unique.py

###unique
#Copyright 2005-2019
#Author Nathan Salomonis - nsalomonis@gmail.com

#Permission is hereby granted, free of charge, to any person obtaining a copy 
#of this software and associated documentation files (the "Software"), to deal 
#in the Software without restriction, including without limitation the rights 
#to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 
#copies of the Software, and to permit persons to whom the Software is furnished 
#to do so, subject to the following conditions:

#THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, 
#INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A 
#PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT 
#HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION 
#OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE 
#SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

"""This module contains instructions for recalling operating system file and directory paths,
eliminating redundant list entries, removing unecessary file paths from py2app or py2exe
and reading the propper Ensembl database version to allow for version specific access."""

import sys, string
import os.path, platform
import traceback
from os.path import expanduser
userHomeDir = expanduser("~")+'/altanalyze/'

ignoreHome = False

py2app_adj = '/GO_Elite.app/Contents/Resources/Python/site-packages.zip'
py2app_adj1 = '/GO_Elite.app/Contents/Resources/lib/python2.4/site-packages.zip'
py2app_adj2 = '/GO_Elite.app/Contents/Resources/lib/python2.5/site-packages.zip'
py2app_adj3 = '/GO_Elite.app/Contents/Resources/lib/python2.6/site-packages.zip'
py2app_adj4 = '/GO_Elite.app/Contents/Resources/lib/python2.7/site-packages.zip'
py2exe_adj = '\\library.zip' ###py2exe
cx_Freeze_adj = '/library.zip'
pyinstaller_adj = '/GO_Elite.app/Contents/MacOS'
py2app_ge_dirs = [py2app_adj,py2exe_adj,py2app_adj1,py2app_adj2,py2app_adj3,py2app_adj4,cx_Freeze_adj,pyinstaller_adj]

py2app_adj = '/AltAnalyze.app/Contents/Resources/Python/site-packages.zip'
py2app_adj1 = '/AltAnalyze.app/Contents/Resources/lib/python2.4/site-packages.zip'
py2app_adj2 = '/AltAnalyze.app/Contents/Resources/lib/python2.5/site-packages.zip'
py2app_adj3 = '/AltAnalyze.app/Contents/Resources/lib/python2.6/site-packages.zip'
py2app_adj4 = '/AltAnalyze.app/Contents/Resources/lib/python2.7/site-packages.zip'

py2exe_adj = '\\library.zip' ###py2exe
cx_Freeze_adj = '/library.zip'
pyinstaller_adj = '/AltAnalyze.app/Contents/MacOS'
pyinstaller_adj2 = '/AltAnalyze.app/Contents/Resources'
py2app_aa_dirs = [py2app_adj,py2app_adj1,py2exe_adj,py2app_adj2,py2app_adj3,py2app_adj4,cx_Freeze_adj,pyinstaller_adj,pyinstaller_adj2]
py2app_dirs = py2app_ge_dirs + py2app_aa_dirs

for i in py2app_aa_dirs:    
    i = string.replace(i,'AltAnalyze.app','AltAnalyzeViewer.app')
    py2app_dirs.append(i)

if ('linux' in sys.platform or 'posix' in sys.platform) and getattr(sys, 'frozen', False): ### For PyInstaller
    application_path = os.path.dirname(sys.executable)
    #application_path = sys._MEIPASS  ### should be the same as the above
else:
    if '..' in __file__:
        """ Indicates the file callin unique.py is in a subdirectory """
        try:
            if '.py' in __file__:
                import export
                application_path = export.findParentDir(string.split(__file__,'..')[0][:-1])
            else:
                application_path = os.getcwd()
        except Exception:
            application_path = os.getcwd()
    else:
        application_path = os.path.dirname(__file__)

if len(application_path)==0:
    application_path = os.getcwd()

if 'AltAnalyze?' in application_path:
    application_path = string.replace(application_path,'//','/')
    application_path = string.replace(application_path,'\\','/') ### If /// present
    application_path = string.split(application_path,'AltAnalyze?')[0]

if 'GO_Elite?' in application_path:
    application_path = string.replace(application_path,'//','/')
    application_path = string.replace(application_path,'\\','/') ### If /// present
    application_path = string.split(application_path,'GO_Elite?')[0]

for py2app_dir in py2app_dirs:
    application_path = string.replace(application_path,py2app_dir,'')

def applicationPath():
    return application_path

def filepath(filename,force=None):
    altDatabaseCheck = True
    #dir=os.path.dirname(dirfile.__file__)       #directory file is input as a variable under the main
    dir = application_path
    """
    if os.path.isfile(filename):
        fn = filename
        return fn
    elif os.path.isfile(dir+'/'+filename):
        fn = filename
        return fn
    #"""

