def resolve_conflicts(fpath, strat, force=False, verbose=True):
"""
Parses merge conflits and takes either version
"""
import utool as ut
import re
top_pat = re.escape('<' * 7)
mid_pat = re.escape('=' * 7)
bot_pat = re.escape('>' * 7)
flags = re.MULTILINE | re.DOTALL
# Pattern to remove the top part
theirs_pat1 = re.compile('^%s.*?%s.*?$\n' % (top_pat, mid_pat), flags=flags)
theirs_pat2 = re.compile('^%s.*?$\n' % (bot_pat), flags=flags)
# Pattern to remove the bottom part
ours_pat1 = re.compile('^%s.*?%s.*?$\n' % (mid_pat, bot_pat), flags=flags)
ours_pat2 = re.compile('^%s.*?$\n' % (top_pat), flags=flags)
strat_pats = {
'theirs': [theirs_pat1, theirs_pat2],
'ours': [ours_pat1, ours_pat2],
}
text_in = ut.readfrom(fpath)
text_out = text_in
strat = 'ours'
strat = 'theirs'
for pat in strat_pats[strat]:
text_out = pat.sub('', text_out)
if verbose:
ut.print_difftext(ut.difftext(text_in, text_out, num_context_lines=3))
if force:
ut.writeto(fpath, text_out)
def get_bibtex_dict(bib_fpath):
r"""
Args:
bib_fpath (str):
Returns:
dict: bibtex_dict
CommandLine:
python -m utool.util_latex --test-get_bibtex_dict
pip install bibtexparser
Example:
>>> # DISABLE_DOCTEST
>>> from utool.util_latex import * # NOQA
>>> import utool as ut
>>> bib_fpath = ut.truepath('~/latex/crall-candidacy-2015/My_Library_clean.bib')
>>> bibtex_dict = get_bibtex_dict(bib_fpath)
>>> result = ('bibtex_dict = %s' % (str(bibtex_dict),))
>>> print(result)
"""
import bibtexparser
import utool as ut
bibtex_str = ut.readfrom(bib_fpath, verbose=False)
bib_database = bibtexparser.loads(bibtex_str)
bibtex_dict = bib_database.get_entry_dict()
return bibtex_dict
def get_bibtex_dict(bib_fpath):
r"""
Args:
bib_fpath (str):
Returns:
dict: bibtex_dict
CommandLine:
python -m utool.util_latex --test-get_bibtex_dict
pip install bibtexparser
Example:
>>> # DISABLE_DOCTEST
>>> from utool.util_latex import * # NOQA
>>> import utool as ut
>>> bib_fpath = ut.truepath('~/latex/crall-candidacy-2015/My_Library_clean.bib')
>>> bibtex_dict = get_bibtex_dict(bib_fpath)
>>> result = ('bibtex_dict = %s' % (str(bibtex_dict),))
>>> print(result)
"""
import bibtexparser
import utool as ut
bibtex_str = ut.readfrom(bib_fpath, verbose=False)
bib_database = bibtexparser.loads(bibtex_str)
bibtex_dict = bib_database.get_entry_dict()
return bibtex_dict
def outline():
"""
./texfix.py --fpaths chapter4-application.tex --outline --asmarkdown --numlines=999 -w --ignoreinputstartswith=def,Crall,header,colordef,figdef
"""
fpaths = testdata_fpaths()
print('fpaths = %r' % (fpaths, ))
for fpath in fpaths:
text = ut.readfrom(fpath)
root = latex_parser.LatexDocPart.parse_text(text, debug=None)
# HACK
new_text = '\n'.join(root.reformat_blocks(debug=None))
# remove trailing spaces
new_text = re.sub(' *$', '', new_text, flags=re.MULTILINE)
# remove double newlines
new_text = re.sub('(\n *)+\n+',
'\n\n',
new_text,
flags=re.MULTILINE)
document = root.find_descendant_type('document')
#document = root.find_descendant_type('section', pat='Identification')
print('document = %r' % (document, ))
if document is not None:
root = document
sectionpat = ut.get_argval('--section', default=None)
if sectionpat is not None:
root = root.find_descendant_type('section', pat=sectionpat)
print('root = %r' % (root, ))
if root is None:
# import utool
# utool.embed()
raise Exception('section %r does not exist' % (sectionpat))
#print(root.get_debug_tree_text())
#ut.colorprint(root.summary_str(outline=True), 'yellow')
print('---outline---')
outline = True
# outline = False
outline_text = root.summary_str(outline=outline, highlight=False)
summary = root.summary_str(outline=outline, highlight=True)
if not ut.get_argflag('-w'):
print(summary)
print('---/outline---')
if root._config['asmarkdown']:
codetype = 'markdown'
newext = '.md'
else:
codetype = 'latex'
newext = None
ut.dump_autogen_code(ut.augpath(fpath,
augpref='outline_',
newext=newext),
outline_text,
codetype=codetype,
fullprint=False)
def inject_python_code2(fpath, patch_code, tag):
""" Does autogeneration stuff """
import utool as ut
text = ut.readfrom(fpath)
start_tag = '# <%s>' % tag
end_tag = '# </%s>' % tag
new_text = ut.replace_between_tags(text, patch_code, start_tag, end_tag)
ut.writeto(fpath, new_text)
def inject_python_code2(fpath, patch_code, tag):
""" Does autogeneration stuff """
import utool as ut
text = ut.readfrom(fpath)
start_tag = '# <%s>' % tag
end_tag = '# </%s>' % tag
new_text = ut.replace_between_tags(text, patch_code, start_tag, end_tag)
ut.writeto(fpath, new_text)
def caption_sentences(fpath):
text = ut.readfrom(fpath)
tokenstream = Tokenizer(text).tokenize()
self = DocParser(tokenstream, fpath)
tree = self.parse()
for node in tree.walk():
if isinstance(node, FigureNode):
for x in node.walk():
if isinstance(x, CaptionNode):
for sent in ut.split_sentences2(x.resolve()):
yield sent
def research(r,
start_line_str=None,
rate='3',
sentence_mode=True,
open_file=False):
fname = join(split(__file__)[0], 'to_speak.txt')
if start_line_str == "prep":
os.system(fname)
return
if open_file is True:
os.system(fname)
import utool as ut
input_str = preprocess_research(ut.readfrom(fname))
if sentence_mode:
input_str = input_str.replace('\n', ' ').replace('. ', '.\n')
input_str = re.sub(' *', ' ', input_str)
line_count = 0
page = 0
page_re = re.compile(' *--- Page [0-9]* *--- *')
if start_line_str is None:
try:
start_page = 0
start_line = int(input('Did you forget the start line?'))
