Merge branch 'master' of ssh://git-annex.branchable.com

doc/bugs/git_annex_assistant_exits_with_failure/comment_7_63b3ec113d52501237abbe6ee1ef5fa5._comment

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+[[!comment format=mdwn
+ username="lasitus"
+ avatar="http://cdn.libravatar.org/avatar/dfe778f28027aeb75876172022aa5de3"
+ subject="comment 7"
+ date="2017-02-17T03:23:46Z"
+ content="""
+Ok, I have a script that generates the error. This generates a repository and 30 GB of random binary files with many folders 2 layers deep. Just put in an empty folder and run with python. No remotes are necessary. This was run in Windows 10 in a git bash window.
+
+```
+#!/usr/bin/env python
+
+import logging
+import os
+import shutil
+import subprocess
+import uuid
+
+logging.basicConfig(level=logging.DEBUG)
+
+repositoryPath = os.path.abspath(\"./bigRepoTest\")	
+os.makedirs(repositoryPath)
+
+subprocess.call(\"git init\", cwd=repositoryPath)
+subprocess.call(\"git annex init pc\", cwd=repositoryPath)
+
+def makeRandomDirectories(level1FolderCount, level2FolderCount, fileCount):
+	for directoryIndex in range(0, level1FolderCount):
+		logging.info(\"Adding top level folder \" + str(directoryIndex + 1) + \" of \" + str(level1FolderCount))
+		newDirectory = os.path.join(repositoryPath, str(uuid.uuid1()))
+		os.makedirs(newDirectory)
+		for directoryIndex in range(0, level2FolderCount):
+			newNestedDirectory = os.path.join(newDirectory, str(uuid.uuid1()))
+			os.makedirs(newNestedDirectory)
+			for fileIndex in range(0, fileCount):
+				newFile = os.path.join(newNestedDirectory, str(uuid.uuid1()) + \".bin\")
+				with open(newFile, 'wb') as fileOut:
+					fileOut.write(os.urandom(500000))
+
+makeRandomDirectories(32, 1000, 1)
+with open(os.path.join(repositoryPath, \"assistant.log\"), 'w') as output:
+	subprocess.Popen([\"git\", \"annex\", \"assistant\", \"--debug\"], cwd=repositoryPath, stdout=output, stderr=output)
+	makeRandomDirectories(32, 1000, 1)
+	subprocess.call(\"tail -f daemon.log\", cwd=os.path.join(repositoryPath, \".git\", \"annex\"))
+```
+"""]]

doc/bugs/mysterious_dependency_of_git_annex_status_output_of_the_added_file.mdwn

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+### Please describe the problem.
+
+in v6 mode -- Result depends on having a good sleep before running 'git annex add'.
+
+Without sleep, git annex manages first to stage file to be committed into git, but then also modifies it to be added into annex  (this is not shown above -- just inspect that repository obtained without having any sleep)
+
+I guess relates to http://git-annex.branchable.com/bugs/Too_difficult_if_not_impossible_to_explicitly_add__47__keep_file_under_git___40__not_annex__41___in_v6_without_employing_.gitattributes/
+
+### What steps will reproduce the problem?
+
+Run http://www.onerussian.com/tmp/ga-3.sh  twice:  once giving 0 secs to sleep, and then 1 (or about 0.3 might work as well)
+
+
+### What version of git-annex are you using? On what operating system?
+
+6.20170209+gitg16be7b5cc-1~ndall+1
+
+### Please provide any additional information below.
+
+if we just proceed with the script (init, add, status) without any delays -- git annex status would report it 
+[[!format sh """
+$> ./ga-3.sh 0
++ s=0
+++ mktemp -d
++ d=/home/yoh/.tmp/tmp.d6g0E7scxt
++ echo 'directory: /home/yoh/.tmp/tmp.d6g0E7scxt'
+directory: /home/yoh/.tmp/tmp.d6g0E7scxt
++ cd /home/yoh/.tmp/tmp.d6g0E7scxt
++ git init
+Initialized empty Git repository in /tmp/tmp.d6g0E7scxt/.git/
++ git annex init --version=6
+init  ok
+(recording state in git...)
++ sed -i -e 's,pre-commit ,pre-commit --debug ,g' .git/hooks/pre-commit
++ echo 'I: creating a file'
+I: creating a file
++ echo whatever
++ sleep 0
++ git -c annex.largefiles=nothing annex --debug add file5
+[2017-02-17 10:19:48.91932971] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","ls-files","--others","--exclude-standard","-z","--","file5"]
+add file5 (non-large file; adding content to git repository) ok
+[2017-02-17 10:19:48.923428344] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","ls-files","--modified","-z","--","file5"]
+(recording state in git...)
+[2017-02-17 10:19:48.927922289] feed: xargs ["-0","git","--git-dir=.git","--work-tree=.","--literal-pathspecs","add","--"]
+[2017-02-17 10:19:48.956812867] process done ExitSuccess
++ git annex status
+M file5
+"""]]
+
+And if we wait just a bit before running add -- we would get it reported added
+[[!format sh """
+hopa:~/.tmp
+$> ./ga-3.sh 1
++ s=1
+++ mktemp -d
++ d=/home/yoh/.tmp/tmp.4I7ym6dSx2
++ echo 'directory: /home/yoh/.tmp/tmp.4I7ym6dSx2'
+directory: /home/yoh/.tmp/tmp.4I7ym6dSx2
++ cd /home/yoh/.tmp/tmp.4I7ym6dSx2
++ git init
+Initialized empty Git repository in /tmp/tmp.4I7ym6dSx2/.git/
++ git annex init --version=6
+init  ok
+(recording state in git...)
++ sed -i -e 's,pre-commit ,pre-commit --debug ,g' .git/hooks/pre-commit
++ echo 'I: creating a file'
+I: creating a file
++ echo whatever
++ sleep 1
++ git -c annex.largefiles=nothing annex --debug add file5
+[2017-02-17 10:19:52.529445464] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","ls-files","--others","--exclude-standard","-z","--","file5"]
+add file5 (non-large file; adding content to git repository) ok
+[2017-02-17 10:19:52.533532166] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","ls-files","--modified","-z","--","file5"]
+(recording state in git...)
+[2017-02-17 10:19:52.537789158] feed: xargs ["-0","git","--git-dir=.git","--work-tree=.","--literal-pathspecs","add","--"]
+[2017-02-17 10:19:52.567222419] process done ExitSuccess
++ git annex status
+A file5
+"""]]
+
+[[!meta author=yoh]]

