cmd = expand_list(p, p["command"])
+    if "task.foreach" in jobp:
+        if args.dry_run or arvados.current_task()['sequence'] == 0:
+            # This is the first task to start the other tasks and exit
+            fvars = jobp["task.foreach"]
+            if isinstance(fvars, basestring):
+                fvars = [fvars]
+            if not isinstance(fvars, list) or len(fvars) == 0:
+                logger.error("value of task.foreach must be a string or non-empty list")
+                sys.exit(1)
+            recursive_foreach(jobp, jobp["task.foreach"])
+            if not args.dry_run:
+                if "task.vwd" in jobp:
+                    # Set output of the first task to the base vwd collection so it
+                    # will be merged with output fragments from the other tasks by
+                    # crunch.
+                    arvados.current_task().set_output(subst.do_substitution(jobp, jobp["task.vwd"]))
+                else:
+                    arvados.current_task().set_output(None)
+            sys.exit(0)
+    else:
+        # This is the only task so taskp/jobp are the same
+        taskp = jobp
+
+    if not args.dry_run:
+        if "task.vwd" in taskp:
+            # Populate output directory with symlinks to files in collection
+            vwd.checkout(subst.do_substitution(taskp, taskp["task.vwd"]), outdir)

 
 

-    stdoutname = None
-    stdoutfile = None
-    if "save.stdout" in p:
-        stdoutname = subst.do_substitution(p, p["save.stdout"])
-        stdoutfile = open(stdoutname, "wb")
+        if "task.cwd" in taskp:
+            os.chdir(subst.do_substitution(taskp, taskp["task.cwd"]))

 
 

-    print("run-command: {}{}".format(' '.join(cmd), (" > " + stdoutname) if stdoutname != None else ""))
+    cmd = expand_list(taskp, taskp["command"])

 
 

-    sp = subprocess.Popen(cmd, shell=False, stdout=stdoutfile)
+    if not args.dry_run:
+        if "task.stdin" in taskp:
+            stdinname = subst.do_substitution(taskp, taskp["task.stdin"])
+            stdinfile = open(stdinname, "rb")
+
+        if "task.stdout" in taskp:
+            stdoutname = subst.do_substitution(taskp, taskp["task.stdout"])
+            stdoutfile = open(stdoutname, "wb")
+
+    logger.info("{}{}{}".format(' '.join(cmd), (" < " + stdinname) if stdinname is not None else "", (" > " + stdoutname) if stdoutname is not None else ""))
+
+    if args.dry_run:
+        sys.exit(0)
+except subst.SubstitutionError as e:
+    logger.error(str(e))
+    logger.error("task parameters were:")
+    logger.error(pprint.pformat(taskp))
+    sys.exit(1)
+except Exception as e:
+    logger.exception("caught exception")
+    logger.error("task parameters were:")
+    logger.error(pprint.pformat(taskp))
+    sys.exit(1)
+
+try:
+    sp = subprocess.Popen(cmd, shell=False, stdin=stdinfile, stdout=stdoutfile)

     sig = SigHandler()
 
     # forward signals to the process.
     sig = SigHandler()
 
     # forward signals to the process.


@@ -155,15 +273,14 @@ try:
     # wait for process to complete.
     rcode = sp.wait()
 
     # wait for process to complete.
     rcode = sp.wait()
 

-    if sig.sig != None:
-        print("run-command: terminating on signal %s" % sig.sig)
+    if sig.sig is not None:
+        logger.critical("terminating on signal %s" % sig.sig)

         sys.exit(2)
     else:
         sys.exit(2)
     else:

-        print("run-command: completed with exit code %i (%s)" % (rcode, "success" if rcode == 0 else "failed"))
+        logger.info("completed with exit code %i (%s)" % (rcode, "success" if rcode == 0 else "failed"))

 
 except Exception as e:
 
 except Exception as e:

-    print("run-command: caught exception:")
-    traceback.print_exc(file=sys.stdout)
+    logger.exception("caught exception")

 
 # restore default signal handlers.
 signal.signal(signal.SIGINT, signal.SIG_DFL)
 
 # restore default signal handlers.
 signal.signal(signal.SIGINT, signal.SIG_DFL)


@@ -173,35 +290,27 @@ signal.signal(signal.SIGQUIT, signal.SIG_DFL)
 for l in links:
     os.unlink(l)
 
 for l in links:
     os.unlink(l)
 

-print("run-command: the following output files will be saved to keep:")
-
-subprocess.call(["find", ".", "-type", "f", "-printf", "run-command: %12.12s %h/%f\\n"])
-
-print("run-command: start writing output to keep")
-
-done = False
-resume_cache = put.ResumeCache(os.path.join(arvados.current_task().tmpdir, "upload-output-checkpoint"))
-reporter = put.progress_writer(machine_progress)
-bytes_expected = put.expected_bytes_for(".")
-while not done:
-    try:
-        out = put.ArvPutCollectionWriter.from_cache(resume_cache, reporter, bytes_expected)
-        out.do_queued_work()
-        out.write_directory_tree(".", max_manifest_depth=0)
-        outuuid = out.finish()
-        api.job_tasks().update(uuid=arvados.current_task()['uuid'],
-                                             body={
-                                                 'output':outuuid,
-                                                 'success': (rcode == 0),
-                                                 'progress':1.0
-                                             }).execute()
-        done = True
-    except KeyboardInterrupt:
-        print("run-command: terminating on signal 2")
-        sys.exit(2)
-    except Exception as e:
-        print("run-command: caught exception:")
-        traceback.print_exc(file=sys.stdout)
-        time.sleep(5)
+logger.info("the following output files will be saved to keep:")
+
+subprocess.call(["find", ".", "-type", "f", "-printf", "run-command: %12.12s %h/%f\\n"], stdout=sys.stderr)
+
+logger.info("start writing output to keep")
+
+if "task.vwd" in taskp:
+    if "task.foreach" in jobp:
+        # This is a subtask, so don't merge with the original collection, that will happen at the end
+        outcollection = vwd.checkin(subst.do_substitution(taskp, taskp["task.vwd"]), outdir, merge=False).manifest_text()
+    else:
+        # Just a single task, so do merge with the original collection
+        outcollection = vwd.checkin(subst.do_substitution(taskp, taskp["task.vwd"]), outdir, merge=True).manifest_text()
+else:
+    outcollection = robust_put.upload(outdir, logger)
+
+api.job_tasks().update(uuid=arvados.current_task()['uuid'],
+                                     body={
+                                         'output': outcollection,
+                                         'success': (rcode == 0),
+                                         'progress':1.0
+                                     }).execute()

 
 sys.exit(rcode)
 
 sys.exit(rcode)