except Exception:
pass
elif start_line_str.find('page') != -1:
start_page = int(start_line_str.replace('page', ''))
start_line = 0
else:
start_page = 0
start_line = int(start_line_str)
print('Starting on line: %d' % (start_line))
print('Starting on page: %d' % (start_page))
for line in input_str.split('\n'):
print('____')
# Check for page marker
if page_re.findall(line) != []:
page = int(re.sub(' *--- Page ', '', line).replace('---', ''))
# Print out what is being read
line_count += 1
print('%d, %d > %s' % (page, line_count, line))
if start_line > line_count or start_page > page:
continue
# Preprocess the line
line = process_research_line(line)
if line == '':
continue
print('--')
robos.speak(r, line, rate)
def reformat():
"""
./texfix.py --reformat --fpaths NewParts.tex
>>> from texfix import * # NOQA
"""
fpaths = testdata_fpaths()
for fpath in fpaths:
text = ut.readfrom(fpath)
root = latex_parser.LatexDocPart.parse_text(text, debug=None)
if ut.get_argflag('--fixcref'):
root.find(' \\\\cref')
continue
#print(root.children)
#root.children = root.children[0:5]
#print('Parsed Str Short')
new_text = '\n'.join(root.reformat_blocks(debug=None))
# remove trailing spaces
new_text = re.sub(' *$', '', new_text, flags=re.MULTILINE)
# remove double newlines
new_text = re.sub('(\n *)+\n+',
'\n\n',
new_text,
flags=re.MULTILINE)
if ut.get_argflag('--summary'):
print('---summary---')
root.print_summary()
print('---/summary---')
# ut.colorprint(root.summary_str(), 'blue')
numchars1 = len(text.replace(' ', '').replace('\n', ''))
numchars2 = len(new_text.replace(' ', '').replace('\n', ''))
print('numchars1 = %r' % (numchars1, ))
print('numchars2 = %r' % (numchars2, ))
#assert numchars1 == numchars2, '%r == %r' % (numchars1, numchars2)
print('old newlines = %r' % (text.count('\n'), ))
print('new newlines = %r' % (new_text.count('\n'), ))
#import unicodedata
#new_text = unicodedata.normalize('NFKD', new_text).encode('ascii','ignore')
#print('new_text = %r' % (new_text,))
ut.dump_autogen_code(fpath,
new_text,
codetype='latex',
fullprint=False)
def test_body(count, logmode, backspace):
ut.colorprint('\n---- count = %r -----' % (count,), 'yellow')
ut.colorprint('backspace = %r' % (backspace,), 'yellow')
ut.colorprint('logmode = %r' % (logmode,), 'yellow')
if logmode:
ut.delete('test.log')
ut.start_logging('test.log')
print('Start main loop')
import time
for count in ut.ProgressIter(range(20), freq=3, backspace=backspace):
time.sleep(.01)
print('Done with main loop work')
print('Exiting main body')
if logmode:
ut.stop_logging()
#print('-----DONE LOGGING----')
testlog_text = ut.readfrom('test.log')
print(ut.indent(testlog_text.replace('\r', '\n'), ' '))
def test_body(count, logmode, backspace):
ut.colorprint('\n---- count = %r -----' % (count, ), 'yellow')
ut.colorprint('backspace = %r' % (backspace, ), 'yellow')
ut.colorprint('logmode = %r' % (logmode, ), 'yellow')
if logmode:
ut.delete('test.log')
ut.start_logging('test.log')
print('Start main loop')
import time
for count in ut.ProgressIter(range(20), freq=3, backspace=backspace):
time.sleep(.01)
print('Done with main loop work')
print('Exiting main body')
if logmode:
ut.stop_logging()
#print('-----DONE LOGGING----')
testlog_text = ut.readfrom('test.log')
print(ut.indent(testlog_text.replace('\r', '\n'), ' '))
def _read_raw_entries(bibman):
parser = bparser.BibTexParser()
ut.delete_keys(parser.alt_dict, ['url', 'urls'])
parser.ignore_nonstandard_types = False
text = ut.readfrom(bibman.fpath)
# ensure good format
flag = 0
for x in re.finditer('^.*}\n[^}\n]', text, flags=re.MULTILINE):
lineno = x.string[:x.start()].count('\n') + 1
print('DID YOU FORGET A COMMA ON lineno = {!r}'.format(lineno))
print(x.group())
flag += 1
assert not flag, 'fix formating'
database = parser.parse(text)
entries = database.entries
raw_entries = database.get_entry_dict()
raw_entries = ut.order_dict_by(raw_entries, [e['ID'] for e in entries])
bibman.raw_text = text
bibman.raw_entries = raw_entries
def dummy_import_vim(fpath=None):
if fpath is not None:
fpath = abspath(expanduser(fpath))
try:
import vim
dohack = False
except ImportError:
dohack = True
vim = None
if vim is not None:
if getattr(vim, '__ishack__', False):
if fpath != vim.current.buffer.name:
dohack = True
if dohack:
import sys
import utool as ut
vim = ut.DynStruct()
vim.__ishack__ = True
vim.current = ut.DynStruct()
vim.current.window = ut.DynStruct()
vim.current.window.cursor = (0, 0)
if fpath is None:
lines = [
'line1',
'line2',
'line3',
]
else:
lines = ut.readfrom(fpath).splitlines()
vim.current.buffer = DummyVimBuffer(lines)
vim.current.buffer.name = fpath
# VERY HACKY
sys.modules['vim'] = vim
return vim
def main():
try:
opts, args = getopt.getopt(sys.argv[1:], 'f:u:n:h')
except getopt.GetoptError:
usage()
sys.exit(1)
filename = None
url = 'www.whaleshark.org/listImages.jsp'
number = 0
# Handle command-line arguments
for opt, arg in opts:
if opt == '-h':
usage()
sys.exit()
elif opt == '-f':
filename = arg
elif opt == '-u':
url = arg
elif opt == '-n':
try:
number = int(arg)
except ValueError:
usage()
sys.exit()
# Open the XML file and extract its contents as a DOM object
if filename:
XMLdata = ut.readfrom(filename)
else:
XMLdata = ut.url_read(url)
#with open('XMLData.xml', 'w') as file_:
# file_.write(XMLdata)
print('Downloading')
download_sharks(XMLdata, number)
def main():
try:
opts, args = getopt.getopt(sys.argv[1:], 'f:u:n:h')
except getopt.GetoptError:
usage()
sys.exit(1)
filename = None
url = 'www.whaleshark.org/listImages.jsp'
number = 0
# Handle command-line arguments
for opt, arg in opts:
if opt == '-h':
usage()
sys.exit()
elif opt == '-f':
filename = arg
elif opt == '-u':
url = arg
elif opt == '-n':
try:
number = int(arg)
except ValueError:
usage()
sys.exit()
# Open the XML file and extract its contents as a DOM object
if filename:
XMLdata = ut.readfrom(filename)
else:
XMLdata = ut.url_read(url)
#with open('XMLData.xml', 'w') as file_:
# file_.write(XMLdata)
print('Downloading')
download_sharks(XMLdata, number)
def main(bib_fpath=None):
r"""
intro point to fixbib script
CommmandLine:
fixbib
python -m fixtex bib
python -m fixtex bib --dryrun
python -m fixtex bib --dryrun --debug
"""
if bib_fpath is None:
bib_fpath = 'My Library.bib'
# DEBUG = ub.argflag('--debug')
# Read in text and ensure ascii format
dirty_text = ut.readfrom(bib_fpath)
from fixtex.fix_tex import find_used_citations, testdata_fpaths
if exists('custom_extra.bib'):
extra_parser = bparser.BibTexParser(ignore_nonstandard_types=False)
parser = bparser.BibTexParser()
ut.delete_keys(parser.alt_dict, ['url', 'urls'])
print('Parsing extra bibtex file')
extra_text = ut.readfrom('custom_extra.bib')
extra_database = extra_parser.parse(extra_text, partial=False)
print('Finished parsing extra')
extra_dict = extra_database.get_entry_dict()
else:
extra_dict = None
#udata = dirty_text.decode("utf-8")
#dirty_text = udata.encode("ascii", "ignore")
#dirty_text = udata
# parser = bparser.BibTexParser()
# bib_database = parser.parse(dirty_text)
# d = bib_database.get_entry_dict()
print('BIBTEXPARSER LOAD')
parser = bparser.BibTexParser(ignore_nonstandard_types=False,
common_strings=True)
ut.delete_keys(parser.alt_dict, ['url', 'urls'])
print('Parsing bibtex file')
bib_database = parser.parse(dirty_text, partial=False)
print('Finished parsing')
bibtex_dict = bib_database.get_entry_dict()
old_keys = list(bibtex_dict.keys())
new_keys = []
for key in ub.ProgIter(old_keys, label='fixing keys'):
new_key = key
new_key = new_key.replace(':', '')
new_key = new_key.replace('-', '_')
new_key = re.sub('__*', '_', new_key)
new_keys.append(new_key)
# assert len(ut.find_duplicate_items(new_keys)) == 0, 'new keys created conflict'
assert len(ub.find_duplicates(new_keys)) == 0, 'new keys created conflict'
for key, new_key in zip(old_keys, new_keys):
if key != new_key:
entry = bibtex_dict[key]
entry['ID'] = new_key
bibtex_dict[new_key] = entry
del bibtex_dict[key]
# The bibtext is now clean. Print it to stdout
#print(clean_text)
verbose = None
if verbose is None:
verbose = 1
# Find citations from the tex documents
key_list = None
if key_list is None:
cacher = ub.Cacher('texcite1', enabled=0)
data = cacher.tryload()
if data is None:
fpaths = testdata_fpaths()
key_list, inverse = find_used_citations(fpaths,
return_inverse=True)
# ignore = ['JP', '?', 'hendrick']
# for item in ignore:
# try:
# key_list.remove(item)
# except ValueError:
# pass
if verbose:
print('Found %d citations used in the document' %
(len(key_list), ))
data = key_list, inverse
cacher.save(data)
key_list, inverse = data
# else:
# key_list = None
unknown_pubkeys = []
debug_author = ub.argval('--debug-author', default=None)
# ./fix_bib.py --debug_author=Kappes
if verbose:
print('Fixing %d/%d bibtex entries' %
(len(key_list), len(bibtex_dict)))
# debug = True
debug = False
if debug_author is not None:
debug = False
known_keys = list(bibtex_dict.keys())
missing_keys = set(key_list) - set(known_keys)
if extra_dict is not None:
missing_keys.difference_update(set(extra_dict.keys()))
if missing_keys:
print('The library is missing keys found in tex files %s' %
(ub.repr2(missing_keys), ))
# Search for possible typos:
candidate_typos = {}
sedlines = []
for key in missing_keys:
candidates = ut.closet_words(key, known_keys, num=3, subset=True)
if len(candidates) > 1:
top = candidates[0]
if ut.edit_distance(key, top) == 1:
# "sed -i -e 's/{}/{}/g' *.tex".format(key, top)
import os
replpaths = ' '.join(
[relpath(p, os.getcwd()) for p in inverse[key]])
sedlines.append("sed -i -e 's/{}/{}/g' {}".format(
key, top, replpaths))
candidate_typos[key] = candidates
print('Cannot find key = %r' % (key, ))
print('Did you mean? %r' % (candidates, ))
print('Quick fixes')
print('\n'.join(sedlines))
# group by file
just = max([0] + list(map(len, missing_keys)))
missing_fpaths = [inverse[key] for key in missing_keys]
for fpath in sorted(set(ub.flatten(missing_fpaths))):
# ut.fix_embed_globals()
subkeys = [k for k in missing_keys if fpath in inverse[k]]
print('')
ut.cprint('--- Missing Keys ---', 'blue')
ut.cprint('fpath = %r' % (fpath, ), 'blue')
ut.cprint('{} | {}'.format('Missing'.ljust(just), 'Did you mean?'),
'blue')
for key in subkeys:
print('{} | {}'.format(ut.highlight_text(key.ljust(just), 'red'),
' '.join(candidate_typos[key])))
# for key in list(bibtex_dict.keys()):
if extra_dict is not None:
# Extra database takes precidence over regular
key_list = list(ut.unique(key_list + list(extra_dict.keys())))
for k, v in extra_dict.items():
bibtex_dict[k] = v
full = ub.argflag('--full')
for key in key_list:
try:
entry = bibtex_dict[key]
except KeyError:
continue
self = BibTexCleaner(key, entry, full=full)
if debug_author is not None:
debug = debug_author in entry.get('author', '')
if debug:
ut.cprint(' --- ENTRY ---', 'yellow')
print(ub.repr2(entry, nl=1))
entry = self.fix()
# self.clip_abstract()
# self.shorten_keys()
# self.fix_authors()
# self.fix_year()
# old_pubval = self.fix_pubkey()
# if old_pubval:
# unknown_pubkeys.append(old_pubval)
# self.fix_arxiv()
# self.fix_general()
# self.fix_paper_types()
if debug:
print(ub.repr2(entry, nl=1))
ut.cprint(' --- END ENTRY ---', 'yellow')
bibtex_dict[key] = entry
unwanted_keys = set(bibtex_dict.keys()) - set(key_list)
if verbose:
print('Removing unwanted %d entries' % (len(unwanted_keys)))
ut.delete_dict_keys(bibtex_dict, unwanted_keys)
if 0:
d1 = bibtex_dict.copy()
full = True
for key, entry in d1.items():
self = BibTexCleaner(key, entry, full=full)
pub = self.publication()
if pub is None:
print(self.entry['ENTRYTYPE'])
old = self.fix_pubkey()
x1 = self._pubval()
x2 = self.standard_pubval(full=full)
