1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/eae248415389/ changeset: eae248415389 user: clements date: 2012-12-18 22:27:20 summary: First iteration of updating Sphinx RST files. These describe classes and modules (and ...) and are used to generate the Sphinx code documentation. However, they are not updated automatically.

Add the patch.py to automate some of the RST update process, but it is still pretty brutal. Look for cleanup in the next few releases. affected #: 9 files

diff -r de8bc5bde938c937759ced066ef28ce1f6202641 -r eae248415389203907b5b951f139a200024ae069 doc/Makefile --- a/doc/Makefile +++ b/doc/Makefile @@ -6,6 +6,9 @@ SPHINXBUILD = sphinx-build PAPER = BUILDDIR = build +UPDATEWORKDIR = /tmp/galaxySphinxUpdate +UPDATEWORKSOURCELIB = $(UPDATEWORKDIR)/source/lib +SPHINXAPIDOC = sphinx-apidoc

# Internal variables. PAPEROPT_a4 = -D latex_paper_size=a4 @@ -21,7 +24,7 @@ $(TOOLDATASHAREDDIR)/ncbi/builds.txt \ $(TOOLDATASHAREDDIR)/ucsc/publicbuilds.txt

-.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext +.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext updaterst

# Sphinx wants the build files to be there; Copy the sample files into @@ -51,9 +54,13 @@ @echo " changes to make an overview of all changed/added/deprecated items" @echo " linkcheck to check all external links for integrity" @echo " doctest to run all doctests embedded in the documentation (if enabled)" + @echo " updaterst to update sphinx rst to reflect code structure changes"

+ +# might also want to do +# cd source/lib; hg revert; rm *.rst.orig; or not. clean: - -rm -rf $(BUILDDIR)/* + -rm -rf $(BUILDDIR)/* $(UPDATEWORKDIR)

html: $(TOOLDATABUILDFILES) $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html @@ -165,3 +172,20 @@ $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest @echo "Testing of doctests in the sources finished, look at the " \ "results in $(BUILDDIR)/doctest/output.txt." + +# Targets for updating the structure of the Sphinx RST doc for lib/ + +$(UPDATEWORKSOURCELIB): + mkdir -p $(UPDATEWORKSOURCELIB) + +# Create a fresh version of the RST files for the lib, and then create a +# unified patch file (ignore all emacs leftovers). +# Feed that to our custom version of patch.py, which applies patches that +# are only adds, and reports everything else to the user to deal with manually +# +# Note: this is still a very rough process. the run of patch.py gets some +# errors that don't mean anything to us. And the manual process is not fun. +updaterst: $(UPDATEWORKSOURCELIB) + $(SPHINXAPIDOC) -o $(UPDATEWORKSOURCELIB) ../lib + -diff -x '*.rst~' -ru source/lib $(UPDATEWORKSOURCELIB) > $(UPDATEWORKDIR)/alldifs.patch + ./patch.py $(UPDATEWORKDIR)/alldifs.patch

