pymerase-cvs-commit — CVS Commits to Pymerase Project

[Pymerase-cvs-commit] pymerase/pymweb/cgi pymweb.py,1.2,1.3

[<ki...@us...>]

Update of /cvsroot/pymerase/pymerase/pymweb/cgi
In directory sc8-pr-cvs1:/tmp/cvs-serv7499/cgi

Modified Files:
	pymweb.py 
Log Message:
was missing a " in html code. =o(


Index: pymweb.py
===================================================================
RCS file: /cvsroot/pymerase/pymerase/pymweb/cgi/pymweb.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** pymweb.py	4 Apr 2003 23:57:19 -0000	1.2
--- pymweb.py	4 Apr 2003 23:58:14 -0000	1.3
***************
*** 170,174 ****
      else:
        print '<b>Generation Complete</b><br>'
!       print 'Download: <a href="/pymweb/%s/%s>%s</a>' % (myfile,
                                                 form['dest'].value,
                                                 form['dest'].value)
--- 170,174 ----
      else:
        print '<b>Generation Complete</b><br>'
!       print 'Download: <a href="/pymweb/%s/%s">%s</a>' % (myfile,
                                                 form['dest'].value,
                                                 form['dest'].value)

[Pymerase-cvs-commit] pymerase/pymweb/cgi pymweb.py,1.1,1.2

[<ki...@us...>]

Update of /cvsroot/pymerase/pymerase/pymweb/cgi
In directory sc8-pr-cvs1:/tmp/cvs-serv7197/cgi

Modified Files:
	pymweb.py 
Log Message:
updated to handle files uploaded by a windows machine with internet explorer.


Index: pymweb.py
===================================================================
RCS file: /cvsroot/pymerase/pymerase/pymweb/cgi/pymweb.py,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** pymweb.py	4 Apr 2003 03:00:27 -0000	1.1
--- pymweb.py	4 Apr 2003 23:57:19 -0000	1.2
***************
*** 3,7 ****
  #                                                                         #
  # C O P Y R I G H T   N O T I C E                                         #
! #  Copyright (c) 2002 by:                                                 #
  #    * California Institute of Technology                                 #
  #                                                                         #
--- 3,7 ----
  #                                                                         #
  # C O P Y R I G H T   N O T I C E                                         #
! #  Copyright (c) 2003 by:                                                 #
  #    * California Institute of Technology                                 #
  #                                                                         #
***************
*** 104,108 ****
    print "---DEBUG---<br>"
    
!     
  if __name__ == '__main__':
    print "Content-Type: text/html"
--- 104,116 ----
    print "---DEBUG---<br>"
    
! 
! def checkFileName(fileName):
!   #Change windows linesep to linux linesep
!   text = re.sub('\\\\', '/', fileName)
!   path, file = os.path.split(text)
! 
!   return file
!   
! 
  if __name__ == '__main__':
    print "Content-Type: text/html"
***************
*** 119,123 ****
      #print 'File:', file.filename, '<br>'
  
!     saved = saveFile(file.filename, file.file.read())
  
      #print 'File %s saved.<br><br>' % (saved)
--- 127,135 ----
      #print 'File:', file.filename, '<br>'
  
!     fileName = file.filename
! 
!     fileName = checkFileName(fileName)
!     
!     saved = saveFile(fileName, file.file.read())
  
      #print 'File %s saved.<br><br>' % (saved)
***************
*** 126,130 ****
      print '<b>Input:</b> %s<br>' % (form['input'].value)
      print '<b>Output:</b> %s<br>' % (form['output'].value)
!     print '<b>Schema:</b> %s<br>' % (file.filename)
      print '<b>Destination:</b> %s<br>' % (form['dest'].value)
      print '<br>'
--- 138,142 ----
      print '<b>Input:</b> %s<br>' % (form['input'].value)
      print '<b>Output:</b> %s<br>' % (form['output'].value)
!     print '<b>Schema:</b> %s<br>' % (fileName)
      print '<b>Destination:</b> %s<br>' % (form['dest'].value)
      print '<br>'
***************
*** 132,136 ****
      driver = getDriverProgram(form['input'].value,
                                form['output'].value,
!                               file.filename,
                                form['dest'].value)
  
--- 144,148 ----
      driver = getDriverProgram(form['input'].value,
                                form['output'].value,
!                               fileName,
                                form['dest'].value)
  
***************
*** 154,158 ****
  
      if str(text) != '0':
!       print 'ERROR, exit code %s' % (text)
      else:
        print '<b>Generation Complete</b><br>'
--- 166,171 ----
  
      if str(text) != '0':
!       print 'ERROR, exit code %s<br>' % (text)
!       print 'E-mail pymerase-devel at lists.sourceforge.net for help.<br>'
      else:
        print '<b>Generation Complete</b><br>'

[Pymerase-cvs-commit] pymerase/pymweb Makefile,NONE,1.1

[<ki...@us...>]

Update of /cvsroot/pymerase/pymerase/pymweb
In directory sc8-pr-cvs1:/tmp/cvs-serv27245

Added Files:
	Makefile 
Log Message:
make file for installing


--- NEW FILE: Makefile ---
all:
	echo 'make install - Installation'
	echo 'make restart - Restart Apache'

install:
	cp cgi/pymweb.py /usr/lib/cgi-bin/
	cp www/pymweb.html /var/www/
	cp -r www/images/ /var/www/
	cp conf/pymweb.conf /etc/apache/conf/

restart:
	/etc/init.d/apache restart

[Pymerase-cvs-commit] pymerase/pymweb README,NONE,1.1

[<ki...@us...>]

Update of /cvsroot/pymerase/pymerase/pymweb
In directory sc8-pr-cvs1:/tmp/cvs-serv27023

Added Files:
	README 
Log Message:
install docs for pymweb


--- NEW FILE: README ---
*Pymweb Installation
---------------------

Debian Only Instructions:

1) add 'Include /etc/apache/conf/pymweb.conf' without the quotes to
   your apache httpd.conf file.

