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BBSutils.py
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BBSutils.py
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##############################################################################
###
### This file is part of the BBS software (Bioconductor Build System).
###
### Author: Hervé Pagès <[email protected]>
### Last modification: May 31, 2023
###
### IMPORTANT: The BBSutils.py file is imported by the Single Package Builder:
### https://github.com/Bioconductor/packagebuilder.git
###
import sys
import os
import shutil
#import urllib.request
import hashlib
import logging
import bbs.fileutils
import bbs.jobs
import bbs.rdir
logging.basicConfig(format='%(levelname)s: %(asctime)s %(filename)s - %(message)s',
datefmt='%m/%d/%Y %I:%M:%S %p',
level=logging.DEBUG)
# TODO: Indent the output (use length of stack as the indent level)
class Debug:
def __init__(self, ps='BBS:debug> '):
self.is_on = False
self.ps = ps
self.stack = []
def Print(self, msg):
if not self.is_on:
return
print("%s%s" % (self.ps, msg))
sys.stdout.flush()
return
def Begin(self, f, args=[]):
if not self.is_on:
return
self.stack.append(f)
fargs = f + '('
is_first = True
for arg in args:
if not is_first:
fargs += ', '
fargs += str(arg)
is_first = False
fargs += ')'
self.Print('BEGIN %s' % fargs)
return
def End(self):
if not self.is_on:
return
f = self.stack.pop()
self.Print('END of %s' % f)
return
debug = Debug()
def getenv(name, is_required=True, default=None):
if name in os.environ and os.environ[name] != "":
val = os.environ[name]
elif is_required:
print("BBSutils ERROR: Environment variable %s" % name, end=" ")
if not name in os.environ:
print("not found!")
else:
print("is an empty string!")
sys.exit("==> EXIT")
else:
val = default
debug.Print("%s=%s" % (name, val))
return val
debug.is_on = int(getenv('BBS_DEBUG', False, "0")) != 0
##############################################################################
### GLOBAL CONSTANTS
##############################################################################
meat_index_file = 'meat-index.dcf'
skipped_index_file = 'skipped-index.dcf'
pkg_dep_graph_file = 'pkg_dep_graph.txt'
#sys.path.append(os.path.join(BBS_home, "nodes"))
import nodes.nodespecs
pkgType2FileExt = {
'source': "tar.gz",
'win.binary': "zip",
'win64.binary': "zip",
'mac.binary': "tgz",
'mac.binary.big-sur-x86_64': "tgz",
'mac.binary.big-sur-arm64': "tgz",
'mac.binary.leopard': "tgz",
'mac.binary.mavericks': "tgz",
'mac.binary.el-capitan': "tgz"
}
def getNodeSpec(node_hostname, key, key_is_optional=False):
specs = nodes.nodespecs.allnodes[node_hostname.lower()]
if key == 'pkgFileExt':
return pkgType2FileExt[specs['pkgType']]
if key_is_optional:
return specs.get(key)
return specs[key]
# Return Source node's name to construct a path
def getSourceNode():
source_machines = []
for build in getenv('BBS_OUTGOING_MAP').split(" "):
if build.count("source"):
source_machines.append(build.strip("source:|/buildsrc)"))
return source_machines[0]
