import glob import os import re import sys import time import types from stat import ST_MODE try: from distutils import log from distutils.core import setup from distutils.ccompiler import * from distutils.command.build import build from distutils.command.clean import clean from distutils.command.install import install from distutils.command.install_egg_info import install_egg_info from distutils.command.sdist import sdist from distutils.dep_util import newer from distutils.dir_util import copy_tree, remove_tree from distutils.errors import DistutilsFileError from distutils.versionpredicate import VersionPredicate import distutils.filelist except: sys.exit("Your python distutils version is too old, please try a newer one") ## Basics ... package_nam = 'Mobyle' package_ver = '1.5.3' package_url = 'https://projets.pasteur.fr/wiki/mobyle/' package_aut = 'The Mobyle team' package_mel = 'mobyle@pasteur.fr' package_platforms = ['Unix'] package_license = 'GNU General Public License, version 2 (GPLv2)' ## Prerequisites ... require_pyt = [ 'python (>=2.5, <3.0)' ] require_mod = [ ('Image (>=1.1.5)', 'PIL (>=2.0.0)'), #Imaging or pillow 'lxml (>=2.2.4)', 'simpletal (>=4.1, <5.0)', 'simplejson (>=1.7.1)' ] ## Installation ... core_dat = [ 'Src/Mobyle/*.py', 'Src/Mobyle/Classes/*.py', 'Src/Mobyle/Execution/*.py', 'Src/Mobyle/Converter/*.py', 'Src/Mobyle/Captcha/*', 'Src/Mobyle/Captcha/data/fonts/vera/*', 'Src/Mobyle/Captcha/data/pictures/abstract/*', 'Src/Mobyle/Captcha/data/pictures/nature/*', 'Src/Mobyle/Captcha/data/words/*', 'Schema/*', 'Local/*.py', 'Local/Config/Execution/*.py', 'Local/*/*.py', 'Tools/validation/*.xsl', 'Tools/README', 'Example/Local/*.py', 'Example/Local/*/*.py', 'Doc/Admin/*.pdf', 'Doc/*.pdf', 'Doc/*.html', 'Doc/Admin/*.tex', 'Doc/Admin/*.png', 'Doc/*.tex', 'Doc/*.jpeg'] core_cfg = [ 'Local/Policy.py', 'Local/black_list.py', 'Local/mailTemplate.py', 'Local/CustomClasses/__init__.py' ] core_scr = [ 'Src/Mobyle/RunnerChild.py', 'Tools/mob*', 'Tools/job_updater.py', 'Tools/session_updater.py', 'Local/Config/Execution/__init__.py' ] core_tst = [ 'Src/Mobyle/Test/*.py', 'Src/Mobyle/Test/Converter/*.py', 'Src/Mobyle/Test/Converter/DataSequences/*', 'Src/Mobyle/Test/Converter/DataAlignments/*' ] core_exe = [ 'Tools/setsid.c' ] core_fix = core_scr + [ 'Src/Mobyle/ConfigManager.py', 'Src/Mobyle/Converter/__init__.py', 'Src/Mobyle/Execution/__init__.py' ] core_tre = [ 'Services', 'Services/Programs', 'Services/Viewers', 'Services/Workflows', 'Services/Tutorials', 'Local/Services', 'Local/Services/Programs', 'Local/Services/Viewers', 'Local/Services/Workflows', 'Local/Services/Tutorials' ] cgis_scr = [ 'Src/Portal/cgi-bin/MobylePortal/*' ] cgis_fix = [ 'Src/Portal/cgi-bin/MobylePortal/mb_cgi.py' ] html_dat = [ 'Src/Portal/htdocs/MobylePortal/*/*', 'Src/Portal/htdocs/MobylePortal/*/openid/*' ] html_cfg = [ 'Src/Portal/htdocs/MobylePortal/css/local.css', 'Src/Portal/htdocs/MobylePortal/html/announcement.txt' ] html_tre = [ 'sessions/anonymous', 'sessions/authentified', 'jobs/ADMINDIR' ] misc_dat = [ 'AUTHORS', 'COPYING', 'INSTALL', 'NEWS', 'UPDATE' ] ## Distribution ... dist_lst = core_dat + core_cfg + core_scr + core_exe + core_tst dist_lst += cgis_scr + html_dat + html_cfg + misc_dat excl_lst = [ 'setup.cfg', 'Local/Policy.pasteur.py', 'Local/Config/Config.py' ] ## Let the hard code begins ... core_dir = 'core' cgis_dir = 'cgis' html_dir = 'html' niaid_dir = 'niaid' ############# # # # Utilities # # # ############# def copy_script(src, dst, exe): ## Mostly stolen from distutils.build_scripts.run() ... if not newer(src, dst): return dir = os.path.dirname(dst) log.info("copying and adjusting %s -> %s", src, dir) try: f = open(src, "r") except os.error, (errstr): raise DistutilsFileError, "could not open '%s': %s" % (src, errstr) try: o = open(dst, "w") except: raise DistutilsFileError, "could not create '%s': %s" % (dst, errstr) l = f.readline() l = re.sub("^#!.