[125171] trunk/dports/science/ligo-lvalert
ram at macports.org
ram at macports.org
Mon Sep 8 09:03:55 PDT 2014
Revision: 125171
https://trac.macports.org/changeset/125171
Author: ram at macports.org
Date: 2014-09-08 09:03:55 -0700 (Mon, 08 Sep 2014)
Log Message:
-----------
science/ligo-lvalert: update to 1.1
Modified Paths:
--------------
trunk/dports/science/ligo-lvalert/Portfile
Removed Paths:
-------------
trunk/dports/science/ligo-lvalert/files/patch-disable_server.diff
Modified: trunk/dports/science/ligo-lvalert/Portfile
===================================================================
--- trunk/dports/science/ligo-lvalert/Portfile 2014-09-08 14:46:39 UTC (rev 125170)
+++ trunk/dports/science/ligo-lvalert/Portfile 2014-09-08 16:03:55 UTC (rev 125171)
@@ -4,7 +4,7 @@
PortGroup python27 1.0
name ligo-lvalert
-version 1.0
+version 1.1
categories science
platforms darwin
maintainers ram
@@ -19,12 +19,9 @@
homepage https://www.lsc-group.phys.uwm.edu/daswg/projects/lvalert.html
master_sites http://www.lsc-group.phys.uwm.edu/daswg/download/software/source/
-checksums md5 179776a3576efa70e339a71da107252a \
- sha1 f765da15ed4d3066af70747fd45deb749c2ecedd \
- rmd160 1a86daa2df47843cd12647140f05120b646043ec
+checksums rmd160 0a5dbfed2b7a3a1561d872492ad018242554cefc \
+ sha256 b9fdd20f777abc777945b42a7eebdae045b8c2e860e6fc0da7eb4750bb1f9f97
-patchfiles patch-disable_server.diff
-
depends_lib-append port:ligo-common \
port:py27-pyxmpp \
port:py27-libxml2 \
Deleted: trunk/dports/science/ligo-lvalert/files/patch-disable_server.diff
===================================================================
--- trunk/dports/science/ligo-lvalert/files/patch-disable_server.diff 2014-09-08 14:46:39 UTC (rev 125170)
+++ trunk/dports/science/ligo-lvalert/files/patch-disable_server.diff 2014-09-08 16:03:55 UTC (rev 125171)
@@ -1,207 +0,0 @@
---- ligo/lvalert/__init__.py
-+++ ligo/lvalert/__init__.py
-@@ -16,6 +16,6 @@
-
- __author__ = "LIGO Scientific Collaboration"
-
--__all__ = ["pubsub", "lvstanzaprocessor", "utils"]
-+__all__ = ["pubsub", "lvstanzaprocessor"]
-
- GIT_TAG = 'lvalert-1.0-3'
---- ligo/lvalert/utils.py
-+++ /dev/null
-@@ -1,194 +0,0 @@
--#!/usr/bin/python
--
--import sys
--import os
--import urlparse
--from optparse import *
--from subprocess import Popen,PIPE
--
--# Note that some of these utilities are not available unless glue is installed.
--
--import warnings
--
--try:
-- from glue.ligolw import ligolw
-- from glue.ligolw import table
-- from glue.ligolw.table import Table
-- from glue.ligolw import lsctables
-- from glue.ligolw import utils
--except ImportError:
-- Table = object
-- warnings.warn("Glue is not installed. Some lvalert.utils functions require glue")
--
--##############################################################################
--#
--# definition of the LVAlertTable
--#
--##############################################################################
--
--class LVAlertTable(Table):
-- """
-- for reference, file is written as
-- file: //host/path_to_file/file
-- uid: the unique id assigned by gracedb
-- temp_data_loc: current location (just the directory)
-- of the ouput of the pipeline (this is VOLATILE)
-- """
-- tableName = "LVAlert:table"
-- validcolumns = {
-- "file": "lstring",
-- "uid": "lstring",
-- "temp_data_loc": "lstring",
-- "alert_type": "lstring",
-- "description": "lstring",
-- }
--
--class LVAlertRow(object):
-- __slots__ = LVAlertTable.validcolumns.keys()
--
--LVAlertTable.RowType = LVAlertRow
--
--##############################################################################
--#
--# useful utilities
--#
--##############################################################################
--
--def parse_file_url(file_url):
-- """
-- simple function to parse the file urls of the form:
-- file://host_name/path_to_file/file
-- where path_to_file is assumed to be the /private subdir of a gracedb entry
-- returns:
-- host: host_name in the above example
-- full_path: path_to_file/file in the above example
-- general_dir: the /general subdir of the gracedb entry (where data not