##############################################################################
### copyTheDamnedThingNoMatterWhat()
##############################################################################
### Copying stuff locally can be a **real** challenge on Windows!
### It can fail for various reasons e.g. a process holding on the file to
### copy, or the file path is too long.
###
### Example: shutil.copy2() will fail on Windows if a process is sill holding
### on the file to copy. Similarly shutil.copytree() will fail if a process
### is still holding on a file located inside the directory to copy, or if the
### directory contains files with paths that are too long. The first situation
### has been observed when calling shutil.copytree() on 'NetSAM.Rcheck' on a
### Windows build machine right after 'R CMD check' failed. Note that the
### latter failed with:
### ..
### * checking files in 'vignettes' ... OK
### * checking examples ... ERROR
### Running examples in 'NetSAM-Ex.R' failed
### Warning in file(con, "r") :
### cannot open file 'NetSAM-Ex.Rout': Permission denied
### Error in file(con, "r") : cannot open the connection
### Execution halted
###
### So it failed exactly for the very reason that a process was holding on
### 'NetSAM.Rcheck\NetSAM-Ex.Rout' hence preventing 'R CMD check' from opening
### the file to parse its content for errors.
###
### Then, when almost immediately after that, BBS tried to copy 'NetSAM.Rcheck'
### with shutil.copytree(), it failed with:
###
### [Errno 13] Permission denied: 'NetSAM.Rcheck\NetSAM-Ex.Rout'
###
### because the process holding on 'NetSAM.Rcheck\NetSAM-Ex.Rout' was still
### there!
### The magic bullet is to use rsync to copy stuff locally. Sounds overkill
### but it seems to work no matter what.
def copyTheDamnedThingNoMatterWhat(src, destdir):
bbs.rdir.set_readable_flag(src)
if sys.platform == 'win32':
## rsync should do it no matter what.
rsync_cmd = getenv('BBS_RSYNC_CMD')
src = bbs.fileutils.to_cygwin_style(src)
destdir = bbs.fileutils.to_cygwin_style(destdir)
cmd = '%s -rL %s %s' % (rsync_cmd, src, destdir)
## Looks like rsync can sometimes have hiccups on Windows where it
## gets stuck forever (timeout) even when trying to perform a local
## copy. So we need to try harder (up to 3 attemps before we give up).
#bbs.jobs.runJob(cmd, stdout=None, maxtime=120.0, verbose=True)
bbs.jobs.tryHardToRunJob(cmd, nb_attempts=3, stdout=None,
maxtime=60.0, sleeptime=10.0,
failure_is_fatal=False, verbose=True)
else:
print("BBS> Copying %s to %s/ ..." % (src, destdir), end=" ")
sys.stdout.flush()
if os.path.isdir(src):
dst = os.path.join(destdir, os.path.basename(src))
if os.path.exists(dst):
bbs.fileutils.nuke_tree(dst, ignore_errors=True)
## We use 'dirs_exist_ok=True' in case bbs.fileutils.nuke_tree()
## above failed to nuke 'dst'.
shutil.copytree(src, dst, symlinks=True, dirs_exist_ok=True)
else:
shutil.copy2(src, destdir)
print("OK")
sys.stdout.flush()
return
##############################################################################
### downloadFile()
##############################################################################
### From https://stackoverflow.com/questions/3431825/
def _md5(file):
hash_md5 = hashlib.md5()
with open(file, "rb") as f:
for chunk in iter(lambda: f.read(4096), b""):
hash_md5.update(chunk)
return hash_md5.hexdigest()
def downloadFile(file, baseurl, dest, MD5sum=None, timeout=600):
print('downloading %s' % file, end=' ')
sys.stdout.flush()
url = baseurl + '/' + file
if os.path.isdir(dest):
destfile = os.path.join(dest, file)
else:
destfile = dest
if MD5sum != None and os.path.exists(destfile):
current = _md5(destfile)
if current == MD5sum:
print('--> skip (identical to local)')
return
print('...', end=' ')
sys.stdout.flush()
#urllib.request.urlretrieve(url, destfile)
## An alternative to urllib.request.urlretrieve() above (from
## https://stackoverflow.com/questions/7243750/).
## Unlike urllib.request.urlretrieve(), this allows us to control
## the timeout limit.
#response = urllib.request.urlopen(url, timeout=timeout)
#f = open(destfile, 'wb')
#shutil.copyfileobj(response, f)
#f.close()
## Unfortunately the urllib.request-based solutions above turn out to
## very unreliable, timing out all the time for mysterious reasons.
## So we just use good ol' curl command for the download.
curl_cmd = getenv('BBS_CURL_CMD')
cmd = '%s --silent %s --output %s' % (curl_cmd, url, destfile)
bbs.jobs.tryHardToRunJob(cmd, nb_attempts=3, maxtime=timeout, sleeptime=5.0)
if MD5sum != None:
current = _md5(destfile)
#print('(%s)' % current, end=' ')
#sys.stdout.flush()
assert current == MD5sum
print('ok')
return destfile