#!/usr/bin/env python3
"""
   htmldoc.py - Create web pages for BIRCH documentation from birchdb database

   Synopsis: htmldoc.py

@modified: July 25, 2023
@author: Brian Fristensky and Dale Hamel
@contact: frist@cc.umanitoba.ca
"""

# Automatically converted to Python3 using 2to3. Compliant with Python 2 and 3.

import os
import re
import shutil
import sys

blib = os.environ.get("BIRCHLIB")
sys.path.append(blib)

from birchlib import Birchmod
from birchlib import Htmlutils
from birchlib import HTMLWriter

PROGRAM = "htmldoc.py: "
USAGE = "\n\t USAGE: htmldoc.py [currently takes no paramters]"
BM = Birchmod(PROGRAM, USAGE)
PROGS = []
CATDICT = {}
PROGDICT = {}
PKGDICT = {}
DOCDICT = {}
HT = Htmlutils(CATDICT, PROGDICT)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
class Parameters:
    "Wrapper class for global parameters"

    def __init__(self):
        """
          Get the location of the BIRCH home directory, BIRCHPATH
          Preferrably, we get it from the BIRCH.properties file,
          but if that isn't found, we get it from the BIRCH
          environment variable. The one catch is that since
          we don't already know the location of BIRCHPATH,
          the former will only work if the current working
          directory is install-scripts. Normally, this would
          only be used when installing or updating BIRCH
          Otherwise, the environment variable will be read.
          """
        FN = '../local/admin/BIRCH.properties'
        if  os.path.exists(FN):
            print("htmldoc.py: Reading $BIRCH from BIRCH.properties")
            self.BIRCHPATH = ""
            self.BIRCH_PLATFORM = ""
            FILE = open(FN, 'r')

            for LINE in FILE:
                TOKENS = LINE.split("=")
                if TOKENS[0] == 'BirchProps.homedir':
                    self.BIRCHPATH = TOKENS[1].strip()
                if TOKENS[0] == 'BirchProps.platform':
                    self.BIRCH_PLATFORM = TOKENS[1].strip()
            FILE.close()
        else:
            print("htmldoc.py: Reading $BIRCH and $BIRCH_PLATFORM environment variables.")
            self.BIRCHPATH = os.environ['BIRCH']

        # If BIRCH_PLATFORM is set in the environment, we want that
        # to supersede the value in BIRCH.properties
        plat = ""
        try:
            plat = os.environ['BIRCH_PLATFORM']
        except:
            pass
        if plat != "":
            self.BIRCH_PLATFORM = plat

        # Everything else depends on BIRCHPATH
        print("htmldoc.py: BIRCHPATH set to: " + self.BIRCHPATH)
        print("htmldoc.py: BIRCH_PLATFORM set to: " + self.BIRCH_PLATFORM)
        self.BIRCHWEBPATH = self.BIRCHPATH + '/public_html'
        self.BIRCHDBPATH = self.BIRCHPATH + '/public_html/birchdb'
        self.BIRCHLOCALDBPATH = self.BIRCHPATH + '/local/public_html/birchdb'
        self.BFN = "" # birchdb.ace
        self.LFN = "" # birchdb.local.ace
        self.INFILE = ""
        self.OFN = ""
        self.OUTFILE = ""
        # default prefix for http path to birch documentation
        #self.DOCPREFIX = 'file://' + self.BIRCHWEBPATH + '/doc'


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def DUMPTOACE(P):
    """
    Dump the core BIRCH and local databases to .ace files
    @param P: Instasnce of Paramters object
    @type P: Parameters
    """
    import subprocess

    os.chdir(P.BIRCHDBPATH)
    TACEDIR = P.BIRCHPATH + "/bin-" + P.BIRCH_PLATFORM

    # Call tace to dump the core birch data to .ace files:
    #         category.ace, package.ace, program.ace, file.ace
    p = subprocess.Popen(['./tbirchdb.sh', P.BIRCHPATH, P.BIRCHDBPATH, TACEDIR, 'tace.input'])
    p.wait()

    # Call tace to dump the core birch data to a .ace files
    #         category.ace, package.ace, program.ace, file.ace
    if os.path.exists(P.BIRCHLOCALDBPATH + '/database/ACEDB.wrm'):
        os.chdir(P.BIRCHLOCALDBPATH)
        p = subprocess.Popen(['./tbirchdb.sh', P.BIRCHPATH, P.BIRCHLOCALDBPATH, TACEDIR, 'tace.input'])
        p.wait()



# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def GetStr(LINE):
    """
    Read the first string delimited by double quotes
    @param LINE: The line to be cleaned up
    @type LINE: str

    Each quoted line is modified as follows:
         escape characters \\ added by ACEDB are deleted
         '>' and '<' characters are changed to '&gt;' and '&lt;' so
         they are not accidentally recognized by HTML as tag delimiters.
    """

    I = LINE.find('"')
    J = LINE.rfind('"')
    LINE = LINE[I + 1:J]
    # Get rid of \ escape characters added by ACEDB
    LINE = LINE.replace('\\', '')
    # Change > and < characters to HTML &gt; and &lt;
    LINE = LINE.replace('>', '&gt;')
    LINE = LINE.replace('<', '&lt;')
    return LINE