# if x2 is not None and len(x2) > 5:
# print(ub.repr2(self.entry))
if x1 != x2:
print('x2 = %r' % (x2, ))
print('x1 = %r' % (x1, ))
print(ub.repr2(self.entry))
# if 'CVPR' in self.entry.get('booktitle', ''):
# if 'CVPR' != self.entry.get('booktitle', ''):
# break
if old:
print('old = %r' % (old, ))
d1[key] = self.entry
if full:
d1 = bibtex_dict.copy()
import numpy as np
import pandas as pd
df = pd.DataFrame.from_dict(d1, orient='index')
paged_items = df[~pd.isnull(df['pub_accro'])]
has_pages = ~pd.isnull(paged_items['pages'])
print('have pages {} / {}'.format(has_pages.sum(), len(has_pages)))
print(ub.repr2(paged_items[~has_pages]['title'].values.tolist()))
entrytypes = dict(list(df.groupby('pub_type')))
if False:
# entrytypes['misc']
g = entrytypes['online']
g = g[g.columns[~np.all(pd.isnull(g), axis=0)]]
entrytypes['book']
entrytypes['thesis']
g = entrytypes['article']
g = entrytypes['incollection']
g = entrytypes['conference']
def lookup_pub(e):
if e == 'article':
return 'journal', 'journal'
elif e == 'incollection':
return 'booksection', 'booktitle'
elif e == 'conference':
return 'conference', 'booktitle'
return None, None
for e, g in entrytypes.items():
print('e = %r' % (e, ))
g = g[g.columns[~np.all(pd.isnull(g), axis=0)]]
if 'pub_full' in g.columns:
place_title = g['pub_full'].tolist()
print(ub.repr2(ub.dict_hist(place_title)))
else:
print('Unknown publications')
if 'report' in entrytypes:
g = entrytypes['report']
missing = g[pd.isnull(g['title'])]
if len(missing):
print('Missing Title')
print(ub.repr2(missing[['title', 'author']].values.tolist()))
if 'journal' in entrytypes:
g = entrytypes['journal']
g = g[g.columns[~np.all(pd.isnull(g), axis=0)]]
missing = g[pd.isnull(g['journal'])]
if len(missing):
print('Missing Journal')
print(ub.repr2(missing[['title', 'author']].values.tolist()))
if 'conference' in entrytypes:
g = entrytypes['conference']
g = g[g.columns[~np.all(pd.isnull(g), axis=0)]]
missing = g[pd.isnull(g['booktitle'])]
if len(missing):
print('Missing Booktitle')
print(ub.repr2(missing[['title', 'author']].values.tolist()))
if 'incollection' in entrytypes:
g = entrytypes['incollection']
g = g[g.columns[~np.all(pd.isnull(g), axis=0)]]
missing = g[pd.isnull(g['booktitle'])]
if len(missing):
print('Missing Booktitle')
print(ub.repr2(missing[['title', 'author']].values.tolist()))
if 'thesis' in entrytypes:
g = entrytypes['thesis']
g = g[g.columns[~np.all(pd.isnull(g), axis=0)]]
missing = g[pd.isnull(g['institution'])]
if len(missing):
print('Missing Institution')
print(ub.repr2(missing[['title', 'author']].values.tolist()))
# import utool
# utool.embed()
# Overwrite BibDatabase structure
bib_database._entries_dict = bibtex_dict
bib_database.entries = list(bibtex_dict.values())
#conftitle_to_types_set_hist = {key: set(val) for key, val in conftitle_to_types_hist.items()}
#print(ub.repr2(conftitle_to_types_set_hist))
print('Unknown conference keys:')
print(ub.repr2(sorted(unknown_pubkeys)))
print('len(unknown_pubkeys) = %r' % (len(unknown_pubkeys), ))
writer = BibTexWriter()
writer.contents = ['comments', 'entries']
writer.indent = ' '
writer.order_entries_by = ('type', 'author', 'year')
new_bibtex_str = bibtexparser.dumps(bib_database, writer)
# Need to check
#jegou_aggregating_2012
# Fix the Journal Abreviations
# References:
# https://www.ieee.org/documents/trans_journal_names.pdf
# Write out clean bibfile in ascii format
clean_bib_fpath = ub.augpath(bib_fpath.replace(' ', '_'), suffix='_clean')
if not ub.argflag('--dryrun'):
ut.writeto(clean_bib_fpath, new_bibtex_str)
def install_wildbook(verbose=ut.NOT_QUIET):
"""
Script to setup wildbook on a unix based system
(hopefully eventually this will generalize to win32)
CommandLine:
# Reset
python -m ibeis --tf reset_local_wildbook
# Setup
python -m ibeis --tf install_wildbook
# Startup
python -m ibeis --tf startup_wildbook_server --show --exec-mode
# Reset
python -m ibeis.control.manual_wildbook_funcs --test-reset_local_wildbook
# Setup
python -m ibeis.control.manual_wildbook_funcs --test-install_wildbook
# Startup
python -m ibeis.control.manual_wildbook_funcs --test-startup_wildbook_server --show --exec-mode
Example:
>>> # SCRIPT
>>> from ibeis.control.manual_wildbook_funcs import * # NOQA
>>> verbose = True
>>> result = install_wildbook()
>>> print(result)
"""
# TODO: allow custom specified tomcat directory
from os.path import basename, splitext, join
import time
import re
import subprocess
try:
output = subprocess.check_output(['java', '-version'],
stderr=subprocess.STDOUT)
_java_version = output.split('\n')[0]
_java_version = _java_version.replace('java version ', '')
java_version = _java_version.replace('"', '')
print('java_version = %r' % (java_version,))
if not java_version.startswith('1.7'):
print('Warning wildbook is only supported for java 1.7')
except OSError:
output = None
if output is None:
raise ImportError(
'Cannot find java on this machine. '
'Please install java: http://www.java.com/en/download/')
tomcat_dpath = find_or_download_tomcat()
assert tomcat_dpath is not None, 'Could not find tomcat'
war_fpath = find_or_download_wilbook_warfile()
war_fname = basename(war_fpath)
wb_target = splitext(war_fname)[0]
# Ensure environment variables
#os.environ['JAVA_HOME'] = find_java_jvm()
#os.environ['TOMCAT_HOME'] = tomcat_dpath
#os.environ['CATALINA_HOME'] = tomcat_dpath
# Move the war file to tomcat webapps if not there
webapps_dpath = join(tomcat_dpath, 'webapps')
deploy_war_fpath = join(webapps_dpath, war_fname)
if not ut.checkpath(deploy_war_fpath, verbose=verbose):
ut.copy(war_fpath, deploy_war_fpath)
# Ensure that the war file has been unpacked
unpacked_war_dpath = join(webapps_dpath, wb_target)
if not ut.checkpath(unpacked_war_dpath, verbose=verbose):