diff -r de8bc5bde938c937759ced066ef28ce1f6202641 -r eae248415389203907b5b951f139a200024ae069 doc/patch.py --- /dev/null +++ b/doc/patch.py @@ -0,0 +1,1085 @@ +#!/usr/bin/env python +""" Patch utility to apply unified diffs + + Brute-force line-by-line non-recursive parsing + + Copyright (c) 2008-2012 anatoly techtonik + Available under the terms of MIT license + + Project home: http://code.google.com/p/python-patch/ + + + $Id: patch.py 181 2012-11-23 16:03:05Z techtonik $ + $HeadURL: https://python-patch.googlecode.com/svn/trunk/patch.py $ + + This program needs further tweaking for how we use it at Galaxy. +""" + +__author__ = "anatoly techtonik techtonik@gmail.com" +__version__ = "1.12.11" + +import copy +import logging +import re +# cStringIO doesn't support unicode in 2.5 +from StringIO import StringIO +import urllib2 + +from os.path import exists, isfile, abspath +import os +import shutil + +#------------------------------------------------ +# Logging is controlled by logger named after the +# module name (e.g. 'patch' for patch.py module) + +debugmode = False + +logger = logging.getLogger(__name__) + +debug = logger.debug +info = logger.info +warning = logger.warning + +class NullHandler(logging.Handler): + """ Copied from Python 2.7 to avoid getting + `No handlers could be found for logger "patch"` + http://bugs.python.org/issue16539 + """ + def handle(self, record): + pass + def emit(self, record): + pass + def createLock(self): + self.lock = None + +logger.addHandler(NullHandler()) + +#------------------------------------------------ +# Constants for Patch/PatchSet types + +DIFF = PLAIN = "plain" +GIT = "git" +HG = MERCURIAL = "mercurial" +SVN = SUBVERSION = "svn" +# mixed type is only actual when PatchSet contains +# Patches of different type +MIXED = MIXED = "mixed" + + +#------------------------------------------------ +# Helpers (these could come with Python stdlib) + +# x...() function are used to work with paths in +# cross-platform manner - all paths use forward +# slashes even on Windows. + +def xisabs(filename): + """ Cross-platform version of `os.path.isabs()` + Returns True if `filename` is absolute on + Linux, OS X or Windows. + """ + if filename.startswith('/'): # Linux/Unix + return True + elif filename.startswith('\'): # Windows + return True + elif re.match(r'\w:[\/]', filename): # Windows + return True + return False + +def xnormpath(path): + """ Cross-platform version of os.path.normpath """ + return os.path.normpath(path).replace(os.sep, '/') + +def xstrip(filename): + """ Make relative path out of absolute by stripping + prefixes used on Linux, OS X and Windows. + + This function is critical for security. + """ + while xisabs(filename): + # strip windows drive with all slashes + if re.match(r'\w:[\/]', filename): + filename = re.sub(r'^\w+:[\/]+', '', filename) + # strip all slashes + elif re.match(r'[\/]', filename): + filename = re.sub(r'^[\/]+', '', filename) + return filename + +#----------------------------------------------- +# Main API functions + +def fromfile(filename): + """ Parse patch file. If successful, returns + PatchSet() object. Otherwise returns False. + """ + patchset = PatchSet() + debug("reading %s" % filename) + fp = open(filename, "rb") + res = patchset.parse(fp) + fp.close() + if res == True: + return patchset + return False + + +def fromstring(s): + """ Parse text string and return PatchSet() + object (or False if parsing fails) + """ + ps = PatchSet( StringIO(s) ) + if ps.errors == 0: + return ps + return False + + +def fromurl(url): + """ Parse patch from an URL, return False + if an error occured. Note that this also + can throw urlopen() exceptions. + """ + ps = PatchSet( urllib2.urlopen(url) ) + if ps.errors == 0: + return ps + return False + + +# --- Utility functions --- +# [ ] reuse more universal pathsplit() +def pathstrip(path, n): + """ Strip n leading components from the given path """ + pathlist = [path] + while os.path.dirname(pathlist[0]) != '': + pathlist[0:1] = os.path.split(pathlist[0]) + return '/'.join(pathlist[n:]) +# --- /Utility function --- + + +class Hunk(object): + """ Parsed hunk data container (hunk starts with @@ -R +R @@) """ + + def __init__(self): + self.startsrc=None #: line count starts with 1 + self.linessrc=None + self.starttgt=None + self.linestgt=None + self.invalid=False + self.hasplus=False # True if any "+" lines in hunk + self.hasminus=False # True if any "-" lines in hunk + self.text=[] + + def originalText(self): + + return("@@ -" + str(self.startsrc) + + "," + str(self.linessrc) + + " +" + str(self.starttgt) + + "," + str(self.linestgt) + + "\n" + + self.printableText()) + + def printableText(self): + """Reformat text into printable text""" + + # yeah, there must be a better way to do this. + printable = "" + for line in self.text: + printable += line + + return printable + + + +# def apply(self, estream): +# """ write hunk data into enumerable stream +# return strings one by one until hunk is +# over +# +# enumerable stream are tuples (lineno, line) +# where lineno starts with 0 +# """ +# pass + + +class Patch(object): + """ Patch for a single file """ + def __init__(self): + self.source = None + self.target = None + self.hunks = [] + self.hunkends = [] + self.header = [] + + self.type = None + + +class PatchSet(object): + + def __init__(self, stream=None): + # --- API accessible fields --- + + # name of the PatchSet (filename or ...) + self.name = None + # patch set type - one of constants + self.type = None + + # list of Patch objects + self.items = [] + + self.errors = 0 # fatal parsing errors + self.warnings = 0 # non-critical warnings + # --- /API --- + + if stream: + self.parse(stream) + + def __len__(self): + return len(self.items) + + def parse(self, stream): + """ parse unified diff + return True on success + """ + lineends = dict(lf=0, crlf=0, cr=0) + nexthunkno = 0 #: even if index starts with 0 user messages number hunks from 1 + + p = None + hunk = None + # hunkactual variable is used