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def AddToList(L, NAME):
    """
    If a list contains NAME, do nothing
    If it does not exist, append it to the list
    @param L: The list to check for name
    @type L: list
    @param NAME: The name to be checked for
    @type NAME: str
    """

    if NAME in L:
        pass
    else:
        L.append(NAME)

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -



class Category:

    def __init__(self):
        """
          Initializes arguments:
                name=""
                program=[]
                pkg=[]
          """
        self.name = ""
        self.program = []
        self.pkg = []



# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def ReadCategory(FN, CATS):
    """
    Read category.ace into a list of category objects
    @param FN: THe name of the file to be read
    @type FN: str
    @param CATS: The categories object to be read into
    @type CATS: list
    """


    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    def AssignCategory(NAME):
        """
        "If a category called NAME already exists, return a pointer"
        "If it does not exist, create a new category object and return a pointer"
        @param NAME: The name of the category to check for
        @type NAME: str
        """

        if NAME in CATDICT:
            C = CATDICT[NAME]
        else:
            C = Category()
            CATS.append(C)
            C.name = NAME
        return C

    if os.path.exists(FN):
        FILE = open(FN, 'r')


        for LINE in FILE:
            if re.match('Category\\s:\\s".+"', LINE):
                C = AssignCategory(GetStr(LINE))
            elif re.match('Program\\s+".+"', LINE):
                TOKENS = HT.tokenize(LINE)
                AddToList(C.program, TOKENS[1])
            elif re.match('Package\\s+".+"', LINE):
                TOKENS = HT.tokenize(LINE)
                AddToList(C.pkg, TOKENS[1])


        FILE.close()
        #print "CATDICT: "
        #print CATDICT



# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
class Package:

    def __init__(self):
        """
          Initializes arguments:
                name=""
                description=""
                category=[]
                doc=[]
                program=[]
                data=[]
                platform=[]
                installation=[]
          """
        self.name = ""
        self.description = ""
        self.category = []
        self.doc = []
        self.program = []
        self.data = []
        self.platform = []
        self.installation = []

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def ReadPackage(FN, PKGS):
    """
    Read package.ace into a list of Package objects
    @param FN: The name of the file to be read in
    @type FN: str
    @param PKGS: The list of package objects to be read into
    @type PKGS:list
    """


    # -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -
    def AssignPackage(NAME):
        """
        If a package called NAME already exists, return a pointer
        If it does not exist, create a new package object and return a pointer
        @param NAME:The name to attempt to assign
        @type NAME:str
        """

        if NAME in PKGDICT:
            PK = PKGDICT[NAME]
        else:
            PK = Package()
            PKGS.append(PK)
            PK.name = NAME
        return PK

    if os.path.exists(FN):
        FILE = open(FN, 'r')
        for LINE in FILE:
            if re.match('Package\\s:\\s".+"', LINE):
                PK = AssignPackage(GetStr(LINE))
            elif re.match('Description\\s+".+"', LINE):
                PK.description = GetStr(LINE)
            elif re.match('Category\\s+".+"', LINE):
                TOKENS = HT.tokenize(LINE)
                AddToList(PK.category, TOKENS[1])
            elif re.match('Documentation\\s+".+"', LINE):
                TOKENS = HT.tokenize(LINE)
                AddToList(PK.doc, TOKENS[1])
            elif re.match('Program\\s+".+"', LINE):
                TOKENS = HT.tokenize(LINE)
                AddToList(PK.program, TOKENS[1])
            elif re.match('Data\\s+".+"', LINE):
                TOKENS = HT.tokenize(LINE)
                AddToList(PK.data, TOKENS[1])
            elif re.match('Platform\\s+".+"', LINE):
                TOKENS = HT.tokenize(LINE)
                AddToList(PK.platform, TOKENS[1])
            elif re.match('BIRCH', LINE):
                AddToList(PK.installation, "BIRCH")
            elif re.match('local', LINE):
                AddToList(PK.installation, "local")

        FILE.close()

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
class Program:

    def __init__(self):
        """
          Initializes arguments:
                name=""
                description=""
                category=[]
                interface=[]
                package=""
                doc=[]
                data=[]
                sampleinput=[]
                sampleoutput=[]
                platform=[]
          """
        self.name = ""
        self.description = ""
        self.category = []
        self.interface = []
        self.package = ""
        self.doc = []
        self.data = []
        self.sampleinput = []
        self.sampleoutput = []
        self.platform = []

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def ReadProgram(FN, PROGS):
    """
    Read program.ace into a list of Program objects
    @param FN: The name of the file to be read in
    @type FN: str
    @param PROGS: The list of Program objects to read the file into
    @type PROGS: list
    """


    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    def AssignProgram(NAME):
        """
        If a program called NAME already exists, return a pointer
        If it does not exist, create a new program object and return a pointer
        @param NAME: The name to attempt to assign
        @type NAME: str
        """

        if NAME in PROGDICT:
            PR = PROGDICT[NAME]
        else:
            PR = Program()
            PROGS.append(PR)
            PR.name = NAME
        return PR

    if os.path.exists(FN):
        FILE = open(FN, 'r')
        for LINE in FILE:
            if re.match('Program\\s:\\s".+"', LINE):
                PR = AssignProgram(GetStr(LINE))
            elif re.match('Description\\s+".+"', LINE):
                PR.description = GetStr(LINE)
            elif re.match('Category\\s+".+"', LINE):
                TOKENS = HT.tokenize(LINE)
                AddToList(PR.category, TOKENS[1])