2) run 'make install' as root.

3) restart apache with the command '/etc/init.d/apache restart' as root.

Other Installation:

You will need to modify the make file to have it put the files in the
correct places. E-mail the pymerase-devel at lists.sourceforge.net
mailing list for help.

[Pymerase-cvs-commit] pymerase/examples __init__.py,NONE,1.1

[<de...@us...>]

Update of /cvsroot/pymerase/pymerase/examples
In directory sc8-pr-cvs1:/tmp/cvs-serv1046

Added Files:
	__init__.py 
Log Message:
add 2 __init__ modules to allow the moved TestSchool to import the school example and run it as a test.

--- NEW FILE: __init__.py ---

[Pymerase-cvs-commit] pymerase/examples/school __init__.py,NONE,1.1

[<de...@us...>]

Update of /cvsroot/pymerase/pymerase/examples/school
In directory sc8-pr-cvs1:/tmp/cvs-serv1046/school

Added Files:
	__init__.py 
Log Message:
add 2 __init__ modules to allow the moved TestSchool to import the school example and run it as a test.

--- NEW FILE: __init__.py ---

[Pymerase-cvs-commit] pymerase/tests TestSchool.py,1.1,1.2

[<de...@us...>]

Update of /cvsroot/pymerase/pymerase/tests
In directory sc8-pr-cvs1:/tmp/cvs-serv2262

Modified Files:
	TestSchool.py 
Log Message:
Changed how I locate the examples/school directory from importing to
just assuming its at ../examples/school. (Not good but might work
better for brandon)


Index: TestSchool.py
===================================================================
RCS file: /cvsroot/pymerase/pymerase/tests/TestSchool.py,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** TestSchool.py	3 Apr 2003 00:51:35 -0000	1.1
--- TestSchool.py	3 Apr 2003 01:15:53 -0000	1.2
***************
*** 48,53 ****
      """Initialize
      """
!     import examples.school
!     self.school_dir = examples.school.__path__[0]
  
      unittest.TestCase.__init__(self, name)
--- 48,52 ----
      """Initialize
      """
!     self.school_dir = os.path.join(os.getcwd(), "../examples/school")
  
      unittest.TestCase.__init__(self, name)

[Pymerase-cvs-commit] pymerase/tests TestSchool.py,NONE,1.1

[<de...@us...>]

Update of /cvsroot/pymerase/pymerase/tests
In directory sc8-pr-cvs1:/tmp/cvs-serv24932

Added Files:
	TestSchool.py 
Log Message:
Moved TestSchool.py to pymerase/tests

Also moved the database initialization into the test code instead of
being seperate sql insert table statements. (So as to cut down on the
number of places I need to keep updated for my test suite).

Made a loop for testing two different name manglers for the database
field and table names.

Not all test cases pass yet, but I'm getting closer.


--- NEW FILE: TestSchool.py ---
#!/usr/bin/env python
from __future__ import nested_scopes
import copy
import sys
import os
import string
import unittest

# CHANGE TO HOST RUNNING POSTGRESQL
host='localhost'
database='school_d0'

# import components needed to build the sql & api
# FIXME: need to set path to pymerase code
#sys.path.append(os.path.abspath(".."))
import pymerase                
from pymerase.util import NameMangling

# import code to use api
from mx import DateTime

def getHouses(session):
  """Returns dictionary of houses indexed by house name
  """
  houses_list = session.getAllObjects(session.Houses)
  houses = {}
  for h in houses_list:
    houses[string.lower(h.getHouseName())] = h
  return houses

def getFaculty(session):
  """Returns dictionary of houses indexed by professor
  """
  prof_list = session.getAllObjects(session.Faculty)
  faculty = {}
  for p in prof_list:
    faculty[string.lower(p.getGivenName())] = p
  return faculty

def getEmployee(session, givenName):
  givenNameQuery = "%s = '%s'" % (givenNameFieldName, givenName)
  employees = session.getObjectsWhere(session.Employees, givenNameQuery)
  return employees

  
class CreatePyGenexTestCases(unittest.TestCase):
  def __init__(self, name):
    """Initialize
    """
    import examples.school
    self.school_dir = examples.school.__path__[0]

    unittest.TestCase.__init__(self, name)
    
  def setUp(self):
    """Perform setup
    """
    self.current_dir = os.getcwd()
    os.chdir(self.school_dir)
    self.current_python_path = sys.path
    sys.path.append(self.school_dir)

  def tearDown(self):
    """Clean up after ourselves. 
    """
    os.chdir(self.current_dir)
    sys.path = self.current_python_path
    
  def resetDirectory(self):
    """Reset the environemnt for testing a different API
    """
    # remove the generated API
    api_dir = os.path.join(self.school_dir, 'school')
    if os.path.isdir(api_dir):
      for file in os.listdir(api_dir):
        os.remove(os.path.join(api_dir,file))
      os.rmdir(api_dir)
      
    sql_file = os.path.join(self.school_dir, 'school.sql')
    if os.path.isfile(sql_file):
      os.remove(sql_file)

    #os.system("sleep 10")
              
  def testCreate_underscore_API(self):
    """Test generating python api with the sql part using underscore_word.
    """
    self.resetDirectory()
    
    # Figure out path information
    schema = os.path.abspath("./schema")
    api_output = os.path.abspath("./school")
    sql_output = os.path.abspath("./school.sql")