to calculate hunk lines for comparison + hunkactual = dict(linessrc=None, linestgt=None) + + + class wrapumerate(enumerate): + """Enumerate wrapper that uses boolean end of stream status instead of + StopIteration exception, and properties to access line information. + """ + + def __init__(self, *args, **kwargs): + # we don't call parent, it is magically created by __new__ method + + self._exhausted = False + self._lineno = False # after end of stream equal to the num of lines + self._line = False # will be reset to False after end of stream + + def next(self): + """Try to read the next line and return True if it is available, + False if end of stream is reached.""" + if self._exhausted: + return False + + try: + self._lineno, self._line = super(wrapumerate, self).next() + except StopIteration: + self._exhausted = True + self._line = False + return False + return True + + @property + def is_empty(self): + return self._exhausted + + @property + def line(self): + return self._line + + @property + def lineno(self): + return self._lineno + + # define states (possible file regions) that direct parse flow + headscan = True # start with scanning header + filenames = False # lines starting with --- and +++ + + hunkhead = False # @@ -R +R @@ sequence + hunkbody = False # + hunkskip = False # skipping invalid hunk mode + + hunkparsed = False # state after successfully parsed hunk + + # regexp to match start of hunk, used groups - 1,3,4,6 + re_hunk_start = re.compile("^@@ -(\d+)(,(\d+))? +(\d+)(,(\d+))?") + + self.errors = 0 + # temp buffers for header and filenames info + header = [] + srcname = None + tgtname = None + + # start of main cycle + # each parsing block already has line available in fe.line + fe = wrapumerate(stream) + while fe.next(): + + # -- deciders: these only switch state to decide who should process + # -- line fetched at the start of this cycle + if hunkparsed: + hunkparsed = False + if re_hunk_start.match(fe.line): + hunkhead = True + elif fe.line.startswith("--- "): + filenames = True + else: + headscan = True + # -- ------------------------------------ + + # read out header + if headscan: + while not fe.is_empty and not fe.line.startswith("--- "): + header.append(fe.line) + fe.next() + if fe.is_empty: + if p == None: + debug("no patch data found") # error is shown later + self.errors += 1 + else: + info("%d unparsed bytes left at the end of stream" % len(''.join(header))) + self.warnings += 1 + # TODO check for \No new line at the end.. + # TODO test for unparsed bytes + # otherwise error += 1 + # this is actually a loop exit + continue + + headscan = False + # switch to filenames state + filenames = True + + line = fe.line + lineno = fe.lineno + + + # hunkskip and hunkbody code skipped until definition of hunkhead is parsed + if hunkbody: + # [x] treat empty lines inside hunks as containing single space + # (this happens when diff is saved by copy/pasting to editor + # that strips trailing whitespace) + if line.strip("\r\n") == "": + debug("expanding empty line in a middle of hunk body") + self.warnings += 1 + line = ' ' + line + + # process line first + if re.match(r"^[- +\]", line): + # gather stats about line endings + if line.endswith("\r\n"): + p.hunkends["crlf"] += 1 + elif line.endswith("\n"): + p.hunkends["lf"] += 1 + elif line.endswith("\r"): + p.hunkends["cr"] += 1 + + if line.startswith("-"): + hunkactual["linessrc"] += 1 + hunk.hasminus = True + elif line.startswith("+"): + hunkactual["linestgt"] += 1 + hunk.hasplus = True + elif not line.startswith("\"): + hunkactual["linessrc"] += 1 + hunkactual["linestgt"] += 1 + hunk.text.append(line) + # todo: handle \ No newline cases + else: + warning("invalid hunk no.%d at %d for target file %s" % (nexthunkno, lineno+1, p.target)) + # add hunk status node + hunk.invalid = True + p.hunks.append(hunk) + self.errors += 1 + # switch to hunkskip state + hunkbody = False + hunkskip = True + + # check exit conditions + if hunkactual["linessrc"] > hunk.linessrc or hunkactual["linestgt"] > hunk.linestgt: + warning("extra lines for hunk no.%d at %d for target %s" % (nexthunkno, lineno+1, p.target)) + # add hunk status node + hunk.invalid = True + p.hunks.append(hunk) + self.errors += 1 + # switch to hunkskip state + hunkbody = False + hunkskip = True + elif hunk.linessrc == hunkactual["linessrc"] and hunk.linestgt == hunkactual["linestgt"]: + # hunk parsed successfully + p.hunks.append(hunk) + # switch to hunkparsed state + hunkbody = False + hunkparsed = True + + # detect mixed window/unix line ends + ends = p.hunkends + if ((ends["cr"]!=0) + (ends["crlf"]!=0) + (ends["lf"]!=0)) > 1: + warning("inconsistent line ends in patch hunks for %s" % p.source) + self.warnings += 1 + if debugmode: + debuglines = dict(ends) + debuglines.update(file=p.target, hunk=nexthunkno) + debug("crlf: %(crlf)d lf: %(lf)d cr: %(cr)d\t - file: %(file)s hunk: %(hunk)d" % debuglines) + # fetch next line + continue + + if hunkskip: + if re_hunk_start.match(line): + # switch to hunkhead state + hunkskip = False + hunkhead = True + elif line.startswith("--- "): + # switch to filenames state + hunkskip = False + filenames = True + if debugmode and len(self.items) > 0: + debug("- %2d hunks for %s" % (len(p.hunks), p.source)) + + if filenames: + if line.startswith("--- "): + if srcname != None: + # XXX testcase + warning("skipping false patch for %s" % srcname) + srcname = None + # XXX header += srcname + # double source filename line is encountered + # attempt to restart from this second line + re_filename = "^--- ([^\t]+)" + match = re.match(re_filename, line) + # todo: support spaces in filenames + if match: + srcname = match.group(1).strip() + else: + warning("skipping invalid filename at line %d" % lineno) + self.errors += 1 + # XXX p.header += line + # switch back to headscan state + filenames = False + headscan = True + elif not line.startswith("+++ "): + if srcname != None: + warning("skipping invalid patch with no target for %s" % srcname) + self.errors += 1 + srcname = None + # XXX header += srcname + # XXX header += line + else: + # this should be unreachable + warning("skipping invalid target patch") + filenames = False + headscan = True + else: + if tgtname != None: + # XXX seems to be a dead branch + warning("skipping invalid patch - double target at line %d" % lineno) + self.errors += 1 + srcname = None + tgtname = None + # XXX header += srcname + # XXX header += tgtname + # XXX header += line + # double target filename line is encountered + # switch back to headscan state + filenames = False + headscan = True + else: + re_filename = "^+++ ([^\t]+)" + match = re.match(re_filename, line) + if not match: + warning("skipping invalid patch - no target filename at line %d" % lineno) + self.errors += 1 + srcname = None + # switch back to headscan state + filenames = False + headscan = True + else: + if p: # for the first run p is None + self.items.append(p) + p = Patch() + p.source = srcname + srcname = None + p.target = match.group(1).strip() + p.header = header + header = [] + # switch to hunkhead state + filenames = False + hunkhead = True + nexthunkno = 0 + p.hunkends = lineends.copy() + continue + + if hunkhead: + match = re.match("^@@ -(\d+)(,(\d+))? +(\d+)(,(\d+))?", line) + if not match: + if not p.hunks: + warning("skipping invalid patch with no hunks for file %s" % p.source) + self.errors += 1 + # XXX review switch + # switch to headscan state + hunkhead = False + headscan = True + continue + else: + # TODO review condition case + # switch to headscan state + hunkhead = False + headscan = True + else: + hunk = Hunk() + hunk.startsrc = int(match.group(1)) + hunk.linessrc = 1 + if match.group(3): hunk.linessrc = int(match.group(3)) + hunk.starttgt = int(match.group(4)) + hunk.linestgt = 1 + if match.group(6): hunk.linestgt = int(match.group(6)) + hunk.invalid = False + hunk.text = [] + + hunkactual["linessrc"] = hunkactual["linestgt"] = 0 + + # switch to hunkbody state + hunkhead = False + hunkbody = True + nexthunkno += 1 + continue + + # /while fe.next() + + if p: + self.items.append(p) + + if not hunkparsed: + if hunkskip: + warning("warning: finished with errors, some hunks may be invalid") + elif headscan: + if len(self.items) == 0: + warning("error: no patch data found!") + return False + else: # extra data at the end of file + pass + else: + warning("error: patch stream is incomplete!") + self.errors += 1 + if len(self.items) == 0: + return False + + if debugmode and len(self.items) > 0: + debug("- %2d hunks for %s" % (len(p.hunks), p.source)) + + # XXX fix total hunks calculation + debug("total files: %d total hunks: %d" % (len(self.items), + sum(len(p.hunks) for p in self.items))) + + # ---- detect patch and patchset types ---- + for idx, p in enumerate(self.items): + self.items[idx].type = self._detect_type(p) + + types = set([p.type for p in self.items]) + if len(types) > 1: + self.type = MIXED + else: + self.type = types.pop() + # -------- + + self._normalize_filenames() + + return (self.errors == 0) + + def _detect_type(self, p): + """ detect and return type for the specified Patch object + analyzes header and filenames info + + NOTE: must be run before filenames are normalized + """ + + # check for SVN + # - header starts with Index: + # - next line is ===... delimiter + # - filename is followed by revision number + # TODO add SVN revision + if (len(p.header) > 1 and p.header[-2].startswith("Index: ") + and p.header[-1].startswith("="*67)): + return SVN + + # common checks for both HG and GIT + DVCS = ((p.source.startswith('a/') or p.source == '/dev/null') + and (p.target.startswith('b/') or p.target == '/dev/null')) + + # GIT type check + # - header[-2] is like "diff --git a/oldname b/newname" + # - header[-1] is like "index <hash>..<hash><mode>" + # TODO add git rename diffs and add/remove diffs + # add git diff with spaced filename + # TODO http://www.kernel.org/pub/software/scm/git/docs/git-diff.html + + # detect the start of diff header - there might be some comments before + if len(p.header) > 1: + for idx in reversed(range(len(p.header))): + if p.header[idx].startswith("diff --git"): + break + if re.match(r'diff --git a/[\w/.]+ b/[\w/.]+', p.header[idx]): + if (idx+1 < len(p.header) + and re.match(r'index \w{7}..\w{7} \d{6}', p.header[idx+1])): + if DVCS: + return GIT + + # HG check + # + # - for plain HG format header is like "diff -r b2d9961ff1f5 filename" + # - for Git-style HG patches it is "diff --git a/oldname b/newname" + # - filename starts with a/, b/ or is equal to /dev/null + # - exported changesets also contain the header + # # HG changeset patch + # # User name@example.com + # ... + # TODO add MQ + # TODO add revision info + if len(p.header) > 0: + if DVCS and re.match(r'diff -r \w{12} .*', p.header[-1]): + return HG + if DVCS and p.header[-1].startswith('diff --git a/'): + if len(p.header) == 1: # native Git patch header len is 2 + return HG + elif p.header[0].startswith('# HG changeset patch'): + return HG + + return PLAIN + + + def _normalize_filenames(self): + """ sanitize filenames, normalizing paths, i.e.: + 1. strip a/ and b/ prefixes from GIT and HG style patches + 2. remove all references to parent directories (with warning) + 3. translate any absolute paths to relative (with warning) + + [x] always use forward slashes to be crossplatform + (diff/patch were born as a unix utility after all) + + return None + """ + for i,p in enumerate(self.items): + if p.type in (HG, GIT): + # TODO: figure out how to deal with /dev/null entries + debug("stripping a/ and b/ prefixes") + if p.source != '/dev/null': + if not p.source.startswith("a/"): + warning("invalid source filename") + else: + p.source = p.source[2:] + if p.target != '/dev/null': + if not p.target.startswith("b/"): + warning("invalid target filename") + else: + p.target = p.target[2:] + + p.source = xnormpath(p.source) + p.target = xnormpath(p.target) + + sep = '/' # sep value can be hardcoded, but it looks nice this way + + # references to parent are not allowed + if p.source.startswith(".." + sep): + warning("error: stripping parent path for source file patch no.