            # In ACeDB .ace files, constants the Interface field
            # does not actually contain the tag 'Interface'
            # It simply contains the values of the field.
            elif re.match('command\\s+".+"', LINE):
                PR.interface.append(['command', GetStr(LINE)])
            elif re.match('interactive\\s+".+"', LINE):
                PR.interface.append(['interactive', GetStr(LINE)])
            elif re.match('gui\\s+".+"', LINE):
                PR.interface.append(['gui', GetStr(LINE)])
            # underscore characters had to be added to represent birch in birchdb/wspec/wspec.wrm
            # To eliminate confusion for those reading the documentation, we
            # delete the underscores when adding 'birch' to the program
            # dictionary
            elif re.match('_birch_\\s+".+"', LINE):
                LINE.replace('_birch_','birch')
                PR.interface.append(['birch', GetStr(LINE)])
            elif re.match('birchadmin\\s+".+"', LINE):
                PR.interface.append(['birchadmin', GetStr(LINE)])
            elif re.match('bldna\\s+".+"', LINE):
                PR.interface.append(['bldna', GetStr(LINE)])
            elif re.match('blnalign\\s+".+"', LINE):
                PR.interface.append(['blnalign', GetStr(LINE)])
            elif re.match('blprotein\\s+".+"', LINE):
                PR.interface.append(['blprotein', GetStr(LINE)])
            elif re.match('blpalign\\s+".+"', LINE):
                PR.interface.append(['blpalign', GetStr(LINE)])
            elif re.match('bldata\\s+".+"', LINE):
                PR.interface.append(['bldata', GetStr(LINE)])
            elif re.match('blmarker\\s+".+"', LINE):
                PR.interface.append(['blmarker', GetStr(LINE)])
            elif re.match('blnfetch\\s+".+"', LINE):
                PR.interface.append(['blnfetch', GetStr(LINE)])
            elif re.match('blpfetch\\s+".+"', LINE):
                PR.interface.append(['blpfetch', GetStr(LINE)])
            elif re.match('blreads\\s+".+"', LINE):
                PR.interface.append(['blreads', GetStr(LINE)])
            elif re.match('blncbi\\s+".+"', LINE):
                PR.interface.append(['blncbi', GetStr(LINE)])
            elif re.match('bltable\\s+".+"', LINE):
                PR.interface.append(['bltable', GetStr(LINE)])
            elif re.match('bltree\\s+".+"', LINE):
                PR.interface.append(['bltree', GetStr(LINE)])
            elif re.match('Package\\s+".+"', LINE):
                TOKENS = HT.tokenize(LINE)
                PR.package = TOKENS[1]
            elif re.match('Documentation\\s+".+"', LINE):
                TOKENS = HT.tokenize(LINE)
                AddToList(PR.doc, TOKENS[1])
            elif re.match('Data\\s+".+"', LINE):
                TOKENS = HT.tokenize(LINE)
                AddToList(PR.data, TOKENS[1])
            elif re.match('Sample_input\\s+".+"', LINE):
                TOKENS = HT.tokenize(LINE)
                AddToList(PR.sampleinput, TOKENS[1])
            elif re.match('Sample_output\\s+".+"', LINE):
                TOKENS = HT.tokenize(LINE)
                AddToList(PR.sampleoutput, TOKENS[1])
            elif re.match('Platform\\s+".+"', LINE):
                TOKENS = HT.tokenize(LINE)
                AddToList(PR.platform, TOKENS[1])

        FILE.close()

def write_category_page(catfn):
    """
            FIXME
            @param catfn:
            @type catfn:
            """
    "write html page listing program categories."

# -   -   -   -   -   -   -   -   -   -   -
    def writecat(c):
        """
         FIXME
         @param c:
         @type c:
         """
        "write a page for a given category"

        catfn = c.name + '.html'
        catpagefile = open(catfn, 'w')
        h = HTMLWriter ()
        h.start_page(catpagefile, 'category: ' + c.name)
        h.start(catpagefile, 'hr', '')
        h.start(catpagefile, 'h1', '')
        catpagefile.write('programs:')
        h.end(catpagefile, 'h1')
        h.start(catpagefile, 'ul', '')
        #c.program.sort(key=HT.cmp_to_key(lambda x, y: cmp(x.lower(), y.lower())))
        #c.program.sort(key=lambda x: x.lower())
        c.program.sort(key=lambda name: name.lower())
        for pname in c.program:
            #print 'pname: ' + pname
            h.start(catpagefile, 'li', '')
            url = '../program/' + pname + '.html'
            #print("Progdict length:"+str(len(PROGDICT)))
            # The try/except clause is here because of a so-far unsolved KeyError problem.
            # See BIRCH mozilla bug 1141
            # I think this is solved now, but we'll keep this code for the time being.
            try:
                text = pname + ' - ' + PROGDICT[pname].description + '\n'
                h.link(catpagefile, url, '', text)
            except KeyError :
                print('In writecat: KeyError: ' + pname)
                h.link(catpagefile, '', '', 'KeyError: ' + pname)
        h.end(catpagefile, 'li')
        h.end(catpagefile, 'ul')
        h.end_page(catpagefile)
        catpagefile.close()
        os.chmod(catfn, 0o664)


    catfile = open(catfn, 'w')
    h = HTMLWriter ()
    h.start_page(catfile, 'programs by category')
    h.start(catfile, 'hr', '')
    h.start(catfile, 'br', '')