    # construct pymerase object
    translator = pymerase.Pymerase()
    translator.setDefaultPackage("school")
    
    # set mangler convetion
    #mangler = NameMangling.underscore_word()
    #translator.setNameMangler(mangler, 'CreateSQL')

    # do the translation
    classesInModel={}
    parsed_input = translator.read(schema, 'parseGenexSchemaXML', classesInModel)
    translator.write(parsed_input, api_output, 'CreateDBAPI')
    translator.write(parsed_input, sql_output, 'CreateSQL')

    # one of the later tests needs to know what the actual field name is
    global givenNameFieldName
    givenNameFieldName="given_name"
    global dataSourceName
    dataSourceName = "data.sql"

    
  def testCreateCapsAPI(self):
    """Test generating python api with the sql part using CapWord.
    """
    self.resetDirectory()

    # Figure out path information
    schema = os.path.abspath("./schema")
    api_output = os.path.abspath("./school")
    sql_output = os.path.abspath("./school.sql")

    # construct pymerase object
    translator = pymerase.Pymerase()
    translator.setDefaultPackage("school")

    # set mangler convetion
    mangler = NameMangling.CapWord()
    translator.setNameMangler(mangler, 'CreateSQL')

    # do the translation 
    classesInModel={}
    parsed_input = translator.read(schema, 'parseGenexSchemaXML', classesInModel)
    print "*** parsed_input: ",parsed_input
    translator.write(parsed_input, api_output, 'CreateDBAPI')
    translator.write(parsed_input, sql_output, 'CreateSQL')

    # one of the later tests needs to know what the actual field name is
    global givenNameFieldName
    givenNameFieldName='"GivenName"'
    global dataSourceName
    dataSourceName = "dataCapWord.sql"


  def testCreateDB(self):
    """Construct the set of commands needed to tell postgresql to load data
    """
    createDBName = "createdb.sql"
    createdb = open(createDBName, "w")

    createDBText = []
    createDBText.append("drop database school_d0;")
    createDBText.append("create database school_d0;")
    createDBText.append("\c school_d0")
    createDBText.append("\i school.sql")
    #createDBText.append("\i %s" % (dataSourceName))
    createdb.write(string.join(createDBText, os.linesep))
    createdb.close()
                   
    exit = os.system("sleep 0 ; psql -h %s -f createdb.sql template1" % (host))

    self.failUnless(exit == 0)
    
    #os.remove(createDBName)

  def testSimpleInsert(self):
    """Insert objects with all attributes manual initialized
    """
    # also known as try to get rid of the using psql to load data
    import school
    s = school.DBSession(host, database)

    # define some faculty
    xavier = s.Faculty()
    xavier.setGivenName('Xavier')
    xavier.setFamilyName('Xal')
    xavier.setStatus('Associate')
    xavier.commit()

    yolanda = s.Faculty()
    yolanda.setGivenName('Yolanda')
    yolanda.setFamilyName('Yetti')
    yolanda.setStatus('Visiting')
    yolanda.commit()

    zaphod = s.Faculty()
    zaphod.setGivenName('Zaphod')
    zaphod.setFamilyName('Zim')
    zaphod.setStatus('Full')
    zaphod.commit()

    # define some houses
    for house_name in ('Blacker', 'Dabney', 'Flemming', 'Lloyd', 'Page', 
                       'Ricketts', 'Ruddock'):
      house = s.Houses()
      house.setHouseName(house_name)
      house.commit()

    for student_values in [('Ann', 'Arbor', 1, 2),
                           ('Ben', 'Blartfast', 2, 1),
                           ('Charles', 'Cooper', 3, 3),
                           ('Daria', 'Darwin', 4, 2),]:
      student = s.Students()
      student.setGivenName(student_values[0])
      student.setFamilyName(student_values[1])
      student.setHouseFk(student_values[2])
      student.setAdvisorFk(student_values[3])
      student.commit()

    courses_list = [('Bi/CS 164', 'Lecture, discussion, and projects in bioinformatics. Students will create, extend, and integrate bioinformatic software tools. Topics include genome-scale mRNA expression analysis, signal transduction pathway modeling, genome database analysis tools, and modeling morphogenesis from gene expression patterns. Each project will link into a larger Web application framework.'),
                    ('Bi 188', 'Introduction to the genetics of humans. Subjects covered include human genome structure, genetic diseases and predispositions, the human genome project, forensic use of human genetic markers, human variability, and human evolution.')
                    ]
    for course_value in courses_list:
      course = s.Courses()
      course.setCode(course_value[0])
      course.setDescription(course_value[1])
      course.commit()

    for class_values in [(1,1,'2002-04-01',3.3),
                         (2,1,'2002-04-01',3.0),
                         ]:
      c = s.Classes()
      c.setUidFk(class_values[0])
      c.setCourseFk(class_values[1])
      c.setTerm(class_values[2])
      c.setGrade(class_values[3])
      c.commit()


    for employee_value in [('diane', 'trout', 'code monkey'),
                           ('kevin', 'cooper', 'lab tech'),
                           ('jason', 'stewart', 'software consultant'),
                           ('amanda', 'jones', 'music')]:
      employee = s.Employees()
      employee.setGivenName(employee_value[0])
      employee.setFamilyName(employee_value[1])
      #employee.setJobDescription(employee_value[2])
      employee.commit()
    
    s.close()
    
  def testReadObject(self):
    import school
    s = school.DBSession(host, database)