# Need to make sure you start catalina in the same directory otherwise
# the derby databsae gets put in in cwd
tomcat_startup_dir = get_tomcat_startup_tmpdir()
with ut.ChdirContext(tomcat_startup_dir):
# Starting and stoping catalina should be sufficient to unpack the
# war
startup_fpath = join(tomcat_dpath, 'bin', 'startup.sh')
shutdown_fpath = join(tomcat_dpath, 'bin', 'shutdown.sh')
ut.cmd(ut.quote_single_command(startup_fpath))
print('It is NOT ok if the startup.sh fails\n')
# wait for the war to be unpacked
for retry_count in range(0, 6):
time.sleep(1)
if ut.checkpath(unpacked_war_dpath, verbose=True):
break
else:
print('Retrying')
# ensure that the server is ruuning
import requests
print('Checking if we can ping the server')
response = requests.get('http://localhost:8080')
if response is None or response.status_code != 200:
print('There may be an error starting the server')
else:
print('Seem able to ping the server')
# assert tht the war was unpacked
ut.assertpath(unpacked_war_dpath, (
'Wildbook war might have not unpacked correctly. This may '
'be ok. Try again. If it fails a second time, then there is a '
'problem.'), verbose=True)
# shutdown the server
ut.cmd(ut.quote_single_command(shutdown_fpath))
print('It is ok if the shutdown.sh fails')
time.sleep(.5)
# Make sure permissions are correctly set in wildbook
# Comment out the line that requires authentication
permission_fpath = join(unpacked_war_dpath, 'WEB-INF/web.xml')
ut.assertpath(permission_fpath)
permission_text = ut.readfrom(permission_fpath)
lines_to_remove = [
'/EncounterSetMarkedIndividual = authc, roles[admin]'
]
new_permission_text = permission_text[:]
for line in lines_to_remove:
re.search(re.escape(line), permission_text)
prefix = ut.named_field('prefix', '\\s*')
suffix = ut.named_field('suffix', '\\s*\n')
pattern = ('^' + prefix + re.escape(line) + suffix)
match = re.search(pattern, permission_text,
flags=re.MULTILINE | re.DOTALL)
if match is None:
continue
newline = '<!--%s -->' % (line,)
repl = ut.bref_field('prefix') + newline + ut.bref_field('suffix')
new_permission_text = re.sub(pattern, repl, permission_text,
flags=re.MULTILINE | re.DOTALL)
assert new_permission_text != permission_text, (
'text should have changed')
if new_permission_text != permission_text:
print('Need to write new permission texts')
ut.writeto(permission_fpath, new_permission_text)
else:
print('Permission file seems to be ok')
print('Wildbook is installed and waiting to be started')
def total_purge_developed_repo(repodir):
r"""
Outputs commands to help purge a repo
Args:
repodir (str): path to developed repository
CommandLine:
python -m utool.util_sysreq total_purge_installed_repo --show
Ignore:
repodir = ut.truepath('~/code/Lasagne')
Example:
>>> # DISABLE_DOCTEST
>>> from utool.util_sysreq import * # NOQA
>>> import utool as ut
>>> repodir = ut.get_argval('--repodir', default=None)
>>> result = total_purge_installed_repo(repodir)
"""
assert repodir is not None
import utool as ut
import os
repo = ut.util_git.Repo(dpath=repodir)
user = os.environ['USER']
fmtdict = dict(
user=user,
modname=repo.modname,
reponame=repo.reponame,
dpath=repo.dpath,
global_site_pkgs=ut.get_global_dist_packages_dir(),
local_site_pkgs=ut.get_local_dist_packages_dir(),
venv_site_pkgs=ut.get_site_packages_dir(),
)
commands = [
_.format(**fmtdict) for _ in [
'pip uninstall {modname}',
'sudo -H pip uninstall {modname}',
'sudo pip uninstall {modname}',
'easy_install -m {modname}',
'cd {dpath} && python setup.py develop --uninstall',
# If they still exist try chowning to current user
'sudo chown -R {user}:{user} {dpath}',
]
]
print('Normal uninstall commands')
print('\n'.join(commands))
possible_link_paths = [
_.format(**fmtdict) for _ in [
'{dpath}/{modname}.egg-info',
'{dpath}/build',
'{venv_site_pkgs}/{reponame}.egg-info',
'{local_site_pkgs}/{reponame}.egg-info',
'{venv_site_pkgs}/{reponame}.egg-info',
]
]
from os.path import exists, basename
existing_link_paths = [path for path in possible_link_paths]
print('# Delete paths and eggs')
for path in existing_link_paths:
if exists(path):
if ut.get_file_info(path)['owner'] != user:
print('sudo /bin/rm -rf {path}'.format(path=path))
else:
print('/bin/rm -rf {path}'.format(path=path))
#ut.delete(path)
print('# Make sure nothing is in the easy install paths')
easyinstall_paths = [
_.format(**fmtdict) for _ in [
'{venv_site_pkgs}/easy-install.pth',
'{local_site_pkgs}/easy-install.pth',
'{venv_site_pkgs}/easy-install.pth',
]
]
for path in easyinstall_paths:
if exists(path):
easy_install_list = ut.readfrom(path,
verbose=False).strip().split('\n')
easy_install_list_ = [basename(p) for p in easy_install_list]
index1 = ut.listfind(easy_install_list_, repo.reponame)
index2 = ut.listfind(easy_install_list_, repo.modname)
if index1 is not None or index2 is not None:
print('Found at index1=%r, index=%r' % (index1, index2))
if ut.get_file_info(path)['owner'] != user:
print('sudo gvim {path}'.format(path=path))
else:
print('gvim {path}'.format(path=path))
checkcmds = [
_.format(**fmtdict)
for _ in ['python -c "import {modname}; print({modname}.__file__)"']
]
import sys
assert repo.modname not in sys.modules
print("# CHECK STATUS")
for cmd in checkcmds:
print(cmd)
def total_purge_developed_repo(repodir):
r"""
Outputs commands to help purge a repo
Args:
repodir (str): path to developed repository
CommandLine:
python -m utool.util_sysreq total_purge_installed_repo --show
Ignore:
repodir = ut.truepath('~/code/Lasagne')
Example:
>>> # DISABLE_DOCTEST
>>> from utool.util_sysreq import * # NOQA
>>> import utool as ut
>>> repodir = ut.get_argval('--repodir', default=None)
>>> result = total_purge_installed_repo(repodir)
"""
assert repodir is not None
import utool as ut
import os
repo = ut.util_git.Repo(dpath=repodir)
user = os.environ['USER']
fmtdict = dict(
user=user,
modname=repo.modname,