    # for each category, write an html page containing
    # a list of programs in that category
    h.start(catfile, 'ul', '')
    catlist = list(CATDICT.keys())
    #catlist.sort(key=HT.cmp_to_key(lambda x, y: cmp(x.lower(), y.lower())))
    #catlist.sort(key=lambda x: x.lower())
    catlist.sort(key=lambda name: name.lower())
    for catkey in catlist:
        c = CATDICT[catkey]
        writecat(c)
        h.start(catfile, 'li', '')
        url = c.name + '.html'
        text = c.name + '\n'
        h.link(catfile, url, '', text)
        h.end(catfile, 'li')
    h.end(catfile, 'ul')
    h.end_page(catfile)
    catfile.close()
    os.chmod(catfn, 0o664)

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
class File:

    def __init__(self):
        """
          Initializes arguments:
                name=""
                description=""
                command='\"$ACE_FILE_LAUNCHER\" '
                path=""
          """
        self.name = ""
        self.description = ""
        self.command = '\"$ACE_FILE_LAUNCHER\" '
        self.path = ""

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def ReadDocFiles(FN, DOCFILES):
    """
    Read file.ace into a list of file objects
    @param FN: The name of the file to be read in
    @type FN: str
    @param DOCFILES: the list of file objects to be read into
    @type DOCFILES: list
    """


    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    def AssignFile(NAME):
        """
        If a file called NAME already exists, return a pointer
If it does not exist, create a new file object and return a pointer
        @param NAME: The name to attempt to assign
        @type NAME: str
        """

        if NAME in DOCDICT:
            FL = DOCDICT[NAME]
        else:
            FL = File()
            DOCFILES.append(FL)
            FL.name = NAME
        return FL

    if os.path.exists(FN):
        FILE = open(FN, 'r')
        for LINE in FILE:
            if re.match('File\\s:\\s".+"', LINE):
                FL = AssignFile(GetStr(LINE))
            elif re.match('Description\\s+".+"', LINE):
                FL.description = GetStr(LINE)
            elif re.match('Pick_me_to_call\\s+".+"', LINE):
                TOKENS = HT.tokenize(LINE)
                FL.path = (TOKENS[2])


        FILE.close()

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -



def FreshDir(DIRNAME):
    """
    Delete an existing directory and create an empty directory
    with the same name.
    @param DIRNAME: The name of the directory to be refreshed
    @type DIRNAME: str
    """

    if os.path.isdir(DIRNAME):
        shutil.rmtree(DIRNAME)
    os.mkdir(DIRNAME)
    os.chmod(DIRNAME, 0o775)

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

def WritePackagePage(PKGFN, P):
    """
    Write HTML page listing program packages.
    @param PKGFN: The name of the html page to be created
    @type PKGFN: str
    @param P: An instance of the Paramaters object
    @type P: Paramters object
    """


    # -   -   -   -   -   -   -   -   -   -   -
    def WritePkg(PK):
        """
        Write a page for a given package
        @param PK: The name of the package
        @type PK: str
        """

        PKGFN = PK.name + '.html'
        PKGPAGEFILE = open(PKGFN, 'w')
        H = HTMLWriter ()
        H.start_page(PKGPAGEFILE, 'Package: ' + PK.name)

    # Program information is in a table.
#       ATTRIBUTES = ' style="border: 1px solid";'
        ATTRIBUTES = ' style="font-family: helvetica,arial,sans-serif;"'
        H.start(PKGPAGEFILE, 'table', ATTRIBUTES)
        ATTRIBUTES = ''
        H.start(PKGPAGEFILE, 'tr', ATTRIBUTES)

    # Title row
        ATTRIBUTES = ''
        H.start(PKGPAGEFILE, 'tr', ATTRIBUTES)
        ATTRIBUTES = ' colspan="2" rowspan="1" style= "background-color: rgb(51, 255, 51);"'
        H.start(PKGPAGEFILE, 'td', ATTRIBUTES)
        ATTRIBUTES = ''
        H.start(PKGPAGEFILE, 'big', ATTRIBUTES)
        PKGPAGEFILE.write(PK.name + ' - ' + PK.description)
        H.end(PKGPAGEFILE, 'big')
        H.end(PKGPAGEFILE, 'td')
        H.end(PKGPAGEFILE, 'tr')