    """ If a local file without the full path (e.g., Config/options.txt). Checks in the software directory."""
    import export
    parent_dir = export.findParentDir(filename)
    actual_file = export.findFilename(filename)
    try:
        #if os.path.exists(dir+'/'+parent_dir):
        dir_list = os.listdir(dir+'/'+parent_dir)
        fn = dir+'/'+parent_dir+'/'+actual_file
        if '.txt' in fn or '.log' in fn:
            return fn
    except:
        pass

    if filename== '':  ### Windows will actually recognize '' as the AltAnalyze root in certain situations but not others
        fn = dir
    elif ':' in filename:
        fn = filename
    else:
        try:
            try:
                dir_list = os.listdir(dir+'/'+filename)
                fn = dir+'/'+filename
            except:
                dir_list = os.listdir(filename)
                fn = filename ### test to see if the path can be found (then it is the full path)
        except Exception:
            fn=os.path.join(dir,filename)
            fileExists = os.path.isfile(fn)
            #print 'filename:',filename, fileExists
            """"When AltAnalyze installed through pypi - AltDatabase and possibly Config in user-directory """
            if 'Config' in fn:
                if fileExists == False and force !='application-path' and ignoreHome==False:
                    fn=os.path.join(userHomeDir,filename)
            if 'AltDatabase' in fn:
                getCurrentGeneDatabaseVersion()
                fn = correctGeneDatabaseDir(fn)
                altanalyze_dir = string.split(fn,'AltDatabase')[0]+'AltDatabase'
                ### Check the AltDatabase dir not the fn, since the fn may not exist yet
                fileExists = os.path.isfile(altanalyze_dir)
                try:
                    dir_list = os.listdir(altanalyze_dir)
                    fileExists=True
                except Exception: pass
                #print 2, [fn],fileExists
                if fileExists == False and ignoreHome==False:
                    fn=os.path.join(userHomeDir,filename)
                    fn = correctGeneDatabaseDir(fn)
                altDatabaseCheck = False 
    
    if '/Volumes/' in filename and altDatabaseCheck:
        filenames = string.split(filename,'/Volumes/'); fn = '/Volumes/'+filenames[-1]
    for py2app_dir in py2app_dirs: fn = string.replace(fn,py2app_dir,'')
    if (('Databases' in fn) or ('AltDatabase' in fn)) and altDatabaseCheck:
        getCurrentGeneDatabaseVersion()
        fn = correctGeneDatabaseDir(fn)
    fn = string.replace(fn,'.txt.txt','.txt')
    fn = string.replace(fn,'//','/')
    fn = string.replace(fn,'//','/') ### If /// present
    return fn

def read_directory(sub_dir):
    dir=application_path
    for py2app_dir in py2app_dirs: dir = string.replace(dir,py2app_dir,'')
    if 'Databases' in sub_dir or 'AltDatabase' in sub_dir:
        getCurrentGeneDatabaseVersion()
        sub_dir = correctGeneDatabaseDir(sub_dir)

    try: dir_list = os.listdir(dir+sub_dir)
    except Exception:
        try: dir_list = os.listdir(sub_dir) ### For linux
        except Exception:
            dir = userHomeDir  ### When AltAnalyze installed through pypi - AltDatabase in user-directory
            dir_list = os.listdir(dir+sub_dir)
    try: dir_list.remove('.DS_Store') ### This is needed on a mac
    except Exception: null=[]
    #print dir, sub_dir
    return dir_list
    
def returnDirectories(sub_dir):
    dir=application_path
    if 'Databases' in sub_dir or 'AltDatabase' in sub_dir:
        getCurrentGeneDatabaseVersion()
        sub_dir = correctGeneDatabaseDir(sub_dir)
    for py2app_dir in py2app_dirs:
        dir = string.replace(dir,py2app_dir,'')
    try: dir_list = os.listdir(dir + sub_dir)
    except Exception:
        try: dir_list = os.listdir(sub_dir) ### For linux
        except Exception: print dir, sub_dir; bad_exit
    return dir_list

def returnDirectoriesNoReplace(sub_dir,search=None):
    dir=application_path
    for py2app_dir in py2app_dirs:
        dir = string.replace(dir,py2app_dir,'')