reponame=repo.reponame,
dpath=repo.dpath,
global_site_pkgs=ut.get_global_dist_packages_dir(),
local_site_pkgs=ut.get_local_dist_packages_dir(),
venv_site_pkgs=ut.get_site_packages_dir(),
)
commands = [_.format(**fmtdict) for _ in [
'pip uninstall {modname}',
'sudo -H pip uninstall {modname}',
'sudo pip uninstall {modname}',
'easy_install -m {modname}',
'cd {dpath} && python setup.py develop --uninstall',
# If they still exist try chowning to current user
'sudo chown -R {user}:{user} {dpath}',
]]
print('Normal uninstall commands')
print('\n'.join(commands))
possible_link_paths = [_.format(**fmtdict) for _ in [
'{dpath}/{modname}.egg-info',
'{dpath}/build',
'{venv_site_pkgs}/{reponame}.egg-info',
'{local_site_pkgs}/{reponame}.egg-info',
'{venv_site_pkgs}/{reponame}.egg-info',
]]
from os.path import exists, basename
existing_link_paths = [path for path in possible_link_paths]
print('# Delete paths and eggs')
for path in existing_link_paths:
if exists(path):
if ut.get_file_info(path)['owner'] != user:
print('sudo /bin/rm -rf {path}'.format(path=path))
else:
print('/bin/rm -rf {path}'.format(path=path))
#ut.delete(path)
print('# Make sure nothing is in the easy install paths')
easyinstall_paths = [_.format(**fmtdict) for _ in [
'{venv_site_pkgs}/easy-install.pth',
'{local_site_pkgs}/easy-install.pth',
'{venv_site_pkgs}/easy-install.pth',
]]
for path in easyinstall_paths:
if exists(path):
easy_install_list = ut.readfrom(path, verbose=False).strip().split('\n')
easy_install_list_ = [basename(p) for p in easy_install_list]
index1 = ut.listfind(easy_install_list_, repo.reponame)
index2 = ut.listfind(easy_install_list_, repo.modname)
if index1 is not None or index2 is not None:
print('Found at index1=%r, index=%r' % (index1, index2))
if ut.get_file_info(path)['owner'] != user:
print('sudo gvim {path}'.format(path=path))
else:
print('gvim {path}'.format(path=path))
checkcmds = [_.format(**fmtdict) for _ in [
'python -c "import {modname}; print({modname}.__file__)"'
]]
import sys
assert repo.modname not in sys.modules
print("# CHECK STATUS")
for cmd in checkcmds:
print(cmd)
'graph-id.tex',
'appendix.tex',
'main.tex',
'graph_id.tex',
]
exclude_dirs = ['guts']
tex_fpath_list = sorted(
ut.glob(dpath, patterns, recursive=True, exclude_dirs=exclude_dirs)
)
tex_fpath_list = ut.get_argval('--fpaths', type_=list, default=tex_fpath_list)
return tex_fpath_list
fpaths = testdata_fpaths()
fpath = 'main.tex'
text = ut.readfrom(fpath)
root = latex_parser.LatexDocPart.parse_text(text, debug=None)
# root._config['asmarkdown'] = True
# root._config['numlines'] = float('inf')
commands = list(root.find_descendant_types('newcommand'))
figcommands = []
for self in commands:
if self.fpath_root() in {'colordef.tex', 'def.tex', 'CrallDef.tex'}:
continue
figcommands.append(self)
cmd_to_fpaths = ut.ddict(list)
for self in figcommands:
def update_wildbook_install_config(webapps_dpath, unpacked_war_dpath):
"""
CommandLine:
python -m ibeis ensure_local_war
python -m ibeis update_wildbook_install_config
python -m ibeis update_wildbook_install_config --show
Example:
>>> from ibeis.control.wildbook_manager import * # NOQA
>>> import ibeis
>>> tomcat_dpath = find_installed_tomcat()
>>> webapps_dpath = join(tomcat_dpath, 'webapps')
>>> wb_target = ibeis.const.WILDBOOK_TARGET
>>> unpacked_war_dpath = join(webapps_dpath, wb_target)
>>> locals_ = ut.exec_func_src(update_wildbook_install_config, globals())
>>> #update_wildbook_install_config(webapps_dpath, unpacked_war_dpath)
>>> ut.quit_if_noshow()
>>> ut.vd(unpacked_war_dpath)
>>> ut.editfile(locals_['permission_fpath'])
>>> ut.editfile(locals_['jdoconfig_fpath'])
>>> ut.editfile(locals_['asset_store_fpath'])
"""
mysql_mode = not ut.get_argflag('--nomysql')
#if ut.get_argflag('--vd'):
# ut.vd(unpacked_war_dpath)
#find_installed_tomcat
# Make sure permissions are correctly set in wildbook
# Comment out the line that requires authentication
permission_fpath = join(unpacked_war_dpath, 'WEB-INF/web.xml')
ut.assertpath(permission_fpath)
permission_text = ut.readfrom(permission_fpath)
lines_to_remove = [
# '/ImageSetSetMarkedIndividual = authc, roles[admin]'
'/EncounterSetMarkedIndividual = authc, roles[admin]'
]
new_permission_text = permission_text[:]
for line in lines_to_remove:
re.search(re.escape(line), permission_text)
prefix = ut.named_field('prefix', '\\s*')
suffix = ut.named_field('suffix', '\\s*\n')
pattern = ('^' + prefix + re.escape(line) + suffix)
match = re.search(pattern,
permission_text,
flags=re.MULTILINE | re.DOTALL)
if match is None:
continue
newline = '<!--%s -->' % (line, )
repl = ut.bref_field('prefix') + newline + ut.bref_field('suffix')
new_permission_text = re.sub(pattern,
repl,
permission_text,
flags=re.MULTILINE | re.DOTALL)
assert new_permission_text != permission_text, (
'text should have changed')
if new_permission_text != permission_text:
print('Need to write new permission texts')
ut.writeto(permission_fpath, new_permission_text)
else:
print('Permission file seems to be ok')
# Make sure we are using a non-process based database
jdoconfig_fpath = join(unpacked_war_dpath,
'WEB-INF/classes/bundles/jdoconfig.properties')
print('Fixing backend database config')
print('jdoconfig_fpath = %r' % (jdoconfig_fpath, ))
ut.assertpath(jdoconfig_fpath)
jdoconfig_text = ut.readfrom(jdoconfig_fpath)
#ut.vd(dirname(jdoconfig_fpath))
#ut.editfile(jdoconfig_fpath)
if mysql_mode:
jdoconfig_text = ut.toggle_comment_lines(jdoconfig_text, 'mysql',
False)
jdoconfig_text = ut.toggle_comment_lines(jdoconfig_text, 'derby', 1)
jdoconfig_text = ut.toggle_comment_lines(jdoconfig_text, 'sqlite', 1)
mysql_user = '******'
mysql_passwd = 'somepassword'
mysql_dbname = 'ibeiswbtestdb'
# Use mysql
jdoconfig_text = re.sub('datanucleus.ConnectionUserName = .*$',