    # Documentation rows
        DocRows(PKGPAGEFILE, H, 'Documentation', PK.doc, DOCDICT, P)

    # Datafile rows
        DocRows(PKGPAGEFILE, H, 'Data', PK.data, DOCDICT, P)


    # Platform row
        ATTRIBUTES = ''
        H.start(PKGPAGEFILE, 'tr', ATTRIBUTES)
        ATTRIBUTES = ' colspan="2" rowspan="1" style= "background-color: rgb(204, 204, 204);"'
        H.start(PKGPAGEFILE, 'td', ATTRIBUTES)
        ATTRIBUTES = ''
        H.start(PKGPAGEFILE, 'big', ATTRIBUTES)
        URL = '../Doc_definitions.html#Platforms'
        TEXT =  'Platforms'
        ATTRIBUTES = 'target="FrameWindow"'
        H.link(PKGPAGEFILE, URL, ATTRIBUTES, TEXT)
        PKGPAGEFILE.write(': ')

        H.end(PKGPAGEFILE, 'big')
        I = 0
        for PLAT in PK.platform:
            PKGPAGEFILE.write(PLAT)
            I = I + 1
            if I < len(PK.platform):
                PKGPAGEFILE.write(', ')
        H.end(PKGPAGEFILE, 'td')
        H.end(PKGPAGEFILE, 'tr')

                # Installation row
        ATTRIBUTES = ''
        H.start(PKGPAGEFILE, 'tr', ATTRIBUTES)
        ATTRIBUTES = ' colspan="2" rowspan="1" style= "background-color: rgb(204, 204, 204);"'
        H.start(PKGPAGEFILE, 'td', ATTRIBUTES)
        ATTRIBUTES = ''
        H.start(PKGPAGEFILE, 'big', ATTRIBUTES)
        URL = '../Doc_definitions.html#Installation'
        TEXT =  'Installation'
        ATTRIBUTES = 'target="FrameWindow"'
        H.link(PKGPAGEFILE, URL, ATTRIBUTES, TEXT)
        PKGPAGEFILE.write(': ')

        H.end(PKGPAGEFILE, 'big')
        I = 0
        for INST in PK.installation:
            PKGPAGEFILE.write(INST)
            I = I + 1
            if I < len(PK.installation):
                PKGPAGEFILE.write(', ')
        H.end(PKGPAGEFILE, 'td')
        H.end(PKGPAGEFILE, 'tr')

        # Program rows
        ATTRIBUTES = ''
        H.start(PKGPAGEFILE, 'tr', ATTRIBUTES)
        ATTRIBUTES = ' colspan="2" rowspan="1" style= "background-color: rgb(204, 204, 204);"'
        H.start(PKGPAGEFILE, 'td', ATTRIBUTES)
        ATTRIBUTES = ''
        H.start(PKGPAGEFILE, 'big', ATTRIBUTES)
        URL = '../Doc_definitions.html#Programs'
        TEXT =  'Programs'
        ATTRIBUTES = 'target="FrameWindow"'
        H.link(PKGPAGEFILE, URL, ATTRIBUTES, TEXT)
        PKGPAGEFILE.write(': ')

        H.end(PKGPAGEFILE, 'big')
        H.end(PKGPAGEFILE, 'td')
        H.end(PKGPAGEFILE, 'tr')

        ATTRIBUTES = ''
        H.start(PKGPAGEFILE, 'tr', ATTRIBUTES)
        ATTRIBUTES = ' colspan="2" rowspan="1" style= "background-color: rgb(255, 255, 255);"'
        H.start(PKGPAGEFILE, 'td', ATTRIBUTES)
        H.start(PKGPAGEFILE, 'ul', '')
        #PK.program.sort(key=HT.cmp_to_key(lambda x, y: cmp(x.lower(), y.lower())))
        #PK.program.sort(key=lambda x: x.lower())
        PK.program.sort(key=lambda name: name.lower())
        for PNAME in PK.program:
            H.start(PKGPAGEFILE, 'li', '')
            URL = '../program/' + PNAME + '.html'
            TEXT = PNAME + ' - ' + PROGDICT[PNAME].description + '\n'
            H.link(PKGPAGEFILE, URL, '', TEXT)
            H.end(PKGPAGEFILE, 'li')
        H.end(PKGPAGEFILE, 'ul')
        H.end(PKGPAGEFILE, 'td')
        H.end(PKGPAGEFILE, 'tr')
        H.end(PKGPAGEFILE, 'table')

        H.end_page(PKGPAGEFILE)
        PKGPAGEFILE.close()
        os.chmod(PKGFN, 0o664)


    PKGFILE = open(PKGFN, 'w')
    H = HTMLWriter ()
    H.start_page(PKGFILE, 'Programs by Package')
    H.start(PKGFILE, 'hr', '')
    H.start(PKGFILE, 'br', '')

    # For each package, write an HTML page containing
    # a list of programs in that package
    H.start(PKGFILE, 'ul', '')
    PKGLIST = list(PKGDICT.keys())

    #PKGLIST.sort(key=HT.cmp_to_key(lambda x, y: cmp(x.lower(), y.lower())))
    #PKGLIST.sort(key=lambda x: x.lower())
    PKGLIST.sort(key=lambda name: name.lower())
    for PKGKEY in PKGLIST:
        PK = PKGDICT[PKGKEY]
        WritePkg(PK)
        H.start(PKGFILE, 'li', '')
        URL = PK.name + '.html'
        TEXT = PK.name + ' - ' + PKGDICT[PK.name].description + '\n'
        H.link(PKGFILE, URL, '', TEXT)
        H.end(PKGFILE, 'li')