*python", "#!" + exe, l) o.write(l) o.writelines(f.readlines()) o.close() f.close() omod = os.stat(dst)[ST_MODE] & 07777 nmod = (omod | 0555) & 07777 if nmod != omod: log.info("changing mode of %s from %o to %o", dst, omod, nmod) os.chmod(dst, nmod) def fix_script(src, dst, mob, htm): log.info("adjusting %s -> %s", src, dst) try: f = open(src, "r") except os.error, (errstr): raise DistutilsFileError, "could not open '%s': %s" % (src, errstr) try: g = open(dst, "w") except os.error, (errstr): raise DistutilsFileError, "could not create '%s': %s" % (dst, errstr) while True: l = f.readline() if not l: break if mob and l == 'MOBYLEHOME = None\n': l = l.replace('None', "'debian/mobyle/usr/share/mobyle/core'", 1) if htm and l == 'MOBYLEHTDOCS = None\n': l = l.replace('None', "'debian/mobyle/usr/share/mobyle/htdocs'", 1) g.write(l) g.close() f.close() mod = os.stat(src)[ST_MODE] & 07777 os.chmod(dst, mod) def find_file(src, msk): lst = distutils.filelist.FileList() lst.findall(src) lst.include_pattern(msk, anchor=False) return lst.files ################### # # # building Mobyle # # # ################### class build_mobyle(build): def run(self): chk = True for req in require_pyt: chk &= self.chkpython(req) for req in require_mod: if isinstance(req, types.StringTypes): req = [req] chk = False for alt in req: predicate = VersionPredicate(alt) if self.chkmodule(predicate): print >> sys.stderr, "%s python module found" % predicate.name chk = True break if not chk: print >> sys.stderr, "Missing mandatory %s python module" % predicate.name sys.exit(1) build.run(self) def chkpython(self, req): chk = VersionPredicate(req) ver = '.'.join([str(v) for v in sys.version_info[:2]]) if not chk.satisfied_by(ver): print >> sys.stderr, "Invalid python version, expected %s" % req return False return True def chkmodule(self, predicate): try: mod = __import__(predicate.name) except: return False for v in [ '__version__', 'version' ]: ver = getattr(mod, v, None) break try: if ver and not predicate.satisfied_by(ver): print >> sys.stderr, "Invalid module version, expected %s" % req return False except: pass return True class build_core(build): build.sub_commands += [('build_core', lambda self:True)] def run(self): base = os.path.join(self.build_base, core_dir) self.mkpath(base) (dat, cfg, scr, exe) = ([], [], [], []) for m in core_dat: dat += glob.glob(m) for m in core_cfg: cfg += glob.glob(m) for m in core_scr: scr += glob.glob(m) for m in core_exe: exe += glob.glob(m) for f in dat: if f in scr + cfg + exe: continue if not os.path.isfile(f): continue dst = os.path.join(base, f) self.mkpath(os.path.dirname(dst)) self.copy_file(f, dst, preserve_mode=0) for f in cfg: if not os.path.isfile(f): continue dst = os.path.join(base, f + '.new') self.mkpath(os.path.dirname(dst)) self.copy_file(f, dst, preserve_mode=0) for f in scr: if f in exe: continue if not os.path.isfile(f): continue dst = os.path.join(base, f) self.mkpath(os.path.dirname(dst)) copy_script(f, dst, self.executable) cc = new_compiler() for f in core_exe: objs = cc.compile([f], self.build_temp) cc.link_executable(objs, f[0:-2], base) for