development/validation/comp_md.py

import sys
import math
import logging
import os
import subprocess

fraw_list = []#List of all .md files found (even the includes).
fmd_list = []#List of all config .md files that can be run (not the includes).
fmd_base_list = []#List of the names of the .md files that can be run.

dir_cwd = ""#Current working directory.
dir_openmd = ""#Absolute path for openmd
dir_base = ""#Directory where the script is run from.

"""
Function sets up the dir_base and dir_openmd. If an openmd executable is not
found, script exits. Function looks for the openmd in the relative location
../build/bin but stores the openmd location as an absolute path.
@author Samuel Njoroge
"""
def setupDirectories():
        global dir_base, dir_openmd, dir_cwd
        dir_base = os.getcwd()
        if(os.path.isfile("../build/bin/openmd")):
                os.chdir("../build/bin/")
                dir_openmd = os.getcwd()
                os.chdir(dir_base)
        else:
                print "OpenMD executable not found."
                sys.exit()
        
        
"""
Function checks if the sample_file and validate_file (.md files) have the same
statusTime = interval time for the stats file.
@author Samuel Njoroge
@param string sample_file - .md file that is being run.
@param string validate_file - .md file the result is being compared to.
@return boolean
"""
def validate_md_time(sample_file, validate_file):
  sample_status_time = 0
  sample_sample_time = 0
  sample_run_time = 0
  validate_status_time = 0
  validate_sample_time = 0
  validate_run_time = 0
  
  samplefh = open(sample_file, "r")
  validatefh = open(validate_file, "r")
  
  line = samplefh.readline()
  while line:
    if "statusTime" in line:
      arr = line.split('=')
      temp = arr[1]
      sample_status_time = float(temp.replace(';', ''))
    elif "sampleTime" in line:
      arr = line.split('=')
      temp = arr[1]
      sample_sample_time = float(temp.replace(';', ''))
    elif "runTime" in line:
      arr = line.split('=')
      temp = arr[1]
      sample_run_time = float(temp.replace(';', ''))

    line = samplefh.readline()

  line = validatefh.readline()
  while line:
    if "statusTime" in line:
      arr = line.split('=')
      temp = arr[1]
      validate_status_time = float(temp.replace(';', ''))
    elif "sampleTime" in line:
      arr = line.split('=')
      temp = arr[1]
      validate_sample_time = float(temp.replace(';', ''))
    elif "runTime" in line:
      arr = line.split('=')
      temp = arr[1]
      validate_run_time = float(temp.replace(';', ''))

    line = validatefh.readline()

  if (sample_status_time > 0) or (validate_status_time > 0):
    if sample_status_time == validate_status_time:
      return True
    else:
      return False

  if (sample_sample_time > 0) or (validate_sample_time > 0):
    if sample_sample_time == validate_sample_time:
      return True
    else:
      return False

  if (sample_run_time > 0) or (validate_run_time > 0):
    if sample_run_time == validate_run_time:
      return True
    else:
      return False

  return False
  
"""
Function checks if an .md config file and not an include file.
@author Samuel Njoroge
@param string file - .md file name
@return boolean
"""
def file_is_md(filename):
        file_handle = open(filename)
        line = file_handle.readline()
        
        while line:
                if "<OpenMD version=" in line:
                        return True
                line = file_handle.readline()
                        
        return False
        
"""
Function compares two numbers.
@author Samuel Njoroge and ().
@param float one - first number to compare.
@param float two - second number to compare.
@param boolean ignore_sign - if sign is a factor in the comparison.
@return float diff - difference between the two numbers.
"""
def absDiff(one, two, ignore_sign = False):
        if ignore_sign:
                one, two = math.fabs(one), math.fabs(two)
        return max(one, two) - min(one, two)
        