    H.end(PKGFILE, 'ul')
    H.end_page(PKGFILE)
    PKGFILE.close()
    os.chmod(PKGFN, 0o664)


# -   -   -   -   -   -   -   -   -   -   -
def DocRows(OUTFILE, H, HEADING, FILELIST, D, P):
    """
    Write rows for documentation lines:
    Documentation, Data, Sample input, Sample output

    @param OUTFILE: The name of the output file
    @type OUTFILE: str
    @param H: An instance of HTMLWriter
    @type H: HTMLWriter
    @param HEADING: The heading to place in each row
    @type HEADING: str
    @param FILELIST: The list of files to be documented
    @type FILELIST: list
    @param D: The dictionary to use for documentation
    @type D: dictionary
    @param P: An instance of the Parameters class
    @type P: Parameters object
    """


    # Documentation rows - title row is 1 column, other rows are 2 columns
    ATTRIBUTES = ''
    H.start(OUTFILE, 'tr', ATTRIBUTES)
    ATTRIBUTES = ' colspan="2" rowspan="1" style= "background-color: rgb(204, 204, 204);"'
    H.start(OUTFILE, 'td', ATTRIBUTES)
    ATTRIBUTES = ''
    H.start(OUTFILE, 'big', ATTRIBUTES)
    URL = '../Doc_definitions.html#' + HEADING.replace(' ', '_')
    TEXT = HEADING
    ATTRIBUTES = 'target="FrameWindow"'
    H.link(OUTFILE, URL, ATTRIBUTES, TEXT)
    H.end(OUTFILE, 'big')
    H.end(OUTFILE, 'td')
    H.end(OUTFILE, 'tr')


    for DOCNAME in FILELIST:
        ATTRIBUTES = ''
        if DOCNAME in D:
            DOCUMENT = D[DOCNAME]
            if len(DOCUMENT.path) > 0:
                H.start(OUTFILE, 'tr', ATTRIBUTES)
                ATTRIBUTES = ' border="0" colspan="1" rowspan="1" style= "background-color: rgb(255, 255, 255);"'
                H.start(OUTFILE, 'td', ATTRIBUTES)
                DOCTYPE = DOCUMENT.description
                H.indent_text(OUTFILE, DOCTYPE)
                H.end(OUTFILE, 'td')
                ATTRIBUTES = ' border="0" colspan="1" rowspan="1" style= "background-color: rgb(255, 255, 255);"'
                H.start(OUTFILE, 'td', ATTRIBUTES)
                URL = HT.name_to_url(DOCUMENT.path, P.DOCPREFIX)
                TEXT = DOCUMENT.path
                H.link(OUTFILE, URL, '', TEXT)
                H.end(OUTFILE, 'td')
                H.end(OUTFILE, 'tr')

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def WriteProgramPage(PROGFN, P):
    """
    Write HTML page listing programs in alphabetical order.
    @param PROGFN: The basename of the page to be written
    @type PROGFN: str
    @param P: An instance of the Parameters class
    @type P: Paramters object
    """


    # -   -   -   -   -   -   -   -   -   -   -
    def WriteProg(PR, P):
        """
        Write a page for a given program
        @param PR: The name of the program to write the page for
        @type PR: str
        @param P: An instance of the Parameters class
        @type P: Parameters object
        """


        PROGFN = PR.name + '.html'
        PROGPAGEFILE = open(PROGFN, 'w')
        H = HTMLWriter ()
        H.start_page(PROGPAGEFILE, PR.name)

        # Program information is in a table.
#               ATTRIBUTES = ' style="border: 1px solid";'
        ATTRIBUTES = ' style="font-family: helvetica,arial,sans-serif;"'
        H.start(PROGPAGEFILE, 'table', ATTRIBUTES)
        ATTRIBUTES = ''
        H.start(PROGPAGEFILE, 'tr', ATTRIBUTES)

        # Title row
        ATTRIBUTES = ''
        H.start(PROGPAGEFILE, 'tr', ATTRIBUTES)
        ATTRIBUTES = ' colspan="2" rowspan="1" style= "background-color: rgb(51, 255, 51);"'
        H.start(PROGPAGEFILE, 'td', ATTRIBUTES)
        ATTRIBUTES = ''
        H.start(PROGPAGEFILE, 'big', ATTRIBUTES)
        PROGPAGEFILE.write(PR.name + ' - ' + PR.description)
        H.end(PROGPAGEFILE, 'big')
        H.end(PROGPAGEFILE, 'td')
        H.end(PROGPAGEFILE, 'tr')

        # Command rows - title row is 1 column, other rows are 2 columns
        ATTRIBUTES = ''
        H.start(PROGPAGEFILE, 'tr', ATTRIBUTES)
        ATTRIBUTES = ' colspan="2" rowspan="1" style= "background-color: rgb(204, 204, 204);"'
        H.start(PROGPAGEFILE, 'td', ATTRIBUTES)
        ATTRIBUTES = ''
        H.start(PROGPAGEFILE, 'big', ATTRIBUTES)
        URL = '../Doc_definitions.html#Launching'
        TEXT =  'Launching the program'
        ATTRIBUTES = 'target="FrameWindow"'
        H.link(PROGPAGEFILE, URL, ATTRIBUTES, TEXT)