doc/forum/dangling_blobs.mdwn

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+Revisiting an issue I reported a couple of months ago but never figured out. I am trying to use git annex assistant on two separate machines to automatically mirror files between them. But after I start the second assistant and add new files to the annex, I find that git fsck reports dangling blobs. Is there a conflict between the two assistants?
+
+On the server:
+
+    $ mkdir ~/annex
+    $ cd ~/annex
+    $ git init
+    $ git annex init u --version=6
+    $ echo This is test file 1. >testfile1.txt
+    $ git annex add testfile1.txt
+    $ git annex sync
+    $ git remote add ml2 ssh://laptop/Users/username/annex
+    $ git annex assistant
+
+After all that, I do this on the laptop:
+
+    $ cd ~/
+    $ git clone ssh://server/home/username/annex
+    $ cd annex
+    $ git annex init ml2 --version=6
+    $ git annex sync
+    $ git annex assistant
+
+At this point git fsck is happy. But when I add files to the annex on either machine and run git fsck, I get messages like:
+
+    Checking object directories: 100% (256/256), done.
+    dangling blob 31a30177d1e37faf8eac96524302a61713d3d522

doc/todo/more_of_diagnostic_information_in_case_of_failures_into_returned_json.mdwn

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+ATM I am experiencing sporadic failures of the batched  git annex addurl call -- seems to report failure (success: False) once in a while, but succeeds on a retry:
+
+[[!format sh """
+(Pdb) p url
+'http://openneuro.s3.amazonaws.com/ds000001/ds000001_R1.1.0/uncompressed/sub016/BOLD/task001_run003/QA/QA_report.pdf?versionId=null'
+
+(Pdb) p out_json
+{u'note': u'from datalad', u'command': u'addurl', u'file': u'ds000001_R1.1.0/uncompressed/sub016/BOLD/task001_run003/QA/QA_report.pdf', u'success': False}
+
+(Pdb) up
+> /home/yoh/proj/datalad/datalad/datalad/support/gitrepo.py(210)newfunc()
+-> return func(self, file_new, *args, **kwargs)
+
+(Pdb) func(self, file_new, *args, **kwargs)
+{u'note': u'from datalad', u'file': u'ds000001_R1.1.0/uncompressed/sub016/BOLD/task001_run003/QA/QA_report.pdf', u'command': u'addurl', u'key': u'MD5E-s1191419--cb4efab8104b5117f64b58ee6d6a79ba.pdf', u'success': True}
+"""]]
+
+besides me blindly trying to re-run it e.g. 3 times and only then declare total failure, I wondered if json output could provide more information (if any known) about the failure... e.g. if a custom remote crashed/errorred (I guess the case here due to "from datalad") -- what was stderr/exit code for that process if crashed/ERROR msg... if wget -- what was stderr there
+
+[[!meta name=yoh]]