"""
Function compares two files.
@author Samuel Njoroge and ().
@param string fExpected - name of the expected file.
@param string fNew - name of the new test file.
@param float epsilon - Precision of the comparison of the files.
@param boolean ignore_sign - if sign will be a factor in comparing the digits.
@return boolean
"""
def compare(fExpected, fNew, epsilon = 0.00001, ignore_sign=False):
        fone = open(fExpected, 'r')
        ftwo = open(fNew, 'r')

        diffs = 0
        
        i = 0
        for lineone in fone:
                linetwo = ftwo.readline()

                elementsone = lineone.split()
                elementstwo = linetwo.split()

                i = i + 1

                lenone = len(elementsone)
                lentwo = len(elementstwo)

                if lenone != lentwo:
                        diffs = diffs + 1
                        print "Line " + str(i) + " do not match in the files."
                        return True
                else:
                        for j in range(lenone):
                                # used to ignore XYZ meta data such as # of frames and # of atoms
                                try:
                                        feone = int(elementsone[j])
                                        fetwo = int(elementstwo[j])
                                        # these are ints -- skip this pair
                                        continue
                                except ValueError:
                                        pass
                                try:
                                        feone = float(elementsone[j])
                                        fetwo = float(elementstwo[j])

                                        fediff = absDiff(feone, fetwo, ignore_sign)

                                        if fediff > epsilon:
                                                diffs = diffs + 1
                                                print "Line " + str(i) + " do not match in the files."
                                                return True
                                except ValueError:
                                        pass
        return False#diffs == 0
        
"""
Function scans the directory for .md config files which will be run for
testing.
@author Samuel Njoroge
"""
def scanForMdFiles():
        paths = []
        variable = "sam is here"
        for p in os.listdir("../samples/"):
                paths.append(os.path.abspath("../samples/" + p))
        
        while len(paths):
                p = paths.pop()
                if os.path.isfile(p):
                        fraw_list.append(p)
                else:
                        for np in os.listdir(p):
                                paths.append(os.path.abspath(p + "/" + np))
                                
        for f in fraw_list:
                if (".md" in f) and (not ".svn" in f) and file_is_md(f):
                        fmd_list.append(f)
                        temp = os.path.basename(f)
                        temp = temp.replace(".md",'')
                        fmd_base_list.append(temp)
                
"""
Function runs OpenMD on the files the compares them with the already run files (*_v.stat)
@author Samuel Njoroge
"""
def runMdFiles():
        global dir_base, dir_openmd, dir_cwd
        output = []
        for x in range(0, len(fmd_list)):
                #subprocess.call(["export FORCE_PARAM_PATH=/Users/snjoroge/Documents/openmd/development/forceFields"])
                if "argon" in fmd_list[x]:
                        print "Switching to Directory: " + os.path.dirname(fmd_list[x])
                        os.chdir(os.path.dirname(fmd_list[x]))
                        print "Running file: " + fmd_list[x]
                        output = subprocess.call([dir_openmd + "/openmd", fmd_list[x]])
                        if(os.path.exists(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat")):
                                #print "Renaming File: " + fmd_base_list[x] + ".stat - " + fmd_base_list[x] + "_v.stat"
                                #subprocess.call(["cp", os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat", os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + "_v.stat"])
                                print "Comparing: " + fmd_base_list[x] + ".stat <=> " + fmd_base_list[x] + "_v.stat"
                                if(compare(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat", os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + "_v.stat")):
                                        print "Files Do not match."
                                else:
                                        print "Files match."
                os.chdir(dir_base)

def cleanUp():
        print "delete all files generated so not to commit"
        for x in range(0, len(fmd_list)):
                print "DELETE:" + os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".eor"
                os.remove(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".eor")
                print "DELETE:" + os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat"
                os.remove(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat")
                print "DELETE:" + os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".dump"
                os.remove(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".dump")
        