        H.end(PROGPAGEFILE, 'big')
        H.end(PROGPAGEFILE, 'td')
        H.end(PROGPAGEFILE, 'tr')



        for COMMAND in PR.interface:
            ATTRIBUTES = ''
            #print("Trying to write: "+PROGPAGEFILE.name+" file is closed="+str(PROGPAGEFILE.closed))
            H.start(PROGPAGEFILE, 'tr', ATTRIBUTES)
            ATTRIBUTES = ' border="0" colspan="1" rowspan="1" style= "background-color: rgb(255, 255, 255);"'
            H.start(PROGPAGEFILE, 'td', ATTRIBUTES)
            H.indent_text(PROGPAGEFILE, COMMAND[0])
            H.end(PROGPAGEFILE, 'td')
            ATTRIBUTES = ' border="0" colspan="1" rowspan="1" style= "background-color: rgb(255, 255, 255);"'
            H.start(PROGPAGEFILE, 'td', ATTRIBUTES)
            ATTRIBUTES = ' face="Courier New,Courier"'
            H.start(PROGPAGEFILE, 'font', ATTRIBUTES)
            PROGPAGEFILE.write(COMMAND[1])
            H.end(PROGPAGEFILE, 'font')
            H.end(PROGPAGEFILE, 'td')
            H.end(PROGPAGEFILE, 'tr')


        # Documentation rows
        DocRows(PROGPAGEFILE, H, 'Documentation', PR.doc, DOCDICT, P)

        # Datafile rows
        DocRows(PROGPAGEFILE, H, 'Data', PR.data, DOCDICT, P)

        # Sample input rows
        DocRows(PROGPAGEFILE, H, 'Sample input', PR.sampleinput, DOCDICT, P)

        # Sample output rows
        DocRows(PROGPAGEFILE, H, 'Sample output', PR.sampleoutput, DOCDICT, P)


        # Package row
        ATTRIBUTES = ''
        H.start(PROGPAGEFILE, 'tr', ATTRIBUTES)
        ATTRIBUTES = ' colspan="2" rowspan="1" style= "background-color: rgb(204, 204, 204);"'
        H.start(PROGPAGEFILE, 'td', ATTRIBUTES)
        ATTRIBUTES = ''
        H.start(PROGPAGEFILE, 'big', ATTRIBUTES)
        URL = '../Doc_definitions.html#Package'
        TEXT =  'Package'
        ATTRIBUTES = 'target="FrameWindow"'
        H.link(PROGPAGEFILE, URL, ATTRIBUTES, TEXT)
        PROGPAGEFILE.write(': ')
        H.end(PROGPAGEFILE, 'big')
        URL = '../package/' + PR.package + '.html'
        TEXT = PR.package
        H.link(PROGPAGEFILE, URL, '', TEXT)
        H.end(PROGPAGEFILE, 'td')
        H.end(PROGPAGEFILE, 'tr')

        # Platform row
        ATTRIBUTES = ''
        H.start(PROGPAGEFILE, 'tr', ATTRIBUTES)
        ATTRIBUTES = ' colspan="2" rowspan="1" style= "background-color: rgb(204, 204, 204);"'
        H.start(PROGPAGEFILE, 'td', ATTRIBUTES)
        ATTRIBUTES = ''
        H.start(PROGPAGEFILE, 'big', ATTRIBUTES)
        URL = '../Doc_definitions.html#Platforms'
        TEXT =  'Platforms'
        ATTRIBUTES = 'target="FrameWindow"'
        H.link(PROGPAGEFILE, URL, ATTRIBUTES, TEXT)
        PROGPAGEFILE.write(': ')
        H.end(PROGPAGEFILE, 'big')
        I = 0
        for PLAT in PR.platform:
            PROGPAGEFILE.write(PLAT)
            I = I + 1
            if I < len(PR.platform):
                PROGPAGEFILE.write(', ')
        H.end(PROGPAGEFILE, 'td')
        H.end(PROGPAGEFILE, 'tr')

        H.end(PROGPAGEFILE, 'table')
        H.end_page(PROGPAGEFILE)
        PROGPAGEFILE.close()
        os.chmod(PROGFN, 0o664)


    PROGFILE = open(PROGFN, 'w')
    h = HTMLWriter ()
    h.start_page(PROGFILE, 'Program Index')
    h.start(PROGFILE, 'hr', '')
    h.start(PROGFILE, 'ul', '')

    # For each program, write an HTML page containing
    # all information for that program
    PROGLIST = list(PROGDICT.keys())
    #PROGLIST.sort(key=HT.cmp_to_key(lambda x, y: cmp(x.lower(), y.lower())))
    #PROGLIST.sort(key=lambda x: x.lower())
    PROGLIST.sort(key=lambda name: name.lower())
    for PROGKEY in PROGLIST:
        PR = PROGDICT[PROGKEY]
        WriteProg(PR, P)
        h.start(PROGFILE, 'li', '')
        URL = PR.name + '.html'
        TEXT = PR.name + ' - ' + PROGDICT[PR.name].description + '\n'
        h.link(PROGFILE, URL, '', TEXT)
        h.end(PROGFILE, 'li')

    h.end(PROGFILE, 'ul')
    h.end_page(PROGFILE)
    PROGFILE.close()
    os.chmod(PROGFN, 0o664)