f in core_tre: dir = os.path.join(base, f) self.mkpath(dir) class build_html(build): build.sub_commands += [('build_html', lambda self:True)] def run(self): base = os.path.join(self.build_base, html_dir) self.mkpath(base) (dat, cfg) = ([], []) for m in html_dat: dat += glob.glob(m) for m in html_cfg: cfg += glob.glob(m) com = os.path.commonprefix(dat + cfg) for f in dat: if f in cfg: continue if not os.path.isfile(f): continue dst = os.path.join(base, 'portal', f) dst = dst.replace(com, '', 1) self.mkpath(os.path.dirname(dst)) self.copy_file(f, dst, preserve_mode=0) for f in cfg: if not os.path.isfile(f): continue dst = os.path.join(base, 'portal', f + '.new') dst = dst.replace(com, '', 1) self.mkpath(os.path.dirname(dst)) self.copy_file(f, dst, preserve_mode=0) for f in html_tre: dir = os.path.join(base, 'data', f) self.mkpath(dir) class build_cgis(build): build.sub_commands += [('build_cgis', lambda self:True)] def run(self): base = os.path.join(self.build_base, cgis_dir) self.mkpath(base) scr = [] for m in cgis_scr: scr += glob.glob(m) for s in scr: if not os.path.isfile(s): continue dst = os.path.join(base, os.path.basename(s)) copy_script(s, dst, self.executable) class build_bmps(build): build.sub_commands.append( ('build_bmps', lambda self:True) ) def run(self): if not os.path.exists( os.path.join( niaid_dir, 'Workflow' ) ): return workflow_src_dir = os.path.join( niaid_dir, 'Workflow', 'target', 'mobyleWorkflow' ) workflow_dest_dir = os.path.join(self.build_base, html_dir , "workflow") #by default copy_tree preserve permissions copy_tree( workflow_src_dir, workflow_dest_dir ) class build_bmid(build): build.sub_commands.append( ('build_bmid', lambda self:True) ) def run(self): if not os.path.exists( os.path.join( niaid_dir, 'InterfaceDesigner' ) ): return bmid_src_dir = os.path.join( niaid_dir, 'InterfaceDesigner', 'target', 'BMID' ) bmid_dest_dir = os.path.join(self.build_base, html_dir , "BMID") #by default copy_tree preserve permissions copy_tree( bmid_src_dir, bmid_dest_dir ) ####################### # # # Mobyle Installation # # # ####################### class install_core(install): install.sub_commands += [('install_core', lambda self:True)] setattr(install, 'install_core', None) install.user_options.append( ('install-core=', None, 'installation directory for Core files')) def run(self): base = os.path.join(self.build_base, core_dir) inst = self.distribution.command_options.get('install') if not inst.has_key('install_core'): sys.exit('Missing mandatory Core installation directory') if not inst.has_key('install_htdocs'): sys.exit('Missing mandatory htdocs installation directory') self.install_dir = inst['install_core'][1] copy_tree(base, self.install_dir) for f in find_file(base, '*.new'): dst = f.replace(base, self.install_dir, 1)[:-4] if os.path.lexists(dst): continue move_file(dst + '.new', dst) fix = [] for m in core_fix: fix += glob.glob(m) for f in fix: f = os.path.join(self.install_dir, f) n = f + '.tmp' fix_script(f, n, self.install_dir, inst['install_htdocs'][1]) os.unlink(f) move_file(n, f) class install_html(install): install.sub_commands += [('install_html', lambda self:True)] setattr(install, 'install_htdocs', None) install.user_options.append( ('install-htdocs=', None, 'installation directory for HTML files')) def run(self): inst = self.distribution.command_options.get('install') if not inst.has_key('install_htdocs'): sys.exit('Missing mandatory htdocs installation directory') for target_dir in ('portal' , 'data'): build_dir = os.path.join(self.build_base, html_dir, target_dir ) inst_dir = os.path.join(inst['install_htdocs'][1], target_dir) copy_tree(build_dir, inst_dir) for f in find_file(build_dir, '*.new'): dst = f.replace(build_dir, inst_dir, 1)[:-4] if os.path.lexists(dst): continue move_file(dst + '.new', dst) class install_cgis(install): install.sub_commands += [('install_cgis', lambda self:True)] setattr(install, 'install_cgis', None) install.user_options.append(('install-cgis=', None, 'installation directory for CGIs files')) def run(self): cgi_build_dir = os.path.join(self.build_base, cgis_dir) inst = self.distribution.command_options.get('install') if not inst.has_key('install_cgis'): sys.exit('Missing mandatory CGIs installation directory') if not inst.has_key('install_core'): sys.exit('Missing mandatory Core installation directory') cgi_inst_dir = inst['install_cgis'][1] copy_tree(cgi_build_dir, cgi_inst_dir) fix = [] for m in cgis_fix: fix += glob.glob(m) for f in fix: f = os.path.join(cgi_inst_dir, os.path.basename(f)) n = f + '.tmp' fix_script(f, n, inst['install_core'][1], None) os.unlink(f) move_file(n, f) class install_bmps(install): install.sub_commands.append( ('install_bmps', lambda self: self.install_bmps ) ) setattr(install, 'install_bmps', False) install.user_options.append(('install-bmps', None, 'installation of BCBB Mobyle Pipeline System')) def initialize_options(self): install.initialize_options(self) self.install_bmps = False def run(self): inst = self.distribution.command_options.get('install') if not inst.has_key('install_htdocs'): sys.exit('Missing mandatory htdocs installation directory') print "[DEBUG] ",os.path.join( self.build_base, html_dir, 'workflow' ) if not os.path.exists( os.path.join( self.build_base, html_dir, 'workflow' ) ): sys.exit('BMPS is not part of this tarball. Get a tarball with BMPS from Mobyle website (https://projets.pasteur.fr/projects/mobyle/wiki/download)') bmps_build_dir = os.path.join(self.build_base, html_dir , 'workflow') bmps_inst_dir = os.path.join( inst['install_htdocs'][1] , 'workflow') copy_tree(bmps_build_dir, bmps_inst_dir) class install_bmid(install): install.sub_commands.append( ('install_bmid', lambda self: self.install_bmid ) ) setattr(install, 'install_bmid', False) install.user_options.append(('install-bmid', None, 'installation of BCBB Mobyle Interface Designer')) def initialize_options(self): install.initialize_options(self) self.install_bmid = False def run(self): inst = self.distribution.command_options.get('install') if not inst.has_key('install_htdocs'): sys.exit('Missing mandatory htdocs installation directory') if not os.path.exists( os.path.join( self.build_base, html_dir, 'BMID' ) ): sys.exit('BMID is not part of this tarball. Get a tarball with BMID from Mobyle website (https://projets.pasteur.fr/projects/mobyle/wiki/download)') bmid_build_dir = os.path.join(self.build_base, html_dir , 'BMID') bmid_inst_dir = os.path.join( inst['install_htdocs'][1] , 'BMID') copy_tree(bmid_build_dir, bmid_inst_dir) ################################### # # # creation of source distribution # # # ################################### class sdist_mobyle(sdist): user_options = [('with-bmps', None, 'build the gwt libraries for BMPS, as part of mobyle distribution [DEFAULT=False]'), ('with-bmid', None, 'build the gwt libraries for BMID, as part of mobyle distribution [DEFAULT=False]'), ('niaid-home-dir=', None, 'the home directory of niaid BMID and BMPS src project [DEFAULT ./niaid]' ), ('maven-bin-name=', None, 'the maven binary name to use [DEFAULT mvn]')] + sdist.user_options def initialize_options(self): sdist.initialize_options(self) self.with_bmps = False self.with_bmid = False self.niaid_home_dir = os.path.realpath('niaid') self.maven_bin_name = 'mvn' def run(self): self.niaid_link_name = 'niaid' self.must_clean = False if self.with_bmid or self.with_bmps: self.set_up() if self.with_bmid: self.build_bmid() self.distribution.metadata.name = self.distribution.metadata.name + "+BMID" if self.with_bmps: self.build_bmps() self.distribution.metadata.name = self.distribution.metadata.name + "+BMPS" self.mktemplate(dist_lst, excl_lst) sdist.run(self) if self.with_bmid or self.with_bmps: self.clean_up() def mktemplate(self, incl, excl): fd = open('MANIFEST.in', 'w') print >> fd, '# WARNING: This is a generated file, *DO NOT* edit.' for nam in incl: print >> fd, 'include %s' % nam for nam in excl: print >> fd, 'exclude %s' % nam if self.with_bmid: print >> fd, 'recursive-include %s *' % os.path.join( self.niaid_link_name, 'InterfaceDesigner', 'target', 'BMID') if self.with_bmps: print >> fd, 'recursive-include %s *' % os.path.join( self.niaid_link_name, 'Workflow', 'target', 'mobyleWorkflow') fd.close() def set_up(self): if os.path.exists( self.niaid_link_name ): if os.path.realpath(self.niaid_link_name) == os.path.realpath(self.niaid_home_dir): self.must_clean = False return else: raise RuntimeError( "there already exist a 'niaid' path in %s and is different than %s"%( os.getcwd(), self.niaid_home_dir) ) os.symlink( self.niaid_home_dir , self.niaid_link_name ) self.must_clean = True def clean_up(self): if self.must_clean: os.unlink( self.niaid_link_name ) def build_niaid(self, command): from subprocess import Popen, PIPE import select process_ = Popen( command, shell = True , stdout= sys.stdout, stdin = None , stderr = sys.stderr, cwd = self.niaid_home_dir ) process_.wait() if process_.returncode != 0: raise RuntimeError def build_bmps(self): print "\n[INFO] Building BMPS project" command = '%s -pl CommonLib,Workflow package' %self.maven_bin_name try: self.build_niaid( command ) except RuntimeError,err: print >> sys.stderr , "[ERROR] BMPS project BUILD FAILURE" sys.exit(0) def build_bmid(self): print "\n[INFO] Building BMID project" command = '%s -pl CommonLib,InterfaceDesigner package' %self.maven_bin_name try: self.build_niaid( command ) except Exception, err: print >> sys.stderr , "[ERROR] BMID project BUILD FAILURE" ################### # # # clean all stuff # # # ################### class clean_mobyle(clean): def run(self): for d in [ core_dir, cgis_dir, html_dir ]: base = os.path.join(self.build_base, d) if not os.path.exists(base): continue remove_tree(base) clean.run(self) class install_mobyle_egg_info(install_egg_info): def run(self): pass ############################# # Overwrite default methods # ############################# cmdclass = {'build': build_mobyle, 'build_core': build_core, 'build_html': build_html, 'build_cgis': build_cgis, 'build_bmid': build_bmid, 'build_bmps': build_bmps, 'install_egg_info': install_mobyle_egg_info, 'install_core': install_core, 'install_cgis': install_cgis, 'install_html': install_html, 'install_bmid': install_bmid, 'install_bmps': install_bmps, 'sdist': sdist_mobyle, 'clean': clean_mobyle, } setup( name = package_nam, version = package_ver, url = package_url, author = package_aut, author_email = package_mel, platforms = package_platforms , license = package_license, cmdclass = cmdclass )