Revision:	1659
Committed:	Thu Nov 3 13:16:29 2011 UTC (13 years, 5 months ago) by chuckv
Content type:	text/x-python
File size:	7561 byte(s)
Log Message:	Adding validation python code.
#	User	Rev	Content
1	chuckv	1659	import sys
2			import math
3			import logging
4			import os
5			import subprocess
6
7			fraw_list = []#List of all .md files found (even the includes).
8			fmd_list = []#List of all config .md files that can be run (not the includes).
9			fmd_base_list = []#List of the names of the .md files that can be run.
10
11			dir_cwd = ""#Current working directory.
12			dir_openmd = ""#Absolute path for openmd
13			dir_base = ""#Directory where the script is run from.
14
15			"""
16			Function sets up the dir_base and dir_openmd. If an openmd executable is not
17			found, script exits. Function looks for the openmd in the relative location
18			../build/bin but stores the openmd location as an absolute path.
19			@author Samuel Njoroge
20			"""
21			def setupDirectories():
22			global dir_base, dir_openmd, dir_cwd
23			dir_base = os.getcwd()
24			if(os.path.isfile("../build/bin/openmd")):
25			os.chdir("../build/bin/")
26			dir_openmd = os.getcwd()
27			os.chdir(dir_base)
28			else:
29			print "OpenMD executable not found."
30			sys.exit()
31
32
33			"""
34			Function checks if the sample_file and validate_file (.md files) have the same
35			statusTime = interval time for the stats file.
36			@author Samuel Njoroge
37			@param string sample_file - .md file that is being run.
38			@param string validate_file - .md file the result is being compared to.
39			@return boolean
40			"""
41			def validate_md_time(sample_file, validate_file):
42			sample_status_time = 0
43			sample_sample_time = 0
44			sample_run_time = 0
45			validate_status_time = 0
46			validate_sample_time = 0
47			validate_run_time = 0
48
49			samplefh = open(sample_file, "r")
50			validatefh = open(validate_file, "r")
51
52			line = samplefh.readline()
53			while line:
54			if "statusTime" in line:
55			arr = line.split('=')
56			temp = arr[1]
57			sample_status_time = float(temp.replace(';', ''))
58			elif "sampleTime" in line:
59			arr = line.split('=')
60			temp = arr[1]
61			sample_sample_time = float(temp.replace(';', ''))
62			elif "runTime" in line:
63			arr = line.split('=')
64			temp = arr[1]
65			sample_run_time = float(temp.replace(';', ''))
66
67			line = samplefh.readline()
68
69			line = validatefh.readline()
70			while line:
71			if "statusTime" in line:
72			arr = line.split('=')
73			temp = arr[1]
74			validate_status_time = float(temp.replace(';', ''))
75			elif "sampleTime" in line:
76			arr = line.split('=')
77			temp = arr[1]
78			validate_sample_time = float(temp.replace(';', ''))
79			elif "runTime" in line:
80			arr = line.split('=')
81			temp = arr[1]
82			validate_run_time = float(temp.replace(';', ''))
83
84			line = validatefh.readline()
85
86			if (sample_status_time > 0) or (validate_status_time > 0):
87			if sample_status_time == validate_status_time:
88			return True
89			else:
90			return False
91
92			if (sample_sample_time > 0) or (validate_sample_time > 0):
93			if sample_sample_time == validate_sample_time:
94			return True
95			else:
96			return False
97
98			if (sample_run_time > 0) or (validate_run_time > 0):
99			if sample_run_time == validate_run_time:
100			return True
101			else:
102			return False
103
104			return False
105
106			"""
107			Function checks if an .md config file and not an include file.
108			@author Samuel Njoroge
109			@param string file - .md file name
110			@return boolean
111			"""
112			def file_is_md(filename):
113			file_handle = open(filename)
114			line = file_handle.readline()
115
116			while line:
117			if "<OpenMD version=" in line:
118			return True
119			line = file_handle.readline()
120
121			return False
122
123			"""
124			Function compares two numbers.
125			@author Samuel Njoroge and ().
126			@param float one - first number to compare.
127			@param float two - second number to compare.
128			@param boolean ignore_sign - if sign is a factor in the comparison.
129			@return float diff - difference between the two numbers.
130			"""
131			def absDiff(one, two, ignore_sign = False):
132			if ignore_sign:
133			one, two = math.fabs(one), math.fabs(two)