    try: dir_list = os.listdir(dir + sub_dir)
    except Exception:
        try: dir_list = os.listdir(sub_dir) ### For linux
        except Exception:
            try: dir_list = os.listdir(sub_dir[1:]) ### For linux
            except: dir_list = os.listdir(userHomeDir + sub_dir)
    if search!=None:
        for file in dir_list:
            if search in file:
                file = string.replace(file,'.lnk','')
                dir_list = file
    return dir_list

def refDir():
    reference_dir=application_path      #directory file is input as a variable under the main            
    for py2app_dir in py2app_dirs: 
        reference_dir = string.replace(reference_dir,py2app_adj,'')
    return reference_dir

def whatProgramIsThis():
    reference_dir = refDir()
    if 'AltAnalyze' in reference_dir: type = 'AltAnalyze'; database_dir = 'AltDatabase/goelite/'
    elif 'GO-Elite' in reference_dir: type = 'GO-Elite'; database_dir = 'Databases/'
    else: database_dir = 'AltDatabase/goelite/'; type = 'AltAnalyze'
    return type,database_dir

def correctGeneDatabaseDir(fn):
    try:
        proceed = 'no'
        alt_version = 'AltDatabase/'+gene_database_dir
        elite_version = 'Databases/'+gene_database_dir
        fn=string.replace(fn,'//','/'); fn=string.replace(fn,'\\','/')
        if (alt_version not in fn) and (elite_version not in fn): proceed = 'yes' ### If the user creates that contains EnsMart
        if gene_database_dir not in fn: proceed = 'yes'
        if 'EnsMart' in fn: proceed = 'no'
        if proceed == 'yes':
            fn = string.replace(fn,'Databases','Databases/'+gene_database_dir)
            if 'AltDatabase/affymetrix' not in fn and 'NoVersion' not in fn and 'AltDatabase/primer3' not in fn \
                    and 'AltDatabase/TreeView' not in fn and 'AltDatabase/kallisto' not in fn and 'AltDatabase/tools' not in fn \
                    and 'AltDatabase/subreads' not in fn:
                if 'AltDatabase' in fn:
                    fn = string.replace(fn,'AltDatabase','AltDatabase/'+gene_database_dir)
        fn = string.replace(fn,'NoVersion','') ### When the text 'NoVersion' is in a filepath, is tells the program to ignore it for adding the database version
    except Exception: null = ''
    return fn

def getCurrentGeneDatabaseVersion():
    global gene_database_dir
    try:
        filename = 'Config/version.txt'
        fn=filepath(filename)
        for line in open(fn,'r').readlines():
            gene_database_dir, previous_date = string.split(line,'\t')
    except Exception:
        import UI
        gene_database_dir='' 
        try:
            for db_version in db_versions:
                if 'EnsMart' in db_version:
                    gene_database_dir = db_version; UI.exportDBversion(db_version)
                    break
        except Exception:
            pass

    return gene_database_dir

def unique(s):
    #we need to remove duplicates from a list, unsuccessfully tried many different methods
    #so I found the below function at: http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/52560
        n = len(s)
        if n == 0: return []    
        u = {}
        try:
            for x in s: u[x] = 1
        except TypeError: del u  # move on to the next method
        else: return u.keys()
        try: t = list(s); t.sort()
        except TypeError: del t  # move on to the next method
        else:
            assert n > 0
            last = t[0]; lasti = i = 1
            while i < n:
                if t[i] != last: t[lasti] = last = t[i]; lasti += 1
                i += 1
            return t[:lasti]
        u = []
        for x in s:
            if x not in u: u.append(x)
        return u
    
def dictionary(s):
    d={}
    for i in s:
        try: d[i]=[]
        except TypeError: d[tuple(i)]=[]
    return d

def unique_db(s):
    d={}; t=[]
    for i in s:
        try: d[i]=[]
        except TypeError: d[tuple(i)]=[]
    for i in d: t.append(i)
    return t

def list(d):
    t=[]
    for i in d: t.append(i)
    return t

def exportVersionData(version,version_date,dir,force='application-path'):
    new_file = dir+'version.txt'
    new_file_default = filepath(new_file,force=force) ### can use user directory local or application local
    print new_file_default;sys.exit()
    try:
        data.write(str(version)+'\t'+str(version_date)+'\n'); data.close()
    except:
        data = export.ExportFile(new_file)
        data.write(str(version)+'\t'+str(version_date)+'\n'); data.close()
        
if __name__ == '__main__':
    #db = returnDirectoriesNoReplace('/AltDatabase',search='EnsMart')
    exportVersionData('EnsMart72','12/17/19','Config/')
    path = filepath('Config/',force=None)
    print path