Re: Unpredictable bug: "NewHeadline" instead of actual headline

[vitalije]

As I wrote in the #1348 
 
it 
is my belief that this issue is caused by operating system itself. It seems 
that subprocess.call returns before process has fully finished and its file 
operations are actually flushed to disk. In this test script the next 
process sometimes starts before the previous one has finished.

Vitalije 

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Re: Unpredictable bug: "NewHeadline" instead of actual headline

[vitalije]

SegundoBob, when I change in the test03.py script:

# leoPfn = pathlib.Path('test.leo')
# to
leoPfn = pathlib.Path('test.db')

There is no error reported with the phantom NewHeadline. However, every 4-5 
seconds Leo reports a gnx clash. The next thing I am going to look for 
potential places where gnx clash can affect reading .leo xml file. 
Vitalije

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Re: Unpredictable bug: "NewHeadline" instead of actual headline

[Edward K. Ream]

On Tuesday, September 24, 2019 at 4:34:19 AM UTC-5, Edward K. Ream wrote:
>
>
>
> On Mon, Sep 23, 2019 at 5:56 PM SegundoBob  wrote:
>
>> *I think the bug is in Leo-Editor*
>>
>
> Please file a new issue.
>

In the new issue, please pretend I know nothing of the old issue and its 
long history.  That is, please summarize the what is know as succinctly as 
you can.

It will also help me if you could edit the first comment as new data or 
ideas become available.  That way I won't have to wade through new batches 
of comments.

Edward

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Re: Unpredictable bug: "NewHeadline" instead of actual headline

[Edward K. Ream]

On Mon, Sep 23, 2019 at 5:56 PM SegundoBob  wrote:

> *I think the bug is in Leo-Editor*
>

Please file a new issue.

Edward

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Re: Unpredictable bug: "NewHeadline" instead of actual headline

[vitalije]

SegundoBob, it seems that google has stripped your attached files. Clicking 
in the link test03 does nothing.

You can find the three Python files composing test03  here test03
>
> Can you post them in github or directly to my email: vitalijem (at) gmail 
dot (ending as usual).

Vitalije

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Re: Unpredictable bug: "NewHeadline" instead of actual headline

[SegundoBob]

*I think the bug is in Leo-Editor*

test03 produces the same bug symptom as my unit tests of my compare 
Leo-Editor files:

"NewHeadline" is seen by LeoBridge but the disk file is correct and does 
not contain "NewHeadline".

For test03 errors/loops is larger, but the errors are still unpredictable 
with many error free loops.  For example.

31 loops 18 errors 58% errors/loops

51 loops 32 errors 62% errors/loops

Based on the above evidence, I think the bug is in Leo-Editor.

You can find the three Python files composing test03  here test03 ;>>

*Bug Symptoms*

Each of the following should not be:

The root node has two parents.  Both parents are the hidden root node.  
Ordinarily, the root node has exactly one parent.

The root node is the only node and its headline is "NewHeadline".

Note: I believe that Leo-Editor until recently set new node headlines to 
"NewHeadline", but now in most cases Leo-Editor sets new node headlines to 
"newHeadline" (no capital letter).

*Test run breaking on the first error (test03 modified slightly since this 
run, to exit gracefully and to conditionally insert breakpoints)*

>
> 2019-09-23 14:55:24 /pri/git/leo_bug_demos/2019-09-21-Phantom-NewHeadline
$ ./test03.py
Leo 6.1-devel, devel branch, build 53cf6d1bb1
2019-09-23 10:35:13 -0500

Expected:
0 Headline
0.0 Headline
0.0.0 Headline
0.1 Headline
0.2 Headline
0.2.0 Headline
Actual:
NewHeadline
> 
/pri/git/leo_bug_demos/2019-09-21-Phantom-NewHeadline/check_file.py(117)checkOutline()
-> exit(50)
(Pdb) where
  
/pri/git/leo_bug_demos/2019-09-21-Phantom-NewHeadline/check_file.py(121)()
-> main()
  
