def load(wb_id):
wb = get_object_or_404(models.Workbench, id=wb_id)
wbtmis = models.Workbenchtemplatemappingitem.objects.filter(
workbenchtemplate=wb.workbenchtemplate).order_by('vieworder')
if wbtmis.count() > 60:
# mysql won't join more than 61 tables.
# but the following is slower so only use in that case.
return load_gt_61_cols(wb_id)
select_fields = ["r.workbenchrowid"]
for wbtmi in wbtmis:
select_fields.append("cell%d.celldata" % wbtmi.vieworder)
from_clause = ["workbenchrow r"]
for wbtmi in wbtmis:
from_clause.append("left join workbenchdataitem cell%(vieworder)d "
"on cell%(vieworder)d.workbenchrowid = r.workbenchrowid "
"and cell%(vieworder)d.workbenchtemplatemappingitemid = %(wbtmi_id)d"
% {'vieworder': wbtmi.vieworder, 'wbtmi_id': wbtmi.id})
sql = '\n'.join([
"select",
",\n".join(select_fields),
"from",
"\n".join(from_clause),
"where workbenchid = %s",
"order by r.rownumber",
])
cursor = connection.cursor()
cursor.execute(sql, [wb_id])
rows = cursor.fetchall()
return http.HttpResponse(toJson(rows), content_type='application/json')
def rows(request, wb_id):
wb = get_object_or_404(models.Workbench, id=wb_id)
if (wb.specifyuser != request.specify_user):
return http.HttpResponseForbidden()
if request.method == "GET":
return load(wb_id)
elif request.method == "PUT":
data = json.load(request)
return save(wb_id, data)
def upload(request, wb_id, mul_match_action, no_commit, match):
wb = get_object_or_404(models.Workbench, id=wb_id)
if (wb.specifyuser != request.specify_user):
return http.HttpResponseForbidden()
args = [
settings.JAVA_PATH, "-Dfile.encoding=UTF-8", "-classpath",
shellquote(":".join((os.path.join(settings.SPECIFY_THICK_CLIENT, jar)
for jar in CLASSPATH))),
"edu.ku.brc.specify.tasks.subpane.wb.wbuploader.UploadCmdLine", "-u",
shellquote(request.specify_user.name), "-U",
shellquote(settings.MASTER_NAME), "-P",
shellquote(settings.MASTER_PASSWORD), "-d",
shellquote(settings.DATABASE_NAME), "-b", wb_id, "-c",
shellquote(request.specify_collection.collectionname), "-w",
shellquote(settings.SPECIFY_THICK_CLIENT), "-x",
"false" if no_commit else "true", "-k", "true" if match else "false",
"-n",
shellquote(mul_match_action)
]
if settings.DATABASE_HOST != '':
args.extend(["-h", shellquote(settings.DATABASE_HOST)])
output_file = "%s_%s_%s" % (settings.DATABASE_NAME, wb_id, uuid4())
with open(os.path.join(settings.WB_UPLOAD_LOG_DIR, output_file), "w") as f:
# we use the shell to start the uploader process to achieve a double
# fork so that we don't have to wait() on the child process
cmdline = ' '.join(
args
) + ' 2> >(egrep "(ERROR)|(UploaderException)|(UploaderMatchSkipException)" >&1) &'
logger.debug('starting upload w/ cmdline: %s', cmdline)
print cmdline
subprocess.call(['/bin/bash', '-c', cmdline], stdout=f)
log_fnames = glob(
os.path.join(settings.WB_UPLOAD_LOG_DIR, '%s_%s_*' % (
settings.DATABASE_NAME,
wb_id,
)))
for fname in log_fnames:
if os.path.join(settings.WB_UPLOAD_LOG_DIR, output_file) != fname:
try:
os.remove(fname)
except:
pass
return http.HttpResponse(output_file, content_type="text_plain")
def upload(request, wb_id, no_commit, match):
wb = get_object_or_404(models.Workbench, id=wb_id)
if (wb.specifyuser != request.specify_user):
return http.HttpResponseForbidden()
args = [
settings.JAVA_PATH,
"-Dfile.encoding=UTF-8",
"-classpath", shellquote(
":".join((os.path.join(settings.SPECIFY_THICK_CLIENT, jar) for jar in CLASSPATH))
),
"edu.ku.brc.specify.tasks.subpane.wb.wbuploader.UploadCmdLine",
"-u", shellquote(request.specify_user.name),
"-U", shellquote(settings.MASTER_NAME),
"-P", shellquote(settings.MASTER_PASSWORD),
"-d", shellquote(settings.DATABASE_NAME),
"-b", wb_id,
"-c", shellquote(request.specify_collection.collectionname),
"-w", shellquote(settings.SPECIFY_THICK_CLIENT),
"-x", "false" if no_commit else "true",
"-k", "true" if match else "false",
]
if settings.DATABASE_HOST != '':
args.extend(["-h", shellquote(settings.DATABASE_HOST)])
output_file = "%s_%s_%s" % (settings.DATABASE_NAME, wb_id, uuid4())
with open(os.path.join(settings.WB_UPLOAD_LOG_DIR, output_file), "w") as f:
# we use the shell to start the uploader process to achieve a double
# fork so that we don't have to wait() on the child process
cmdline = ' '.join(args) + ' 2> >(egrep "(ERROR)|(UploaderException)|(UploaderMatchSkipException)" >&1) &'
logger.debug('starting upload w/ cmdline: %s', cmdline)
print cmdline
subprocess.call(['/bin/bash', '-c', cmdline], stdout=f)
log_fnames = glob(os.path.join(settings.WB_UPLOAD_LOG_DIR, '%s_%s_*' % (settings.DATABASE_NAME, wb_id,)))
for fname in log_fnames:
if os.path.join(settings.WB_UPLOAD_LOG_DIR, output_file) != fname:
try:
os.remove(fname)
except:
pass
return http.HttpResponse(output_file, content_type="text_plain")