    # grab by primary key and make sure it's our first example student
    ann = s.Students(4)
    self.failUnless(ann.getGivenName() == 'Ann')
    self.failUnless(ann.getFamilyName() == 'Arbor')
    self.failUnless(ann.getHouseFk() == 1)
    self.failUnless(ann.getAdvisorFk() == 2)

    # try to read inherited object via class factory
    zaphod = s.Faculty(3)
    self.failUnless(zaphod.getGivenName() == 'Zaphod')
    self.failUnless(zaphod.getFamilyName() == 'Zim')
    self.failUnless(zaphod.getStatus() == 'Full')

    # The initial load of data installs 4 example students
    print dir(school)
    print dir(school.school)
    student_list = s.getAllObjects(school.Students.Students)
    self.failUnless(len(student_list) == 4)
    s.close()
    

  def testReadOneToOneLink(self):
    import school
    s = school.DBSession(host, database)

    daria = s.Students(7)

    # FIXME: this should read advisor
    advisors = daria.getAdvisor()

    self.failUnless(len(advisors) == 1)
    self.failUnless(advisors[0].getUid() == 2)
    self.failUnless(advisors[0].getGivenName() == 'Yolanda')
    self.failUnless(advisors[0].getFamilyName() == 'Yetti')
    s.close()
    

  def testReadManyToOneLink(self):
    import school
    s = school.DBSession(host, database)

    houses = getHouses(s)
    darbs = houses['dabney'].getStudents()

    self.failUnless(len(darbs) == 1)
    self.failUnless(darbs[0].getGivenName() == "Ben")
    self.failUnless(darbs[0].getFamilyName() == "Blartfast")
    s.close()
    

  def testReadManyToManyLink(self):
    pass
  
  def testOneToOneInsert(self):
    import school
    s = school.DBSession(host, database)
    houses = getHouses(s)
    faculty = getFaculty(s)
    
    #erin = Students(db_session=s)
    erin = s.Students()
    erin.setGivenName("Erin")
    erin.setFamilyName("Ericsson")
    erin.setHouses(houses['page'])

    faculty['yolanda'].appendStudents(erin)
    faculty['yolanda'].commit()

    #erin_list = s.getObjectsWhere(s.Students, "\"GivenName\" = 'Erin'")
    givenNameQuery = "%s = 'Erin'" % ( givenNameFieldName )
    erin_list = s.getObjectsWhere(s.Students, givenNameQuery)
    self.failUnless(len(erin_list) == 1)
    erin_loaded = erin_list[0]

    print erin.id(), erin_loaded.id()
    self.failUnless(erin.id() == erin_loaded.id())
    self.failUnless(erin.getGivenName() == erin_loaded.getGivenName())
    self.failUnless(erin.getFamilyName() == erin_loaded.getFamilyName())
    self.failUnless(erin.getHouseFk() == erin_loaded.getHouseFk())
    self.failUnless(erin.getAdvisorFk() == erin_loaded.getAdvisorFk())
    
    frederick = s.Students()
    frederick.setGivenName("Frederick")
    frederick.setFamilyName("Fergison")
    frederick.setHouses(houses['ricketts'])
    faculty['zaphod'].appendStudents(frederick)
    faculty['zaphod'].commit()

    #frederick_list = s.getObjectsWhere(s.Students,
    #                                     "\"GivenName\" = 'Frederick'")
    givenNameQuery = "%s = 'Frederick'" % (givenNameFieldName)
    frederick_list = s.getObjectsWhere(s.Students, givenNameQuery)
    self.failUnless(len(frederick_list) == 1)
    frederick_loaded = frederick_list[0]

    self.failUnless(frederick.id() == frederick_loaded.id(),
       "frederick primary key failure %s != %s" % (frederick.id(),
                                                   frederick_loaded.id()))
    self.failUnless(frederick.getGivenName() == frederick_loaded.getGivenName())
    self.failUnless(frederick.getFamilyName()==frederick_loaded.getFamilyName())
    self.failUnless(frederick.getHouseFk() == frederick_loaded.getHouseFk())
    self.failUnless(frederick.getAdvisorFk() == frederick_loaded.getAdvisorFk())
    
    s.close()
    
    
  def testManyToOneInsert(self):
    import school
    s = school.DBSession(host, database)
    charles = s.Students(6)
    daria = s.Students(7)
    bi188 = s.Courses(2)

    classes = s.Classes()
    classes.setCourses(bi188)
    classes.setStudents(charles)
    classes.setTerm(DateTime.DateTime(2002,04,01))
    classes.setGrade(3.3)
    classes.commit()

    classes = s.Classes()
    classes.setCourses(bi188)
    classes.setStudents(daria)
    classes.setTerm(DateTime.DateTime(2002,04,01))
    classes.setGrade(3.7)
    classes.commit()

    s.close()
    

  def testTreeInsert(self):
    import school

    def checkEmployee(session, givenName):
      e = getEmployee(session, givenName)
      self.failUnless(len(e) == 1)
      return e[0]

    s = school.DBSession(host, database)
    diane = checkEmployee(s, "diane")
    kevin = checkEmployee(s, "kevin")
    jason = checkEmployee(s, "jason")
    amanda = checkEmployee(s, "amanda")
    yolanda = checkEmployee(s, "Yolanda")