134			return max(one, two) - min(one, two)
135
136			"""
137			Function compares two files.
138			@author Samuel Njoroge and ().
139			@param string fExpected - name of the expected file.
140			@param string fNew - name of the new test file.
141			@param float epsilon - Precision of the comparison of the files.
142			@param boolean ignore_sign - if sign will be a factor in comparing the digits.
143			@return boolean
144			"""
145			def compare(fExpected, fNew, epsilon = 0.00001, ignore_sign=False):
146			fone = open(fExpected, 'r')
147			ftwo = open(fNew, 'r')
148
149			diffs = 0
150
151			i = 0
152			for lineone in fone:
153			linetwo = ftwo.readline()
154
155			elementsone = lineone.split()
156			elementstwo = linetwo.split()
157
158			i = i + 1
159
160			lenone = len(elementsone)
161			lentwo = len(elementstwo)
162
163			if lenone != lentwo:
164			diffs = diffs + 1
165			print "Line " + str(i) + " do not match in the files."
166			return True
167			else:
168			for j in range(lenone):
169			# used to ignore XYZ meta data such as # of frames and # of atoms
170			try:
171			feone = int(elementsone[j])
172			fetwo = int(elementstwo[j])
173			# these are ints -- skip this pair
174			continue
175			except ValueError:
176			pass
177			try:
178			feone = float(elementsone[j])
179			fetwo = float(elementstwo[j])
180
181			fediff = absDiff(feone, fetwo, ignore_sign)
182
183			if fediff > epsilon:
184			diffs = diffs + 1
185			print "Line " + str(i) + " do not match in the files."
186			return True
187			except ValueError:
188			pass
189			return False#diffs == 0
190
191			"""
192			Function scans the directory for .md config files which will be run for
193			testing.
194			@author Samuel Njoroge
195			"""
196			def scanForMdFiles():
197			paths = []
198			variable = "sam is here"
199			for p in os.listdir("../samples/"):
200			paths.append(os.path.abspath("../samples/" + p))
201
202			while len(paths):
203			p = paths.pop()
204			if os.path.isfile(p):
205			fraw_list.append(p)
206			else:
207			for np in os.listdir(p):
208			paths.append(os.path.abspath(p + "/" + np))
209
210			for f in fraw_list:
211			if (".md" in f) and (not ".svn" in f) and file_is_md(f):
212			fmd_list.append(f)
213			temp = os.path.basename(f)
214			temp = temp.replace(".md",'')
215			fmd_base_list.append(temp)
216
217			"""
218			Function runs OpenMD on the files the compares them with the already run files (*_v.stat)
219			@author Samuel Njoroge
220			"""
221			def runMdFiles():
222			global dir_base, dir_openmd, dir_cwd
223			output = []
224			for x in range(0, len(fmd_list)):
225			#subprocess.call(["export FORCE_PARAM_PATH=/Users/snjoroge/Documents/openmd/development/forceFields"])
226			if "argon" in fmd_list[x]:
227			print "Switching to Directory: " + os.path.dirname(fmd_list[x])
228			os.chdir(os.path.dirname(fmd_list[x]))
229			print "Running file: " + fmd_list[x]
230			output = subprocess.call([dir_openmd + "/openmd", fmd_list[x]])
231			if(os.path.exists(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat")):
232			#print "Renaming File: " + fmd_base_list[x] + ".stat - " + fmd_base_list[x] + "_v.stat"
233			#subprocess.call(["cp", os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat", os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + "_v.stat"])
234			print "Comparing: " + fmd_base_list[x] + ".stat <=> " + fmd_base_list[x] + "_v.stat"
235			if(compare(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat", os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + "_v.stat")):
236			print "Files Do not match."
237			else:
238			print "Files match."
239			os.chdir(dir_base)
240
241			def cleanUp():
242			print "delete all files generated so not to commit"
243			for x in range(0, len(fmd_list)):
244			print "DELETE:" + os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".eor"
245			os.remove(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".eor")
246			print "DELETE:" + os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat"
247			os.remove(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat")
248			print "DELETE:" + os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".dump"
249			os.remove(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".dump")
250