'datanucleus.ConnectionUserName = '******'datanucleus.ConnectionPassword = .*$',
'datanucleus.ConnectionPassword = '******'datanucleus.ConnectionURL *= *jdbc:mysql:.*$',
'datanucleus.ConnectionURL = jdbc:mysql://localhost:3306/' +
mysql_dbname,
jdoconfig_text,
flags=re.MULTILINE)
jdoconfig_text = re.sub('^.*jdbc:mysql://localhost:3306/shepherd.*$',
'',
jdoconfig_text,
flags=re.MULTILINE)
else:
# Use SQLIIte
jdoconfig_text = ut.toggle_comment_lines(jdoconfig_text, 'derby', 1)
jdoconfig_text = ut.toggle_comment_lines(jdoconfig_text, 'mysql', 1)
jdoconfig_text = ut.toggle_comment_lines(jdoconfig_text, 'sqlite',
False)
ut.writeto(jdoconfig_fpath, jdoconfig_text)
# Need to make sure wildbook can store information in a reasonalbe place
#tomcat_data_dir = join(tomcat_startup_dir, 'webapps', 'wildbook_data_dir')
tomcat_data_dir = join(webapps_dpath, 'wildbook_data_dir')
ut.ensuredir(tomcat_data_dir)
ut.writeto(join(tomcat_data_dir, 'test.txt'), 'A hosted test file')
asset_store_fpath = join(unpacked_war_dpath, 'createAssetStore.jsp')
asset_store_text = ut.read_from(asset_store_fpath)
#data_path_pat = ut.named_field('data_path', 'new File(".*?").toPath')
new_line = 'LocalAssetStore as = new LocalAssetStore("example Local AssetStore", new File("%s").toPath(), "%s", true);' % (
tomcat_data_dir, 'http://localhost:8080/' + basename(tomcat_data_dir))
# HACKY
asset_store_text2 = re.sub('^LocalAssetStore as = .*$',
new_line,
asset_store_text,
flags=re.MULTILINE)
ut.writeto(asset_store_fpath, asset_store_text2)
def fix_chktex():
"""
./texfix.py --fixcite --fix-chktex
"""
import parse
fpaths = testdata_fpaths()
print('Running chktex')
output_list = [
ut.cmd('chktex', fpath, verbose=False)[0] for fpath in fpaths
]
fixcite = ut.get_argflag('--fixcite')
fixlbl = ut.get_argflag('--fixlbl')
fixcmdterm = ut.get_argflag('--fixcmdterm')
for fpath, output in zip(fpaths, output_list):
text = ut.readfrom(fpath)
buffer = text.split('\n')
pat = '\n' + ut.positive_lookahead('Warning')
warn_list = list(
filter(lambda x: x.startswith('Warning'),
re.split(pat, output)))
delete_linenos = []
if not (fixcmdterm or fixlbl or fixcite):
print(' CHOOSE A FIX ')
modified_lines = []
for warn in warn_list:
warnlines = warn.split('\n')
pres = parse.parse(
'Warning {num} in {fpath} line {lineno}: {warnmsg}',
warnlines[0])
if pres is not None:
fpath_ = pres['fpath']
lineno = int(pres['lineno']) - 1
warnmsg = pres['warnmsg']
try:
assert fpath == fpath_, ('%r != %r' % (fpath, fpath_))
except AssertionError:
continue
if 'No errors printed' in warn:
#print('Cannot fix')
continue
if lineno in modified_lines:
print('Skipping modified line')
continue
if fixcmdterm and warnmsg == 'Command terminated with space.':
print('Fix command termination')
errorline = warnlines[1] # NOQA
carrotline = warnlines[2]
pos = carrotline.find('^')
if 0:
print('pos = %r' % (pos, ))
print('lineno = %r' % (lineno, ))
print('errorline = %r' % (errorline, ))
modified_lines.append(lineno)
line = buffer[lineno]
pre_, post_ = line[:pos], line[pos + 1:]
newline = (pre_ + '{} ' + post_).rstrip(' ')
#print('newline = %r' % (newline,))
buffer[lineno] = newline
elif fixlbl and warnmsg == 'Delete this space to maintain correct pagereferences.':
print('Fix label newline')
fpath_ = pres['fpath']
errorline = warnlines[1] # NOQA
new_prevline = buffer[
lineno - 1].rstrip() + errorline.lstrip(' ')
buffer[lineno - 1] = new_prevline
modified_lines.append(lineno)
delete_linenos.append(lineno)
elif fixcite and re.match(
'Non-breaking space \\(.~.\\) should have been used',
warnmsg):
#print(warnmsg)
#print('\n'.join(warnlines))
print('Fix citation space')
carrotline = warnlines[2]
pos = carrotline.find('^')
modified_lines.append(lineno)
line = buffer[lineno]
if line[pos] == ' ':
pre_, post_ = line[:pos], line[pos + 1:]
newline = (pre_ + '~' + post_).rstrip(' ')
else:
pre_, post_ = line[:pos + 1], line[pos + 1:]
newline = (pre_ + '~' + post_).rstrip(' ')
print(warn)
print(line[pos])
assert False
#assert line[pos] == ' ', '%r' % line[pos]
break
if len(pre_.strip()) == 0:
new_prevline = buffer[
lineno - 1].rstrip() + newline.lstrip(' ')
buffer[lineno - 1] = new_prevline
delete_linenos.append(lineno)
else:
#print('newline = %r' % (newline,))
buffer[lineno] = newline
#print(warn)
if len(delete_linenos) > 0:
mask = ut.index_to_boolmask(delete_linenos, len(buffer))
buffer = ut.compress(buffer, ut.not_list(mask))
newtext = '\n'.join(buffer)
#ut.dump_autogen_code(fpath, newtext, 'tex', fullprint=False)
ut.print_difftext(
ut.get_textdiff(text, newtext, num_context_lines=4))
if ut.get_argflag('-w'):
ut.writeto(fpath, newtext)
else:
print('Specify -w to finialize change')
def load_oxford_2007():
"""
Loads data from
http://www.robots.ox.ac.uk:5000/~vgg/publications/2007/Philbin07/philbin07.pdf
>>> from wbia.algo.smk.script_smk import * # NOQA
"""
from os.path import join, basename, splitext
import pandas as pd
import vtool as vt
dbdir = ut.truepath('/raid/work/Oxford/')
data_fpath0 = join(dbdir, 'data_2007.pkl')
if ut.checkpath(data_fpath0):
data = ut.load_data(data_fpath0)
return data
else:
word_dpath = join(dbdir, 'word_oxc1_hesaff_sift_16M_1M')
_word_fpath_list = ut.ls(word_dpath)
imgid_to_word_fpath = {
splitext(basename(word_fpath))[0]: word_fpath
for word_fpath in _word_fpath_list
}
readme_fpath = join(dbdir, 'README2.txt')
imgid_order = ut.readfrom(readme_fpath).split('\n')[20:-1]
imgid_order = imgid_order
data_uri_order = [x.replace('oxc1_', '') for x in imgid_order]
imgid_to_df = {}
for imgid in ut.ProgIter(imgid_order, label='reading kpts'):
word_fpath = imgid_to_word_fpath[imgid]
row_gen = (map(float,
line.strip('\n').split(' '))
for line in ut.read_lines_from(word_fpath)[2:])
rows = [(int(word_id), x, y, e11, e12, e22)
for (word_id, x, y, e11, e12, e22) in row_gen]
df = pd.DataFrame(
rows, columns=['word_id', 'x', 'y', 'e11', 'e12', 'e22'])