-- produced by the event supplier should be placed)
-- """
-- parsed = urlparse.urlparse(file_url)
-- host = parsed[1]
-- path, fname = os.path.split(parsed[2])
--
-- return host, path, fname
--
--def get_LVAdata_from_stdin(std_in, as_dict=False):
-- """
-- this function takes an LVAlertTable from sys.stdin and it returns:
-- host: the machine the payload file was created on
-- full_path: the full path to (and including) the payload file
-- general_dir: the directory in gracedb that the output of your code should
-- be written to
-- uid: the gracedb unique id associated with the event in the LVAlertTable
-- """
-- doc = utils.load_fileobj(std_in)[0]
-- lvatable = table.get_table(doc, LVAlertTable.tableName)
-- file = lvatable[0].file
-- uid = lvatable[0].uid
-- data_loc = lvatable[0].temp_data_loc
--
-- if as_dict:
-- return {
-- "file" : lvatable[0].file,
-- "uid" : lvatable[0].uid,
-- "data_loc" : lvatable[0].temp_data_loc,
-- "description" : lvatable[0].description,
-- "alert_type" : lvatable[0].alert_type,
-- }
--
-- return file, uid, data_loc
--
--def get_LVAdata_from_file(filename, as_dict=False):
-- """
-- this function takes the name of an xml file containing a single LVAlertTable
-- and it returns:
-- host: the machine the payload file was created on
-- full_path: the full path to (and including) the payload file
-- general_dir: the directory in gracedb that the output of your code should
-- be written to
-- uid: the gracedb unique id associated with the event in the LVAlertTable
-- """
-- doc = utils.load_filename(filename)
-- lvatable = table.get_table(doc, LVAlertTable.tableName)
-- file = lvatable[0].file
-- uid = lvatable[0].uid
-- data_loc = lvatable[0].temp_data_loc
--
-- if as_dict:
-- return {
-- "file" : lvatable[0].file,
-- "uid" : lvatable[0].uid,
-- "data_loc" : lvatable[0].temp_data_loc,
-- "description" : lvatable[0].description,
-- "alert_type" : lvatable[0].alert_type,
-- }
--
-- return file, uid, data_loc
--
--def make_LVAlertTable(file_url, uid, data_loc, alert_type="new", desc=""):
-- """
-- create xml doc which contains an LVAlert Table
-- with submission file file_loc and data located at data_loc
-- """
-- xmldoc = ligolw.Document()
-- xmldoc.appendChild(ligolw.LIGO_LW())
-- lvalerttable = lsctables.New(LVAlertTable)
-- row = lvalerttable.RowType()
-- row.file = file_url
-- row.uid = uid
-- row.temp_data_loc = data_loc
-- row.alert_type = alert_type
-- row.description = desc
-- lvalerttable.append(row)
-- xmldoc.childNodes[0].appendChild(lvalerttable)
--
-- return xmldoc
--
--
--#the following is meant as a template for small jobs
--#notes:
--# * we only use the vanilla universe which is appropriate for python
--# jobs and things not condor-compiled
--# * it only works for single-process jobs; anything more complicated will
--# require a dag
--condor_sub_template = \
-- """
-- universe = vanilla
-- executable = macroexecutible
-- arguments = macroargs
-- log = macrolog
-- error = macroerr
-- output = macroout
-- getenv = True
-- notification = never
-- queue
-- """
--def write_condor_sub(executible, args, logdir, uid):
-- """
-- write a simple condor submission file
-- uid: unique id used in naming the files (to avoid conflicts)
-- executible: the name of the executible file
-- args: a list of arguments to executible
-- logdir: directory to keep log files
-- returns the name of the file
-- """
-- subfile = condor_sub_template.replace('macroexecutible', executible)\
-- .replace('macroargs', args)\
-- .replace('macrolog', os.path.join(logdir,str(uid)+'.log'))\
-- .replace('macroerr', os.path.join(logdir,str(uid)+'.err'))\
-- .replace('macroout', os.path.join(logdir,str(uid)+'.out'))
-- fname = str(uid) + '.sub'
-- f = open(fname,'w')
-- f.write(subfile)
-- f.close()
--
-- return fname
--
--def submit_condor_job(subfile):
-- """
-- submit the subfile to condor
-- returns the process id
-- """
-- p = Popen(["condor_submit "+subfile], shell=True).pid
--
-- return p
--
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