/pri/git/leo_bug_demos/2019-09-21-Phantom-NewHeadline/check_file.py(56)main()
-> checkOutline(cmdrT, outline)
> 
/pri/git/leo_bug_demos/2019-09-21-Phantom-NewHeadline/check_file.py(117)checkOutline()
-> exit(50)
(Pdb) l
112  print(hdr)
113  print('Actual:')
114  for hdr in walkList:
115  print(hdr)
116  import pdb; pdb.set_trace()
117  ->exit(50)
118  #@-others
119  
120  if __name__ == "__main__":
121  main()
122  #@-leo
(Pdb) walkList
['NewHeadline']
(Pdb) root

(Pdb) root.v

(Pdb) root.v.parents
[>, >]
(Pdb) root.v.children
[]
(Pdb) root.v.parents[0]
>
(Pdb) root.v.parents[0].children
[]
(Pdb) cmdrT
Commander 140033515115464: 
'/pri/git/leo_bug_demos/2019-09-21-Phantom-NewHeadline/test.leo'
(Pdb) 


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Re: Unpredictable bug: "NewHeadline" instead of actual headline

[vitalije]

O.k. just add two more lines:
bridge.g.app.commander_cacher = leoCache.CommanderCacher()
bridge.g.app.commander_db = bridge.g.app.commander_cacher.db


HTH Vitalije


On Monday, September 23, 2019 at 1:22:57 AM UTC+2, SegundoBob wrote:
>
> I spoke too soon.  All the easy symptoms turned out to be bugs in my test 
> programs.  No surprise there.
>
> I'm back to trying to produce the "Phantom Headline" symptom, and 
> unfortunately Vitalije's work around doesn't work.  It does get me through 
> the second Leo-Editor file open, but then it fails with the "closed 
> database" error on the second cmdr.save().
>
> phantom_new_Headline_01_passes.py 
>  
> is 
> a test that passes.   Using Vitalije's work around, I made it closer to my 
> unit test that encounters the "Phantom Headline" symptom:  
> phantom_new_Headline_02_work_around_fails.py
>
> Run of phantom_new_Headline_02_work_around_fails.py:
>
>> 2019-09-22 15:56:08 /pri/git/leo_bug_demos/2019-09-21-Phantom-NewHeadline
>> $ ./test02.py
>> ic| test02.py:62 in main()
>> cmdrT: Commander 139729630728768: 
>> '/pri/git/leo_bug_demos/2019-09-21-Phantom-NewHeadline/test.leo'
>> ic| test02.py:62 in main()
>> cmdrT: Commander 139729631145264: 
>> '/pri/git/leo_bug_demos/2019-09-21-Phantom-NewHeadline/test.leo'
>> Traceback (most recent call last):
>>   File "./test02.py", line 172, in 
>> main()
>>   File "./test02.py", line 63, in main
>> cmdrT.save()
>>   File "/pri/git/leo-editor/leo/commands/commanderFileCommands.py", line 
>> 355, in save
>> c.fileCommands.save(c.mFileName)
>>   File "/pri/git/leo-editor/leo/core/leoFileCommands.py", line 1049, in 
>> save
>> g.app.commander_cacher.save(c, fileName, changeName=True)
>>   File "/pri/git/leo-editor/leo/core/leoCache.py", line 99, in save
>> self.commit()
>>   File "/pri/git/leo-editor/leo/core/leoCache.py", line 58, in commit
>> self.db.conn.commit()
>> sqlite3.ProgrammingError: Cannot operate on a closed database.
>
>
>

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Re: Unpredictable bug: "NewHeadline" instead of actual headline

[SegundoBob]

I spoke too soon.  All the easy symptoms turned out to be bugs in my test 
programs.  No surprise there.

I'm back to trying to produce the "Phantom Headline" symptom, and 
unfortunately Vitalije's work around doesn't work.  It does get me through 
the second Leo-Editor file open, but then it fails with the "closed 
database" error on the second cmdr.save().

phantom_new_Headline_01_passes.py 
 is 
a test that passes.   Using Vitalije's work around, I made it closer to my 
unit test that encounters the "Phantom Headline" symptom:  
phantom_new_Headline_02_work_around_fails.py ;>>

Run of phantom_new_Headline_02_work_around_fails.py:

> 2019-09-22 15:56:08 /pri/git/leo_bug_demos/2019-09-21-Phantom-NewHeadline
> $ ./test02.py
> ic| test02.py:62 in main()
> cmdrT: Commander 139729630728768: 
> '/pri/git/leo_bug_demos/2019-09-21-Phantom-NewHeadline/test.leo'
> ic| test02.py:62 in main()
> cmdrT: Commander 139729631145264: 
> '/pri/git/leo_bug_demos/2019-09-21-Phantom-NewHeadline/test.leo'
> Traceback (most recent call last):
>   File "./test02.py", line 172, in 
> main()
>   File "./test02.py", line 63, in main
> cmdrT.save()
>   File "/pri/git/leo-editor/leo/commands/commanderFileCommands.py", line 
> 355, in save
> c.fileCommands.save(c.mFileName)
>   File "/pri/git/leo-editor/leo/core/leoFileCommands.py", line 1049, in 
> save
> g.app.commander_cacher.save(c, fileName, changeName=True)
>   File "/pri/git/leo-editor/leo/core/leoCache.py", line 99, in save
> self.commit()
>   File "/pri/git/leo-editor/leo/core/leoCache.py", line 58, in commit
> self.db.conn.commit()
> sqlite3.ProgrammingError: Cannot operate on a closed database.


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Re: Unpredictable bug: "NewHeadline" instead of actual headline

[vitalije]

On Sunday, September 22, 2019 at 7:26:20 PM UTC+2, SegundoBob wrote:
>
>
>
> On Sunday, September 22, 2019 at 2:12:03 AM UTC-7, Edward K. Ream wrote:
>>
>> On Friday, September 20, 2019 at 5:33:31 AM UTC-5, Edward K. Ream wrote:
>>
>> Sounds like a worthy bug.  Thanks for sharing it with us.
>>>
>>
>> A few more thoughts.
>>
>>
> I spent yesterday trying to put together a small test program and bug 
> report concerning this bug.  I regret to say that the "Phantom NewHeadline" 
> symptom appears to be the wrong symptom to investigate.  It appears that 
> LeoBridge has very serious problems creating and/or changing a Leo-Editor 
> file.  Almost everything I tried failed in some way every time.  I was 
> seriously hampered by your decision not to fix issue #658 
> , which prevented me 
> from writing simple tests.  Not being able to close a LeoBridge commander 
> is a very inconvenient restriction.  It would also help if there was a 
> LeoBridge.close() method. 
>

To avoid triggering #658, manually reopen g.app.db object after closing the 
first commander. Perhaps leoBridge.openLeoFile method could be modified to 
check if g.app.db is closed and if so, reopen it automatically. 

# add an import statement
import leo.core.leoCache as leoCache

# and then after closing first commander
cmdr1.close()
# insert the following two lines
bridge.g.app.global_cacher = leoCache.GlobalCacher()
bridge.g.app.db = bridge.g.app.global_cacher.db
# now you can open another file
cmdr2 = bridge.openLeoFile(...)
#

Vitalije

 

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Re: Unpredictable bug: "NewHeadline" instead of actual headline

[SegundoBob]

On Sunday, September 22, 2019 at 2:12:03 AM UTC-7, Edward K. Ream wrote:
>
> On Friday, September 20, 2019 at 5:33:31 AM UTC-5, Edward K. Ream wrote:
>
> Sounds like a worthy bug.  Thanks for sharing it with us.
>>
>
> A few more thoughts.
>
>
I spent yesterday trying to put together a small test program and bug 
report concerning this bug.  I regret to say that the "Phantom NewHeadline" 
symptom appears to be the wrong symptom to investigate.  It appears that 
LeoBridge has very serious problems creating and/or changing a Leo-Editor 
file.  Almost everything I tried failed in some way every time.  I was 
seriously hampered by your decision not to fix issue #658 
, which prevented me 
from writing simple tests.  Not being able to close a LeoBridge commander 
is a very inconvenient restriction.  It would also help if there was a 
LeoBridge.close() method. 

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Re: Unpredictable bug: "NewHeadline" instead of actual headline

[Edward K. Ream]

On Friday, September 20, 2019 at 5:33:31 AM UTC-5, Edward K. Ream wrote:

Sounds like a worthy bug.  Thanks for sharing it with us.
>

A few more thoughts.