%d" % (i+1)) + self.warnings += 1 + while p.source.startswith(".." + sep): + p.source = p.source.partition(sep)[2] + if p.target.startswith(".." + sep): + warning("error: stripping parent path for target file patch no.%d" % (i+1)) + self.warnings += 1 + while p.target.startswith(".." + sep): + p.target = p.target.partition(sep)[2] + # absolute paths are not allowed + if xisabs(p.source) or xisabs(p.target): + warning("error: absolute paths are not allowed - file no.%d" % (i+1)) + self.warnings += 1 + if xisabs(p.source): + warning("stripping absolute path from source name '%s'" % p.source) + p.source = xstrip(p.source) + if xisabs(p.target): + warning("stripping absolute path from target name '%s'" % p.target) + p.target = xstrip(p.target) + + self.items[i].source = p.source + self.items[i].target = p.target + + + def diffstat(self): + """ calculate diffstat and return as a string + Notes: + - original diffstat ouputs target filename + - single + or - shouldn't escape histogram + """ + names = [] + insert = [] + delete = [] + namelen = 0 + maxdiff = 0 # max number of changes for single file + # (for histogram width calculation) + for patch in self.items: + i,d = 0,0 + for hunk in patch.hunks: + for line in hunk.text: + if line.startswith('+'): + i += 1 + elif line.startswith('-'): + d += 1 + names.append(patch.target) + insert.append(i) + delete.append(d) + namelen = max(namelen, len(patch.target)) + maxdiff = max(maxdiff, i+d) + output = '' + statlen = len(str(maxdiff)) # stats column width + for i,n in enumerate(names): + # %-19s | %-4d %s + format = " %-" + str(namelen) + "s | %" + str(statlen) + "s %s\n" + + hist = '' + # -- calculating histogram -- + width = len(format % ('', '', '')) + histwidth = max(2, 80 - width) + if maxdiff < histwidth: + hist = "+"*insert[i] + "-"*delete[i] + else: + iratio = (float(insert[i]) / maxdiff) * histwidth + dratio = (float(delete[i]) / maxdiff) * histwidth + + # make sure every entry gets at least one + or - + iwidth = 1 if 0 < iratio < 1 else int(iratio) + dwidth = 1 if 0 < dratio < 1 else int(dratio) + #print iratio, dratio, iwidth, dwidth, histwidth + hist = "+"*int(iwidth) + "-"*int(dwidth) + # -- /calculating +- histogram -- + output += (format % (names[i], insert[i] + delete[i], hist)) + + output += (" %d files changed, %d insertions(+), %d deletions(-)" + % (len(names), sum(insert), sum(delete))) + return output + + + def apply(self, strip=0): + """ apply parsed patch + return True on success + """ + + total = len(self.items) + errors = 0 + if strip: + # [ ] test strip level exceeds nesting level + # [ ] test the same only for selected files + # [ ] test if files end up being on the same level + try: + strip = int(strip) + except ValueError: + errors += 1 + warning("error: strip parameter '%s' must be an integer" % strip) + strip = 0 + + #for fileno, filename in enumerate(self.source): + for i,p in enumerate(self.items): + f2patch = p.source + if strip: + debug("stripping %s leading component from '%s'" % (strip, f2patch)) + f2patch = pathstrip(f2patch, strip) + if not exists(f2patch): + f2patch = p.target + if strip: + debug("stripping %s leading component from '%s'" % (strip, f2patch)) + f2patch = pathstrip(f2patch, strip) + if not exists(f2patch): + warning("source/target file does not exist\n--- %s\n+++ %s" % (p.source, f2patch)) + errors += 1 + continue + if not isfile(f2patch): + warning("not a file - %s" % f2patch) + errors += 1 + continue + filename = f2patch + + debug("processing %d/%d:\t %s" % (i+1, total, filename)) + + # validate before patching + f2fp = open(filename) + hunkno = 0 + hunk = p.hunks[hunkno] + hunkfind = [] + hunkreplace = [] + validhunks = 0 + canpatch = False + for lineno, line in enumerate(f2fp): + if lineno+1 < hunk.startsrc: + continue + elif lineno+1 == hunk.startsrc: + hunkfind = [x[1:].rstrip("\r\n") for x in hunk.text if x[0] in " -"] + hunkreplace = [x[1:].rstrip("\r\n") for x in hunk.text if x[0] in " +"] + #pprint(hunkreplace) + hunklineno = 0 + + # todo \ No newline at end of file + + # check hunks in source file + if lineno+1 < hunk.startsrc+len(hunkfind)-1: + if line.rstrip("\r\n") == hunkfind[hunklineno]: + hunklineno+=1 + else: + info("file %d/%d:\t %s" % (i+1, total, filename)) + info(" hunk no.%d doesn't match source file at line %d" % (hunkno+1, lineno)) + info(" expected: %s" % hunkfind[hunklineno]) + info(" actual : %s" % line.rstrip("\r\n")) + # not counting this as error, because file may already be patched. + # check if file is already patched is done after the number of + # invalid hunks if found + # TODO: check hunks against source/target file in one pass + # API - check(stream, srchunks, tgthunks) + # return tuple (srcerrs, tgterrs) + + # continue to check other hunks for completeness + hunkno += 1 + if hunkno < len(p.hunks): + hunk = p.hunks[hunkno] + continue + else: + break + + # check if processed line is the last line + if lineno+1 == hunk.startsrc+len(hunkfind)-1: + debug(" hunk no.%d for file %s -- is ready to be patched" % (hunkno+1, filename)) + hunkno+=1 + validhunks+=1 + if hunkno < len(p.hunks): + hunk = p.hunks[hunkno] + else: + if validhunks == len(p.hunks): + # patch file + canpatch = True + break + else: + if hunkno < len(p.hunks): + warning("premature end of source file %s at hunk %d" % (filename, hunkno+1)) + errors += 1 + + f2fp.close() + + if validhunks < len(p.hunks): + if self._match_file_hunks(filename, p.hunks): + warning("already patched %s" % filename) + else: + warning("source file is different - %s" % filename) + errors += 1 + if canpatch: + backupname = filename+".orig" + if exists(backupname): + warning("can't backup original file to %s - aborting" % backupname) + else: + import shutil + shutil.move(filename, backupname) + if self.write_hunks(backupname, filename, p.hunks): + info("successfully patched %d/%d:\t %s" % (i+1, total, filename)) + os.unlink(backupname) + else: + errors += 1 + warning("error patching file %s" % filename) + shutil.copy(filename, filename+".invalid") + warning("invalid version is saved to %s" % filename+".invalid") + # todo: proper rejects + shutil.move(backupname, filename) + + # todo: check for premature eof + return (errors == 0) + + + def can_patch(self, filename): + """ Check if specified filename can be patched. Returns None if file can + not be found among source filenames. False if patch can not be applied + clearly. True otherwise. + + :returns: True, False or None + """ + filename = abspath(filename) + for p in self.items: + if filename == abspath(p.source): + return self._match_file_hunks(filename, p.hunks) + return None + + + def _match_file_hunks(self, filepath, hunks): + matched = True + fp = open(abspath(filepath)) + + class NoMatch(Exception): + pass + + lineno = 1 + line = fp.readline() + hno = None + try: + for hno, h in enumerate(hunks): + # skip to first line of the hunk + while lineno < h.starttgt: + if not len(line): # eof + debug("check failed - premature eof before hunk: %d" % (hno+1)) + raise NoMatch + line = fp.readline() + lineno += 1 + for hline in h.text: + if hline.startswith("-"): + continue + if not len(line): + debug("check failed - premature eof on hunk: %d" % (hno+1)) + # todo: \ No newline at the end of file + raise NoMatch + if line.rstrip("\r\n") != hline[1:].rstrip("\r\n"): + debug("file is not patched - failed hunk: %d" % (hno+1)) + raise NoMatch + line = fp.readline() + lineno += 1 + + except NoMatch: + matched = False + # todo: display failed hunk, i.e. expected/found + + fp.close() + return matched + + + def patch_stream(self, instream, hunks): + """ Generator that yields stream patched with hunks iterable + + Converts lineends in hunk lines to the best suitable format + autodetected from input + """ + + # todo: At the moment substituted lineends may not be the same + # at the start and at the end of patching. Also issue a + # warning/throw about mixed lineends (is it really needed?) + + hunks = iter(hunks) + + srclineno = 1 + + lineends = {'\n':0, '\r\n':0, '\r':0} + def get_line(): + """ + local utility function - return line from source stream + collecting line end statistics on the way + """ + line = instream.readline() + # 'U' mode works only with text files + if line.endswith("\r\n"): + lineends["\r\n"] += 1 + elif line.endswith("\n"): + lineends["\n"] += 1 + elif line.endswith("\r"): + lineends["\r"] += 1 + return line + + for hno, h in enumerate(hunks): + debug("hunk %d" % (hno+1)) + if h.hasminus: + warning("Change removes/replaces some text; INVESTIGATE AND APPLY (OR NOT) MANUALLY") + warning("Change:") + changeText = h.originalText() + if len(changeText) > 1000: + changeText = changeText[0:999] + "...\n" + warning(changeText) + else: + # skip to line just before hunk starts + while srclineno < h.startsrc: + yield get_line() + srclineno += 1 + + for hline in h.text: + # todo: check \ No newline at the end of file + if hline.startswith("-") or hline.startswith("\"): + get_line() + srclineno += 1 + continue + else: + if not hline.startswith("+"): + get_line() + srclineno += 1 + line2write = hline[1:] + # detect if line ends are consistent in source file + if sum([bool(lineends[x]) for x in lineends]) == 1: + newline = [x for x in lineends if lineends[x] != 0][0] + yield line2write.rstrip("\r\n")+newline + else: # newlines are mixed + yield line2write + + for line in instream: + yield line + + + def write_hunks(self, srcname, tgtname, hunks): + src = open(srcname, "rb") + tgt = open(tgtname, "wb") + + debug("processing target file %s" % tgtname) + + tgt.writelines(self.patch_stream(src, hunks)) + + tgt.close() + src.close() + # [ ] TODO: add test for permission copy + shutil.copymode(srcname, tgtname) + return True + + + +if __name__ == "__main__": + from optparse import OptionParser + from os.path import exists + import sys + + opt = OptionParser(usage="1. %prog [options] unified.diff\n" + " 2. %prog [options] http://host/patch%5Cn" + " 3. %prog [options] -- < unified.diff", + version="python-patch %s" % __version__) + opt.add_option("-q", "--quiet", action="store_const", dest="verbosity", + const=0, help="print only warnings and errors", default=1) + opt.add_option("-v", "--verbose", action="store_const", dest="verbosity", + const=2, help="be verbose") + opt.add_option("--debug", action="store_true", dest="debugmode", help="debug mode") + opt.add_option("--diffstat", action="store_true", dest="diffstat", + help="print diffstat and exit") + opt.add_option("-p", "--strip", type="int", metavar='N', default=0, + help="strip N path components from filenames") + (options, args) = opt.parse_args() + + if not args and sys.argv[-1:] != ['--']: + opt.print_version() + opt.print_help() + sys.exit() + readstdin = (sys.argv[-1:] == ['--'] and not args) + + debugmode = options.debugmode + + verbosity_levels = {0:logging.WARNING, 1:logging.INFO, 2:logging.DEBUG} + loglevel = verbosity_levels[options.verbosity] + logformat = "%(message)s" + if debugmode: + loglevel = logging.DEBUG + logformat = "%(levelname)8s %(message)s" + logger.setLevel(loglevel) + loghandler = logging.StreamHandler() + loghandler.setFormatter(logging.Formatter(logformat)) + logger.addHandler(loghandler) + + + if readstdin: + patch = PatchSet(sys.stdin) + else: + patchfile = args[0] + urltest = patchfile.split(':')[0] + if (':' in patchfile and urltest.isalpha() + and len(urltest) > 1): # one char before : is a windows drive letter + patch = fromurl(patchfile) + else: + if not exists(patchfile) or not isfile(patchfile): + sys.exit("patch file does not exist - %s" % patchfile) + patch = fromfile(patchfile) + + if options.diffstat: + print patch.diffstat() + sys.exit(0) + + #pprint(patch) + patch.apply(options.strip) or sys.exit(-1) + + # todo: document and test line ends handling logic - patch.py detects proper line-endings + # for inserted hunks and issues a warning if patched file has incosistent line ends