    #yolanda.appendManaged(amanda)
    diane.setManager(yolanda)
    kevin.setManager(diane)
    amanda.setManager(yolanda)
 
    diane.commit()
    kevin.commit()
    
    jason.setManager(yolanda)
    jason.commit()
    amanda.commit()
    yolanda.commit()

    s.close()
    
    
  def testTreeRetrieval(self):
    import school
    s = school.DBSession(host, database)
    yolanda = getEmployee(s, "Yolanda")[0]
    managedList = yolanda.getManaged()
    self.failUnless(len(managedList) == 3)

    diane = filter(lambda x: x.getGivenName() == 'diane', managedList)[0]
    managedByDiane = diane.getManaged()
    self.failUnless(len(managedByDiane) == 1)
    kevin = managedByDiane[0]
    self.failUnless(kevin.getGivenName() == 'kevin')

    kevinManager = kevin.getManager()[0]
    self.failUnless(kevinManager.getGivenName() == diane.getGivenName())
    
    amanda = filter(lambda x: x.getGivenName() == 'amanda', managedList)[0]
    amandaDirect = getEmployee(s, "amanda")[0]
    self.failUnless(amanda.getGivenName() == amandaDirect.getGivenName())
    self.failUnless(amanda.getFamilyName() == amandaDirect.getFamilyName())

    s.close()
    

def suite():
  suite = unittest.TestSuite()

  # run through test twice once for underscore_api and once for CapsAPI
  api_tests = [
               CreatePyGenexTestCases("testCreate_underscore_API"),
               CreatePyGenexTestCases("testCreateCapsAPI"),
              ]
  for api in api_tests:
    suite.addTest(api)
    suite.addTest(CreatePyGenexTestCases("testCreateDB"))
    suite.addTest(CreatePyGenexTestCases("testSimpleInsert"))
    suite.addTest(CreatePyGenexTestCases("testReadObject"))
    suite.addTest(CreatePyGenexTestCases("testReadOneToOneLink"))
    suite.addTest(CreatePyGenexTestCases("testReadManyToOneLink"))
    suite.addTest(CreatePyGenexTestCases("testReadManyToManyLink"))
    suite.addTest(CreatePyGenexTestCases("testOneToOneInsert"))
    suite.addTest(CreatePyGenexTestCases("testManyToOneInsert"))
    suite.addTest(CreatePyGenexTestCases("testTreeInsert"))
    suite.addTest(CreatePyGenexTestCases("testTreeRetrieval"))
              
  return suite

if __name__ == "__main__":
  unittest.main(defaultTest="suite")

[Pymerase-cvs-commit] Docs/install Makefile,NONE,1.1

[<ki...@us...>]

Update of /cvsroot/pymerase/Docs/install
In directory sc8-pr-cvs1:/tmp/cvs-serv23271a

Added Files:
	Makefile 
Log Message:
pretty pdf file generation


--- NEW FILE: Makefile ---
install.pdf: install.tex
	latex install.tex
	latex install.tex
	dvips -Ppdf install.dvi
	ps2pdf install.ps
	gv install.pdf

[Pymerase-cvs-commit] Docs/install install.tex,NONE,1.1

[<ki...@us...>]

Update of /cvsroot/pymerase/Docs/install
In directory sc8-pr-cvs1:/tmp/cvs-serv23173

Added Files:
	install.tex 
Log Message:
Installation Docs in latex format


--- NEW FILE: install.tex ---
% Pymerase Docs - Template
% Copyright (c) California Institute of Technology
%
% Authors: Brandon King
% $Revision: 1.1 $
% Modified $Date: 2003/04/03 00:46:58 $

\documentclass{article}
\usepackage{graphicx}
\usepackage{color}
\usepackage[margin=3cm,noheadfoot]{geometry}

\setlength{\parindent}{0in}
\setlength{\parskip}{2mm}

%colors
\newcommand{\cb}{\color{blue}}

%new commands
\newcommand{\pymlink}{http://pymerase.sf.net}

%document
\begin{document}

%title page
\begin{titlepage}
\title{\cb Pymerase Docs - Installation}
\author{Diane Trout \\
Copyright \copyright  California Institute of Technology}
\date{Version 0.1.1\\\today}
\maketitle
\thispagestyle{empty}
\end{titlepage}

\tableofcontents
\thispagestyle{empty}
\newpage

%Document Body
\setcounter{page}{1}

\section{\cb Installation}
\subsection{\cb How to install?}
Pymerase depends on several components depending on what you'd like to
do with it.

\subsubsection{\cb GeneX Table Definition Format}
Currently the GeneX Table definition format is the best supported file
format (As it was the first mode I started developing against.)

However the XMI format is coming along as well.

At minimum it requires an XML parser. The default python XML parser is
called expat, newer versions are available at
http://sourceforge.net/projects/pyxml. Later versions of this might
work with the current table.dtd

2003 Apr 02: default parser seems to work, so the steps to install
pirxx \& xerces seem to be unnecessary. (But I'm leaving the section in
just in case.)  [Well, almost works, since the default xml parser
couldn't find the table.dtd file without using a full URL instead of
just a pathname]

  However the version of expat I was using didn't properly support
  entities with the XML files were using so I ended up using the
  xerces-c XML parser. 
  
  A project called pirxx is providing the python wrapper for xerces-c.
  
  xerces-c: http://xml.apache.org/xerces-c/index.html
  pirxx: http://sourceforge.net/projects/pirxx

END old instructions.

\subsubsection{\cb XMI file format}
The key thing for XMI files is you need to generate them somehow,
ArgoUML is the tool we're currently using for testing. 

http://argouml.tigris.org

The current XMI parser was written by Teemu Toivanen and is available
from the MGED/Mage sourceforge site in the directory lib/Python/pyXMI.

\subsubsection{\cb DB Support}
The code generated by CreateDBAPI, needs the mxTools Date Time
extension as well as the postgresql python db api module.

The mx tools is available from:
http://www.egenix.com/files/python/mxDateTime.html 

The database interface, pgdb, is distributed with postgresql
(http://www.postgresql.org) 

Also, the SQL code generated by CreateSQL is using postgresql's sequence
feature, and so is currently dependent on postgresql. 