#======================== MAIN PROCEDURE ==========================

def main():
    """
    Called when not in documentation mode.
    """
    print ("***** obtaining parameters")
    P = Parameters()
    # Read in the prefix to begin URLs that will be used as links
    # to documentation files.
    print ("***** reading BIRCH.properties")
    P.DOCPREFIX = BM.GetBIRCHProperties(P.BIRCHPATH,"birchURL")
    # When birchprops creates BIRCH.properties, some special characters
    # are escaped with a left slash. We need to eliminate these left slashes
    # which would otherwise cause web browsers to incorrectly interpret URLs
    P.DOCPREFIX=P.DOCPREFIX.replace("\\","");
    #P.DOCPREFIX = BM.GetBIRCHProperties(P.BIRCHPATH,"birchHomeURL")
    #P.DOCPREFIX=""
    print(('P.DOCPREFIX: ' + P.DOCPREFIX))
    if P.DOCPREFIX != "" :
        OKAY = True
    else :
        OKAY = False
    # Use tace to generate birchdb.ace and birchdb.local.ace, which contain
    # a complete dump of both the core birch documentation objects and those
    # from the local implementation.

    print ("***** dumping to ACE")
    DUMPTOACE(P)

    # Read in birchdb.ace, and then birchdb.local.ace. If an object is present
    # in both files, the object from birchdb.local.ace replaces the object
    # from birchdb.ace. Thus, local versions of documentation can replace
    # documents from the birch core.

    # Read Categories
    CATS = []

    print ("***** reading categories")
    os.chdir(P.BIRCHDBPATH)
    ReadCategory('category.ace', CATS)
    print(("Categories:"+str(len(CATS))))
    for C in CATS:
        CATDICT[C.name] = C
    if os.path.exists(P.BIRCHLOCALDBPATH):
        os.chdir(P.BIRCHLOCALDBPATH)
        ReadCategory('category.ace', CATS)
        for C in CATS:
            CATDICT[C.name] = C
    print('CATDICT size: ' + str(len(CATDICT)))

    # Read Packages
    PKGS = []

    print ("***** reading packages")
    os.chdir(P.BIRCHDBPATH)
    ReadPackage('package.ace', PKGS)
    print(("Packages:"+str(len(PKGS))))
    for PK in PKGS:
        PKGDICT[PK.name] = PK
    if os.path.exists(P.BIRCHLOCALDBPATH):
        os.chdir(P.BIRCHLOCALDBPATH)
        ReadPackage('package.ace', PKGS)
        for PK in PKGS:
            PKGDICT[PK.name] = PK
    print('PKGDICT size: ' + str(len(PKGDICT)))

    # Read programs

    print ("***** reading programs")
    os.chdir(P.BIRCHDBPATH)
    ReadProgram('program.ace', PROGS)
    print(("Progs:"+str(len(PROGS))))
    for PR in PROGS:
        PROGDICT[PR.name] = PR
        #print("Read in program:"+str(PR))
    if os.path.exists(P.BIRCHLOCALDBPATH):
        os.chdir(P.BIRCHLOCALDBPATH)
        ReadProgram('program.ace', PROGS)
        for PR in PROGS:
            PROGDICT[PR.name] = PR

    print('PROGDICT size: ' + str(len(PROGDICT)))


    # Read documentation file names
    DOCFILES = []

    print ("***** reading documentation filenames")
    os.chdir(P.BIRCHDBPATH)
    ReadDocFiles('file.ace', DOCFILES)
    for FL in DOCFILES:
        DOCDICT[FL.name] = FL
    if os.path.exists(P.BIRCHLOCALDBPATH):
        os.chdir(P.BIRCHLOCALDBPATH)
        ReadDocFiles('file.ace', DOCFILES)
        for FL in DOCFILES:
            DOCDICT[FL.name] = FL




    # Remove existing directories for category, program and package,
    # and create new empty directories
    # This ensures that old files that are no longer needed (such
    # as files describing programs or packages that have been removed)
    # do not clutter up the directories.
    print ("***** freshdir")
    os.chdir(P.BIRCHPATH + '/public_html/birchdoc')
    FreshDir('category')
    FreshDir('package')
    FreshDir('program')

    #os.chdir(P.BIRCHPATH + '/install-scripts')
    if OKAY:

        print ("***** read OK *****")
        # - - - - - - - - - -  Output to the public_html/birchdb directory - - - - - -

        # For each category write a category page in HTML

        print ("***** writing category pages")
        os.chdir('category')
        CATFN = 'category.html'
        write_category_page(CATFN)

        # For each all programs write an HTML page with an alphabetical list of programs
        print ("***** writing program pages")
        os.chdir('../program')
        PROGFN = 'program.html'
        WriteProgramPage(PROGFN, P)

        # For each package, write a package page in HTML
            # For each category write a category page in HTML
        print ("***** writing package pages")
        os.chdir('../package')
        PKGFN = 'package.html'
        WritePackagePage(PKGFN, P)

if __name__=="__main__":
    if (BM.documentor() or "-test" in sys.argv):
        pass
    else:
        main()
        BM.exit_success()