diff -r de8bc5bde938c937759ced066ef28ce1f6202641 -r eae248415389203907b5b951f139a200024ae069 doc/source/lib/galaxy.jobs.rst --- a/doc/source/lib/galaxy.jobs.rst +++ b/doc/source/lib/galaxy.jobs.rst @@ -48,6 +48,7 @@

galaxy.jobs.actions galaxy.jobs.deferred + galaxy.jobs.rules galaxy.jobs.runners galaxy.jobs.splitters

diff -r de8bc5bde938c937759ced066ef28ce1f6202641 -r eae248415389203907b5b951f139a200024ae069 doc/source/lib/galaxy.jobs.runners.rst --- a/doc/source/lib/galaxy.jobs.runners.rst +++ b/doc/source/lib/galaxy.jobs.runners.rst @@ -57,14 +57,6 @@ :undoc-members: :show-inheritance:

-:mod:`sge` Module ------------------ - -.. automodule:: galaxy.jobs.runners.sge - :members: - :undoc-members: - :show-inheritance: - :mod:`tasks` Module -------------------

diff -r de8bc5bde938c937759ced066ef28ce1f6202641 -r eae248415389203907b5b951f139a200024ae069 doc/source/lib/galaxy.tool_shed.rst --- a/doc/source/lib/galaxy.tool_shed.rst +++ b/doc/source/lib/galaxy.tool_shed.rst @@ -9,6 +9,14 @@ :undoc-members: :show-inheritance:

+:mod:`common_util` Module +------------------------- + +.. automodule:: galaxy.tool_shed.common_util + :members: + :undoc-members: + :show-inheritance: + :mod:`encoding_util` Module ---------------------------

diff -r de8bc5bde938c937759ced066ef28ce1f6202641 -r eae248415389203907b5b951f139a200024ae069 doc/source/lib/galaxy.util.rst --- a/doc/source/lib/galaxy.util.rst +++ b/doc/source/lib/galaxy.util.rst @@ -25,6 +25,14 @@ :undoc-members: :show-inheritance:

+:mod:`debugging` Module +----------------------- + +.. automodule:: galaxy.util.debugging + :members: + :undoc-members: + :show-inheritance: + :mod:`expressions` Module -------------------------

@@ -113,6 +121,14 @@ :undoc-members: :show-inheritance:

+:mod:`shed_util_common` Module +------------------------------ + +.. automodule:: galaxy.util.shed_util_common + :members: + :undoc-members: + :show-inheritance: + :mod:`streamball` Module ------------------------

diff -r de8bc5bde938c937759ced066ef28ce1f6202641 -r eae248415389203907b5b951f139a200024ae069 doc/source/lib/galaxy.webapps.community.rst --- a/doc/source/lib/galaxy.webapps.community.rst +++ b/doc/source/lib/galaxy.webapps.community.rst @@ -42,4 +42,5 @@ galaxy.webapps.community.framework galaxy.webapps.community.model galaxy.webapps.community.security + galaxy.webapps.community.util

diff -r de8bc5bde938c937759ced066ef28ce1f6202641 -r eae248415389203907b5b951f139a200024ae069 doc/source/lib/galaxy.webapps.community.util.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.community.util.rst @@ -0,0 +1,27 @@ +util Package +============ + +:mod:`container_util` Module +---------------------------- + +.. automodule:: galaxy.webapps.community.util.container_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`hgweb_config` Module +-------------------------- + +.. automodule:: galaxy.webapps.community.util.hgweb_config + :members: + :undoc-members: + :show-inheritance: + +:mod:`shed_statistics` Module +----------------------------- + +.. automodule:: galaxy.webapps.community.util.shed_statistics + :members: + :undoc-members: + :show-inheritance: +

diff -r de8bc5bde938c937759ced066ef28ce1f6202641 -r eae248415389203907b5b951f139a200024ae069 doc/source/lib/galaxy.webapps.galaxy.api.rst --- a/doc/source/lib/galaxy.webapps.galaxy.api.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst @@ -293,6 +293,14 @@ :undoc-members: :show-inheritance:

+:mod:`item_tags` Module +----------------------- + +.. automodule:: galaxy.webapps.galaxy.api.item_tags + :members: + :undoc-members: + :show-inheritance: + :mod:`libraries` Module -----------------------

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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