\end{document}

[Pymerase-cvs-commit] Docs/install - New directory

[<ki...@us...>]

Update of /cvsroot/pymerase/Docs/install
In directory sc8-pr-cvs1:/tmp/cvs-serv22792/install

Log Message:
Directory /cvsroot/pymerase/Docs/install added to the repository

[Pymerase-cvs-commit] pymerase/tests pymeraseTestSuite.py,1.1,1.2

[<de...@us...>]

Update of /cvsroot/pymerase/pymerase/tests
In directory sc8-pr-cvs1:/tmp/cvs-serv22078

Modified Files:
	pymeraseTestSuite.py 
Log Message:
Add TestSchool testsuite to the list of tests.


Index: pymeraseTestSuite.py
===================================================================
RCS file: /cvsroot/pymerase/pymerase/tests/pymeraseTestSuite.py,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** pymeraseTestSuite.py	26 Mar 2003 03:13:26 -0000	1.1
--- pymeraseTestSuite.py	3 Apr 2003 00:43:16 -0000	1.2
***************
*** 41,44 ****
--- 41,45 ----
  import TestImportAll
  #Import new test suites here
+ import TestSchool
  
  def suite():
***************
*** 50,53 ****
--- 51,55 ----
    suite = unittest.TestSuite()
    suite.addTest(TestImportAll.suite())
+   suite.addTest(TestSchool.suite())
    #add new suite.addTest(module.suite()) here
    

[Pymerase-cvs-commit] pymerase/tests TestImportAll.py,1.3,1.4

[<de...@us...>]

Update of /cvsroot/pymerase/pymerase/tests
In directory sc8-pr-cvs1:/tmp/cvs-serv21920

Modified Files:
	TestImportAll.py 
Log Message:
For running under python the failure of importing parseXMI is
expected, so if it succeeds we should generate an error.


Index: TestImportAll.py
===================================================================
RCS file: /cvsroot/pymerase/pymerase/tests/TestImportAll.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** TestImportAll.py	26 Mar 2003 03:25:06 -0000	1.3
--- TestImportAll.py	3 Apr 2003 00:42:49 -0000	1.4
***************
*** 53,58 ****
  
    def testInputParseXMI(self):
!     from pymerase.input import parseXMI
! 
    def testOutputCreateDBAPI(self):
      from pymerase.output import CreateDBAPI
--- 53,64 ----
  
    def testInputParseXMI(self):
!     try:
!       from pymerase.input import parseXMI
!     except ImportError, e:
!       return
!     # FIXME: need to differentiate between
!     # FIXME: python & jython
!     self.fail("parseXMI should fail to import under python")
!     
    def testOutputCreateDBAPI(self):
      from pymerase.output import CreateDBAPI

[Pymerase-cvs-commit] pymerase/examples/school TestSchool.py,1.10,NONE

[<de...@us...>]

Update of /cvsroot/pymerase/pymerase/examples/school
In directory sc8-pr-cvs1:/tmp/cvs-serv21637

Removed Files:
	TestSchool.py 
Log Message:
Moved TestSchool.py to pymerase/tests

--- TestSchool.py DELETED ---

[Pymerase-cvs-commit] pymerase INSTALL,1.1,1.2

[<de...@us...>]

Update of /cvsroot/pymerase/pymerase
In directory sc8-pr-cvs1:/tmp/cvs-serv21171

Modified Files:
	INSTALL 
Log Message:
updated install instructions to mention that the newer xml parser
seems to work.


Index: INSTALL
===================================================================
RCS file: /cvsroot/pymerase/pymerase/INSTALL,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** INSTALL	13 Feb 2003 02:47:11 -0000	1.1
--- INSTALL	3 Apr 2003 00:40:03 -0000	1.2
***************
*** 19,30 ****
  work with the current table.dtd
  
! However the version of expat I was using didn't properly support
! entities with the XML files were using so I ended up using the
! xerces-c XML parser. 
  
! A project called pirxx is providing the python wrapper for xerces-c.
  
! xerces-c: http://xml.apache.org/xerces-c/index.html
! pirxx: http://sourceforge.net/projects/pirxx
  
  ** XMI file format
--- 19,38 ----
  work with the current table.dtd
  
! 2003 Apr 02: default parser seems to work, so the steps to install
! pirxx & xerces seem to be unnecessary. (But I'm leaving the section in
! just in case.)  [Well, almost works, since the default xml parser
! couldn't find the table.dtd file without using a full URL instead of
! just a pathname]
  
!   However the version of expat I was using didn't properly support
!   entities with the XML files were using so I ended up using the
!   xerces-c XML parser. 
!   
!   A project called pirxx is providing the python wrapper for xerces-c.
!   
!   xerces-c: http://xml.apache.org/xerces-c/index.html
!   pirxx: http://sourceforge.net/projects/pirxx
  
! END old instructions.
  
  ** XMI file format

[Pymerase-cvs-commit] pymerase/pymerase/input parseGenexSchemaXML.py,1.25,1.26

[<de...@us...>]

Update of /cvsroot/pymerase/pymerase/pymerase/input
In directory sc8-pr-cvs1:/tmp/cvs-serv27899

Modified Files:
	parseGenexSchemaXML.py 
Log Message:
Remove dependency on pirxx as the default python xml parsers seem to
be working now.