1. A good goal would be to drop into the debugger (g.pdb) when the bug 
happens. Easier said than done, surely.

If you *can* do this, then you can look around at the whole environment.  I 
suggest using g.printObj(x) on complex x.

2. I wonder whether this bug could be related to #35 
, which was the result 
of timing issues when opening multiple .leo files from the bridge. The fix 
is ugly enough that it might not be solid.

Edward

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Re: Unpredictable bug: "NewHeadline" instead of actual headline

[vitalije]

  Have you in fact ever seen a phantom vnode?  I have not.
>
> SegundoBob
>

>From time to time I bump on something like this, mostly because I tend to 
search for nodes using c.fileCommands.gnxDict, or when I manually build 
subtree and forget to  create two way binding between children and parents.

Have you tried to disable plugins when loading leoBridge?

Vitalije

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Re: Unpredictable bug: "NewHeadline" instead of actual headline

[SegundoBob]

On Friday, September 20, 2019 at 3:33:31 AM UTC-7, Edward K. Ream wrote:
 

> If your .leo files contain external files, I would also trace 
> fast_at.scan_lines in leoAtFile.py.
>
>
The problem files are small and they do not contain any external files.

Thanks for your suggestions. I'll continue investigating.

SegundoBob

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Re: Unpredictable bug: "NewHeadline" instead of actual headline

[SegundoBob]

On Thursday, September 19, 2019 at 10:41:46 PM UTC-7, vitalije wrote:
>
> I don't know how you go through the nodes of these two files. 
>

I obtain all the vnodes by doing a depth first walk starting at 
cmdr.hiddenRootNode.  The attribute vnode.children gives me the children of 
each vnode.  I use cmdr.clearAllVisited() and vnode.isVisited() to prevent 
visiting cloned sub-trees twice.  I believe Edward suggested more or less 
this strategy a long time ago.

I have also used emacs to examine the Leo-Editor files suffering from 
phantom "NewHeadline" and these files did not contain any "NewHeadline" and 
they contained only what I expected.  The files are small.

Thanks for the suggestion.  I hadn't considered phantom vnodes.  Have you 
in fact ever seen a phantom vnode?  I have not.

SegundoBob

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Re: Unpredictable bug: "NewHeadline" instead of actual headline

[Edward K. Ream]

On Thursday, September 19, 2019 at 5:02:54 PM UTC-5, SegundoBob wrote:

This bug may be in my code or in Leo-Editor code.  I have been seeing 
> occurrences for at least two weeks.
>
> The bug occurs when I run my unit tests for my program that compares two 
> Leo-Editor files.  I have 41 unit tests.  The bug occurs about once every 
> 30 tests.
>

Sounds like a worthy bug.  Thanks for sharing it with us.

I don't have any ideas about causes.  My strategy would be to insert traces 
in Leo as follows:

I would trace fast.readFile in leoFileCommands.py.  This is the code that 
reads .leo files.

If your .leo files contain external files, I would also trace 
fast_at.scan_lines in leoAtFile.py.

My goal would be to have the traces fire only in unexpected situations, so 
I don't get overwhelmed with data.  If you can get that to happen you will 
likely have a handle on what is going on.

Edward

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Re: Unpredictable bug: "NewHeadline" instead of actual headline

[vitalije]

Can you share your code for the second process that compares outlines D and 
expected D. I don't know how you go through the nodes of these two files. A 
phantom node that can't be seen might be a node which is not properly 
connected. Every vnode has to be linked to its parent i.e. its parent node 
must be in v.parents, and also for every parent in v.parents, must be v in 
parent.children. If your code for traversing outline nodes uses values from 
c.fileCommands.gnxDict, it might find some nodes that are not part of the 
outline. Such nodes are not visible in the outline. 

Without looking at actual code I can't think of anything else.

Vitalije

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Re: Unpredictable bug: "NewHeadline" instead of actual headline

[SegundoBob]

On 9/19/19 5:22 PM, Brian Theado wrote:

> It isn't clear from your description what your 2nd subprocess.call is 
executing.

The second subprocess.call() executes my compare Leo-Editor files program.  
This is the same program executed by my first subprocess.call().

Thanks for your suggestions.