imgid_to_df[imgid] = df
df_list = ut.take(imgid_to_df, imgid_order)
nfeat_list = [len(df_) for df_ in df_list]
offset_list = [0] + ut.cumsum(nfeat_list)
shape = (offset_list[-1], 128)
# shape = (16334970, 128)
sift_fpath = join(dbdir, 'OxfordSIFTDescriptors',
'feat_oxc1_hesaff_sift.bin')
try:
file_ = open(sift_fpath, 'rb')
with ut.Timer('Reading SIFT binary file'):
nbytes = np.prod(shape)
all_vecs = np.fromstring(file_.read(nbytes), dtype=np.uint8)
all_vecs = all_vecs.reshape(shape)
finally:
file_.close()
kpts_list = [
df_.loc[:, ('x', 'y', 'e11', 'e12', 'e22')].values
for df_ in df_list
]
wordid_list = [df_.loc[:, 'word_id'].values for df_ in df_list]
kpts_Z = np.vstack(kpts_list)
idx_to_wx = np.hstack(wordid_list)
# assert len(np.unique(idx_to_wx)) == 1E6
# Reqd standard query order
query_files = sorted(
ut.glob(dbdir + '/oxford_groundtruth', '*_query.txt'))
query_uri_order = []
for qpath in query_files:
text = ut.readfrom(qpath, verbose=0)
query_uri = text.split(' ')[0].replace('oxc1_', '')
query_uri_order.append(query_uri)
logger.info('converting to invV')
all_kpts = vt.convert_kptsZ_to_kpts(kpts_Z)
data = {
'offset_list': offset_list,
'all_kpts': all_kpts,
'all_vecs': all_vecs,
'idx_to_wx': idx_to_wx,
'data_uri_order': data_uri_order,
'query_uri_order': query_uri_order,
}
ut.save_data(data_fpath0, data)
return data
def update_wildbook_install_config(webapps_dpath, unpacked_war_dpath):
"""
CommandLine:
python -m ibeis ensure_local_war
python -m ibeis update_wildbook_install_config
python -m ibeis update_wildbook_install_config --show
Example:
>>> from ibeis.control.wildbook_manager import * # NOQA
>>> import ibeis
>>> tomcat_dpath = find_installed_tomcat()
>>> webapps_dpath = join(tomcat_dpath, 'webapps')
>>> wb_target = ibeis.const.WILDBOOK_TARGET
>>> unpacked_war_dpath = join(webapps_dpath, wb_target)
>>> locals_ = ut.exec_func_src(update_wildbook_install_config, globals())
>>> #update_wildbook_install_config(webapps_dpath, unpacked_war_dpath)
>>> ut.quit_if_noshow()
>>> ut.vd(unpacked_war_dpath)
>>> ut.editfile(locals_['permission_fpath'])
>>> ut.editfile(locals_['jdoconfig_fpath'])
>>> ut.editfile(locals_['asset_store_fpath'])
"""
mysql_mode = not ut.get_argflag('--nomysql')
#if ut.get_argflag('--vd'):
# ut.vd(unpacked_war_dpath)
#find_installed_tomcat
# Make sure permissions are correctly set in wildbook
# Comment out the line that requires authentication
permission_fpath = join(unpacked_war_dpath, 'WEB-INF/web.xml')
ut.assertpath(permission_fpath)
permission_text = ut.readfrom(permission_fpath)
lines_to_remove = [
# '/ImageSetSetMarkedIndividual = authc, roles[admin]'
'/EncounterSetMarkedIndividual = authc, roles[admin]'
]
new_permission_text = permission_text[:]
for line in lines_to_remove:
re.search(re.escape(line), permission_text)
prefix = ut.named_field('prefix', '\\s*')
suffix = ut.named_field('suffix', '\\s*\n')
pattern = ('^' + prefix + re.escape(line) + suffix)
match = re.search(pattern, permission_text,
flags=re.MULTILINE | re.DOTALL)
if match is None:
continue
newline = '<!--%s -->' % (line,)
repl = ut.bref_field('prefix') + newline + ut.bref_field('suffix')
new_permission_text = re.sub(pattern, repl, permission_text,
flags=re.MULTILINE | re.DOTALL)
assert new_permission_text != permission_text, (
'text should have changed')
if new_permission_text != permission_text:
print('Need to write new permission texts')
ut.writeto(permission_fpath, new_permission_text)
else:
print('Permission file seems to be ok')
# Make sure we are using a non-process based database
jdoconfig_fpath = join(unpacked_war_dpath,
'WEB-INF/classes/bundles/jdoconfig.properties')
print('Fixing backend database config')
print('jdoconfig_fpath = %r' % (jdoconfig_fpath,))
ut.assertpath(jdoconfig_fpath)
jdoconfig_text = ut.readfrom(jdoconfig_fpath)
#ut.vd(dirname(jdoconfig_fpath))
#ut.editfile(jdoconfig_fpath)
if mysql_mode:
jdoconfig_text = ut.toggle_comment_lines(jdoconfig_text, 'mysql', False)
jdoconfig_text = ut.toggle_comment_lines(jdoconfig_text, 'derby', 1)
jdoconfig_text = ut.toggle_comment_lines(jdoconfig_text, 'sqlite', 1)
mysql_user = '******'
mysql_passwd = 'somepassword'
mysql_dbname = 'ibeiswbtestdb'
# Use mysql
jdoconfig_text = re.sub(
'datanucleus.ConnectionUserName = .*$',
'datanucleus.ConnectionUserName = '******'datanucleus.ConnectionPassword = .*$',
'datanucleus.ConnectionPassword = '******'datanucleus.ConnectionURL *= *jdbc:mysql:.*$',
'datanucleus.ConnectionURL = jdbc:mysql://localhost:3306/' + mysql_dbname,
jdoconfig_text, flags=re.MULTILINE)
jdoconfig_text = re.sub(
'^.*jdbc:mysql://localhost:3306/shepherd.*$', '',
jdoconfig_text, flags=re.MULTILINE)
else:
# Use SQLIIte
jdoconfig_text = ut.toggle_comment_lines(jdoconfig_text, 'derby', 1)
jdoconfig_text = ut.toggle_comment_lines(jdoconfig_text, 'mysql', 1)
jdoconfig_text = ut.toggle_comment_lines(jdoconfig_text, 'sqlite', False)
ut.writeto(jdoconfig_fpath, jdoconfig_text)
# Need to make sure wildbook can store information in a reasonalbe place
#tomcat_data_dir = join(tomcat_startup_dir, 'webapps', 'wildbook_data_dir')
tomcat_data_dir = join(webapps_dpath, 'wildbook_data_dir')
ut.ensuredir(tomcat_data_dir)
ut.writeto(join(tomcat_data_dir, 'test.txt'), 'A hosted test file')
asset_store_fpath = join(unpacked_war_dpath, 'createAssetStore.jsp')
asset_store_text = ut.read_from(asset_store_fpath)
#data_path_pat = ut.named_field('data_path', 'new File(".*?").toPath')
new_line = 'LocalAssetStore as = new LocalAssetStore("example Local AssetStore", new File("%s").toPath(), "%s", true);' % (
tomcat_data_dir,
'http://localhost:8080/' + basename(tomcat_data_dir)
)
# HACKY
asset_store_text2 = re.sub('^LocalAssetStore as = .*$', new_line, asset_store_text, flags=re.MULTILINE)
ut.writeto(asset_store_fpath, asset_store_text2)