Index: parseGenexSchemaXML.py
===================================================================
RCS file: /cvsroot/pymerase/pymerase/pymerase/input/parseGenexSchemaXML.py,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** parseGenexSchemaXML.py	5 Feb 2003 23:04:15 -0000	1.25
--- parseGenexSchemaXML.py	2 Apr 2003 23:26:39 -0000	1.26
***************
*** 202,206 ****
      # create parser
      #print sax2exts.XMLParserFactory.get_parser_list()
!     parser = sax2exts.make_parser('pirxx')
      parser.setFeature(feature_namespaces, 0)
      parser.setContentHandler(self)
--- 202,207 ----
      # create parser
      #print sax2exts.XMLParserFactory.get_parser_list()
!     
!     parser = sax2exts.make_parser()
      parser.setFeature(feature_namespaces, 0)
      parser.setContentHandler(self)

[Pymerase-cvs-commit] pymerase/pymerase/output/dbAPI init.py,1.4,1.5

[<de...@us...>]

Update of /cvsroot/pymerase/pymerase/pymerase/output/dbAPI
In directory sc8-pr-cvs1:/tmp/cvs-serv27505

Modified Files:
	init.py 
Log Message:
Fix bug where DBHOST wasn't actually being used as the environment
variable to set the host name.

Removed the woldlab testing data source defaults and try more
reasonable general defaults.


Index: init.py
===================================================================
RCS file: /cvsroot/pymerase/pymerase/pymerase/output/dbAPI/init.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** init.py	1 Jul 2002 22:38:59 -0000	1.4
--- init.py	2 Apr 2003 23:25:32 -0000	1.5
***************
*** 28,39 ****
    """Manages creating and closing a database session.
    """
!   default_dsn = "thornvalley.caltech.edu"
!   default_user = "diane"
!   default_database = "genex2_d0"
    default_password=None
    
    def __init__(self, dsn=None, database=None, user=None, password=None):
      if dsn is None:
!       self.dsn = os.environ.get('DBUSER', DBSession.default_dsn)
      else:
        self.dsn = dsn
--- 28,39 ----
    """Manages creating and closing a database session.
    """
!   default_dsn = "localhost"
!   default_user = os.getlogin()
!   default_database = None
    default_password=None
    
    def __init__(self, dsn=None, database=None, user=None, password=None):
      if dsn is None:
!       self.dsn = os.environ.get('DBHOST', DBSession.default_dsn)
      else:
        self.dsn = dsn
***************
*** 89,92 ****
--- 89,96 ----
      if self.db is not None:
        self.db.commit()
+ 
+   def close(self):
+     if self.db is not None:
+       self.db.close()
  
    ############################

[Pymerase-cvs-commit] pymerase/pymerase/output/dbAPI dbAPI.py,1.20,1.21

[<de...@us...>]

Update of /cvsroot/pymerase/pymerase/pymerase/output/dbAPI
In directory sc8-pr-cvs1:/tmp/cvs-serv27101

Modified Files:
	dbAPI.py 
Log Message:
For some reason sqlEscapeString was being called with things that
weren't strings. So just return those without modification.


Index: dbAPI.py
===================================================================
RCS file: /cvsroot/pymerase/pymerase/pymerase/output/dbAPI/dbAPI.py,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** dbAPI.py	18 Mar 2003 02:49:42 -0000	1.20
--- dbAPI.py	2 Apr 2003 23:24:27 -0000	1.21
***************
*** 37,40 ****
--- 37,41 ----
  import os
  import pprint
+ import re
  import string
  import sys
***************
*** 58,62 ****
    """Given a string escape any double quote marks \"
    """
!   return re.sub('"', '\"', s)
  
  class Field:
--- 59,66 ----
    """Given a string escape any double quote marks \"
    """
!   if type(s) == types.StringType or type(s) == types.UnicodeType:
!     return re.sub('"', '\"', s)
!   else:
!     return s
  
  class Field:

[Pymerase-cvs-commit] pymerase/pymerase __init__.py,1.30,1.31

[<de...@us...>]

Update of /cvsroot/pymerase/pymerase/pymerase
In directory sc8-pr-cvs1:/tmp/cvs-serv3137

Modified Files:
	__init__.py 
Log Message:
Removed default parameters for the read & write api calls. 
  This was to fix bug #714139, where multiple calls to read would
  accrete the contents of each schema being parsed.


Index: __init__.py
===================================================================
RCS file: /cvsroot/pymerase/pymerase/pymerase/__init__.py,v
retrieving revision 1.30
retrieving revision 1.31
diff -C2 -d -r1.30 -r1.31
*** __init__.py	26 Mar 2003 01:13:14 -0000	1.30
--- __init__.py	2 Apr 2003 22:20:17 -0000	1.31
***************
*** 258,262 ****
  
  
!   def read(self, source, inputTranslator=None, classesInModel={}):
      """Given a translator and source of input, parse object definitions.
      """
--- 258,262 ----
  
  
!   def read(self, source, inputTranslator, classesInModel):
      """Given a translator and source of input, parse object definitions.
      """
***************
*** 273,277 ****
      return parsedInput
  
!   def write(self, parsedInput, destination, outputTranslator=None):
      """Given parsed object definitions write output defined by
      an output_translator.
--- 273,277 ----
      return parsedInput
  
!   def write(self, parsedInput, destination, outputTranslator):
      """Given parsed object definitions write output defined by
      an output_translator.

[Pymerase-cvs-commit] Docs/running_pymerase Makefile,1.2,1.3

[<ki...@us...>]

Update of /cvsroot/pymerase/Docs/running_pymerase
In directory sc8-pr-cvs1:/tmp/cvs-serv5764

Modified Files:
	Makefile 
Log Message:
Nice quality pdf generation.