Segundo Bob

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Re: Unpredictable bug: "NewHeadline" instead of actual headline

[Brian Theado]

Without seeing actual code, I find it difficult to understand your
explanation enough to come up with any guess. But it seems you have 3
things: leo code, your comparison code, and your unit test code. Since this
problem started happening, at least one of those things had to have changed
right? I see you are running a git commit from a month ago, so maybe your
leo code hasn't changed since the problem appeared and so it must be your
unit test or program code? Do you have a history (in git or something) of
your code? When it is a problem which is fairly easy to reliably reproduce
then git bisect is very handy.

It isn't clear from your description what your 2nd subprocess.call is
executing. Whatever it is, maybe you can have extra tracing or set a
debugger breakpoint whenever newHeadline is seen and that way you can get
more information.

On Thu, Sep 19, 2019 at 6:02 PM SegundoBob  wrote:

>
> *Leo-Editor Version:*
> Leo 6.1-devel, devel branch, build f5986d8016
> 2019-08-09 10:23:41 -0500
> Python 3.6.8, PyQt version 5.11.1
>
> *Bug Description:*
>
> This bug may be in my code or in Leo-Editor code.  I have been seeing
> occurrences for at least two weeks.
>
> The bug occurs when I run my unit tests for my program that compares two
> Leo-Editor files.  I have 41 unit tests.  The bug occurs about once every
> 30 tests.
>
> My comparison program uses LeoBridge to access Leo-Editor files.  File
> "Content" as accessed by vnode (not position).  File "structure" is
> analyzed by position (path).  That is, my program gets the headline and
> body from the vnode (vn.h, bn.b).  When my comparison program compares the
> unit test File A and File B, the bug never occurs.  Using LeoBridge my
> comparision program produces a difference file (File D).  The unit tests
> use subprocess.call() to execute my comparision program, so the process
> comparing File A and File B and producing File D ends.  Then the unit tests
> use subprocess.call() to compare the actual File D with the expected File
> D.  This is when the bug occurs.
>
> The bug is always that a headline in File D, is seen to be "NewHeadline."
> But when I look at File D, there is no "NewHeadline" and File D is exactly
> as expected.
>
> There are never two or more bug occurrences in comparing one File D.  The
> bug never occurs on a node body.  There is a slight tendency for bug
> occurrences to cluster.  That is, sometimes it occurs on two tests in a row
> or even three tests in row.
>
> *Help:*
>
> Does anyone have any ideas about how this bug could occur?  Does anyone
> have any ideas about how to chase this bug?
>
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Unpredictable bug: "NewHeadline" instead of actual headline

[SegundoBob]

*Leo-Editor Version:*
Leo 6.1-devel, devel branch, build f5986d8016
2019-08-09 10:23:41 -0500
Python 3.6.8, PyQt version 5.11.1

*Bug Description:*

This bug may be in my code or in Leo-Editor code.  I have been seeing 
occurrences for at least two weeks.

The bug occurs when I run my unit tests for my program that compares two 
Leo-Editor files.  I have 41 unit tests.  The bug occurs about once every 
30 tests.

My comparison program uses LeoBridge to access Leo-Editor files.  File 
"Content" as accessed by vnode (not position).  File "structure" is 
analyzed by position (path).  That is, my program gets the headline and 
body from the vnode (vn.h, bn.b).  When my comparison program compares the 
unit test File A and File B, the bug never occurs.  Using LeoBridge my 
comparision program produces a difference file (File D).  The unit tests 
use subprocess.call() to execute my comparision program, so the process 
comparing File A and File B and producing File D ends.  Then the unit tests 
use subprocess.call() to compare the actual File D with the expected File 
D.  This is when the bug occurs.

The bug is always that a headline in File D, is seen to be "NewHeadline."  
But when I look at File D, there is no "NewHeadline" and File D is exactly 
as expected.

There are never two or more bug occurrences in comparing one File D.  The 
bug never occurs on a node body.  There is a slight tendency for bug 
occurrences to cluster.  That is, sometimes it occurs on two tests in a row 
or even three tests in row.

*Help:*

Does anyone have any ideas about how this bug could occur?  Does anyone 
have any ideas about how to chase this bug?

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