Index: Makefile
===================================================================
RCS file: /cvsroot/pymerase/Docs/running_pymerase/Makefile,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Makefile	21 Mar 2003 02:53:21 -0000	1.2
--- Makefile	2 Apr 2003 21:08:11 -0000	1.3
***************
*** 1,5 ****
  Run_Pymerase.pdf: Run_Pymerase.tex
  	latex Run_Pymerase.tex
! 	dvipdf Run_Pymerase.dvi
  	gv Run_Pymerase.pdf
  
--- 1,7 ----
  Run_Pymerase.pdf: Run_Pymerase.tex
  	latex Run_Pymerase.tex
! 	latex Run_Pymerase.tex
! 	dvips -Ppdf Run_Pymerase.dvi
! 	ps2pdf Run_Pymerase.ps
  	gv Run_Pymerase.pdf
  

[Pymerase-cvs-commit] Docs/template Makefile,1.1,1.2

[<ki...@us...>]

Update of /cvsroot/pymerase/Docs/template
In directory sc8-pr-cvs1:/tmp/cvs-serv5545

Modified Files:
	Makefile 
Log Message:
now generates nice quality pdf files.


Index: Makefile
===================================================================
RCS file: /cvsroot/pymerase/Docs/template/Makefile,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** Makefile	20 Mar 2003 20:55:26 -0000	1.1
--- Makefile	2 Apr 2003 21:07:33 -0000	1.2
***************
*** 2,5 ****
  	latex template.tex
  	latex template.tex
! 	dvipdf template.dvi template.pdf
  	gv template.pdf
--- 2,6 ----
  	latex template.tex
  	latex template.tex
! 	dvips -Ppdf template.dvi
! 	ps2pdf template.ps
  	gv template.pdf

[Pymerase-cvs-commit] Docs/linkDB-tutorial Makefile,1.1,1.2

[<ki...@us...>]

Update of /cvsroot/pymerase/Docs/linkDB-tutorial
In directory sc8-pr-cvs1:/tmp/cvs-serv4142

Modified Files:
	Makefile 
Log Message:
nice quality pdf files. =o)


Index: Makefile
===================================================================
RCS file: /cvsroot/pymerase/Docs/linkDB-tutorial/Makefile,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** Makefile	7 Mar 2003 23:32:23 -0000	1.1
--- Makefile	2 Apr 2003 21:04:21 -0000	1.2
***************
*** 2,5 ****
  	latex linkdb-tutorial.tex
  	latex linkdb-tutorial.tex
! 	dvipdf linkdb-tutorial.dvi
  	gv linkdb-tutorial.pdf
--- 2,6 ----
  	latex linkdb-tutorial.tex
  	latex linkdb-tutorial.tex
! 	dvips -Ppdf linkdb-tutorial.dvi
! 	ps2pdf linkdb-tutorial.ps
  	gv linkdb-tutorial.pdf

[Pymerase-cvs-commit] Docs/faq Makefile,1.3,1.4

[<ki...@us...>]

Update of /cvsroot/pymerase/Docs/faq
In directory sc8-pr-cvs1:/tmp/cvs-serv3813

Modified Files:
	Makefile 
Log Message:
nice quality pdf generation. =o)


Index: Makefile
===================================================================
RCS file: /cvsroot/pymerase/Docs/faq/Makefile,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** Makefile	2 Apr 2003 19:23:09 -0000	1.3
--- Makefile	2 Apr 2003 21:03:41 -0000	1.4
***************
*** 1,5 ****
  faq.pdf: faq.tex
  	latex faq.tex
! 	pdflatex faq.tex
  	gv faq.pdf
  
--- 1,7 ----
  faq.pdf: faq.tex
  	latex faq.tex
! 	latex faq.tex
! 	dvips -Ppdf faq.tex
! 	ps2pdf faq.ps
  	gv faq.pdf
  

[Pymerase-cvs-commit] Docs/argouml Makefile,1.1,1.2

[<ki...@us...>]

Update of /cvsroot/pymerase/Docs/argouml
In directory sc8-pr-cvs1:/tmp/cvs-serv2482

Modified Files:
	Makefile 
Log Message:
Finally generating nice PDF files. =o)


Index: Makefile
===================================================================
RCS file: /cvsroot/pymerase/Docs/argouml/Makefile,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** Makefile	20 Mar 2003 21:53:02 -0000	1.1
--- Makefile	2 Apr 2003 21:00:45 -0000	1.2
***************
*** 2,5 ****
  	latex argouml.tex
  	latex argouml.tex
! 	dvipdf argouml.dvi argo4pymerase.pdf
  	gv argo4pymerase.pdf
--- 2,6 ----
  	latex argouml.tex
  	latex argouml.tex
! 	dvips -Ppdf argouml.dvi
! 	ps2pdf argouml.ps argo4pymerase.pdf
  	gv argo4pymerase.pdf

[Pymerase-cvs-commit] Docs/faq Makefile,1.2,1.3

[<ki...@us...>]

Update of /cvsroot/pymerase/Docs/faq
In directory sc8-pr-cvs1:/tmp/cvs-serv16576

Modified Files:
	Makefile 
Log Message:
dvipdf produced bad pdf files, now using pdflatex.


Index: Makefile
===================================================================
RCS file: /cvsroot/pymerase/Docs/faq/Makefile,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Makefile	21 Mar 2003 02:58:42 -0000	1.2
--- Makefile	2 Apr 2003 19:23:09 -0000	1.3
***************
*** 1,7 ****
! pymerase-faq.pdf: faq.tex
! 	latex faq.tex
  	latex faq.tex
! 	dvipdf faq.dvi pymerase-faq.pdf
! 	gv pymerase-faq.pdf
  
  html:
--- 1,6 ----
! faq.pdf: faq.tex
  	latex faq.tex
! 	pdflatex faq.tex
! 	gv faq.pdf
  
  html: