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pythondev
help
The test file is.
2017-10-05T11:38:23.000732
Kym
pythondev_help_Kym_2017-10-05T11:38:23.000732
1,507,203,503.000732
95,903
pythondev
help
-rw-rw-r-- 1 ghost ghost 69K Oct 3 14:09 test.xml
2017-10-05T11:38:32.000347
Kym
pythondev_help_Kym_2017-10-05T11:38:32.000347
1,507,203,512.000347
95,904
pythondev
help
Have you verified the xml is valid?
2017-10-05T11:38:45.000293
Meghan
pythondev_help_Meghan_2017-10-05T11:38:45.000293
1,507,203,525.000293
95,905
pythondev
help
Yup
2017-10-05T11:38:57.000172
Kym
pythondev_help_Kym_2017-10-05T11:38:57.000172
1,507,203,537.000172
95,906
pythondev
help
A
2017-10-05T11:38:59.000579
Kym
pythondev_help_Kym_2017-10-05T11:38:59.000579
1,507,203,539.000579
95,907
pythondev
help
As I mentioned, it used to work
2017-10-05T11:39:07.000376
Kym
pythondev_help_Kym_2017-10-05T11:39:07.000376
1,507,203,547.000376
95,908
pythondev
help
When I only used Jupyter
2017-10-05T11:39:13.000558
Kym
pythondev_help_Kym_2017-10-05T11:39:13.000558
1,507,203,553.000558
95,909
pythondev
help
Now I took the XML
2017-10-05T11:39:18.000235
Kym
pythondev_help_Kym_2017-10-05T11:39:18.000235
1,507,203,558.000235
95,910
pythondev
help
parsing logic out of the function itself and magically ... broken
2017-10-05T11:39:29.000402
Kym
pythondev_help_Kym_2017-10-05T11:39:29.000402
1,507,203,569.000402
95,911
pythondev
help
Haha :slightly_smiling_face:
2017-10-05T11:39:34.000213
Kym
pythondev_help_Kym_2017-10-05T11:39:34.000213
1,507,203,574.000213
95,912
pythondev
help
It also used to work with the 400mb and the 1.5gb files I have
2017-10-05T11:39:50.000520
Kym
pythondev_help_Kym_2017-10-05T11:39:50.000520
1,507,203,590.00052
95,913
pythondev
help
How have you verified where it stops?
2017-10-05T11:40:44.000421
Vada
pythondev_help_Vada_2017-10-05T11:40:44.000421
1,507,203,644.000421
95,914
pythondev
help
Logging
2017-10-05T11:40:50.000518
Kym
pythondev_help_Kym_2017-10-05T11:40:50.000518
1,507,203,650.000518
95,915
pythondev
help
The funny thing is:
2017-10-05T11:41:38.000803
Kym
pythondev_help_Kym_2017-10-05T11:41:38.000803
1,507,203,698.000803
95,916
pythondev
help
1. execution apparently never leaves instantiation of article=PubmedArticle(elem)
2017-10-05T11:42:02.000579
Kym
pythondev_help_Kym_2017-10-05T11:42:02.000579
1,507,203,722.000579
95,917
pythondev
help
2. magically, the execution continues after the end of the loop
2017-10-05T11:42:16.000324
Kym
pythondev_help_Kym_2017-10-05T11:42:16.000324
1,507,203,736.000324
95,918
pythondev
help
That means,
2017-10-05T11:42:20.000723
Kym
pythondev_help_Kym_2017-10-05T11:42:20.000723
1,507,203,740.000723
95,919
pythondev
help
line 251 STILL gets executed!!
2017-10-05T11:42:38.000311
Kym
pythondev_help_Kym_2017-10-05T11:42:38.000311
1,507,203,758.000311
95,920
pythondev
help
What exception is being raised?
2017-10-05T11:43:25.000098
Meghan
pythondev_help_Meghan_2017-10-05T11:43:25.000098
1,507,203,805.000098
95,921
pythondev
help
NONE!
2017-10-05T11:43:29.000114
Kym
pythondev_help_Kym_2017-10-05T11:43:29.000114
1,507,203,809.000114
95,922
pythondev
help
Which line is that one <@Kym>
2017-10-05T11:43:33.000430
Vada
pythondev_help_Vada_2017-10-05T11:43:33.000430
1,507,203,813.00043
95,923
pythondev
help
incidentally, in that last line of the `__init__`, do you mean `self.authorslist` instead of `self.authors`?
2017-10-05T11:43:49.000436
Sirena
pythondev_help_Sirena_2017-10-05T11:43:49.000436
1,507,203,829.000436
95,924
pythondev
help
<@Vada>, which one do you mean?
2017-10-05T11:44:03.000373
Kym
pythondev_help_Kym_2017-10-05T11:44:03.000373
1,507,203,843.000373
95,925
pythondev
help
<@Sirena>, I'll check sec.
2017-10-05T11:44:11.000290
Kym
pythondev_help_Kym_2017-10-05T11:44:11.000290
1,507,203,851.00029
95,926
pythondev
help
The one you are talking about ion 1
2017-10-05T11:44:15.000373
Vada
pythondev_help_Vada_2017-10-05T11:44:15.000373
1,507,203,855.000373
95,927
pythondev
help
article=PubMedArticle
2017-10-05T11:44:28.000204
Vada
pythondev_help_Vada_2017-10-05T11:44:28.000204
1,507,203,868.000204
95,928
pythondev
help
<@Sirena>, you're right. That point still isn't reached.
2017-10-05T11:45:49.000099
Kym
pythondev_help_Kym_2017-10-05T11:45:49.000099
1,507,203,949.000099
95,929
pythondev
help
I've fixed it, though.
2017-10-05T11:45:55.000774
Kym
pythondev_help_Kym_2017-10-05T11:45:55.000774
1,507,203,955.000774
95,930
pythondev
help
line 188
2017-10-05T11:46:19.000481
Kym
pythondev_help_Kym_2017-10-05T11:46:19.000481
1,507,203,979.000481
95,931
pythondev
help
The print('HELLO') I put in the snippet is never reached.
2017-10-05T11:46:33.000365
Kym
pythondev_help_Kym_2017-10-05T11:46:33.000365
1,507,203,993.000365
95,932
pythondev
help
yah, didn't really think it was the issue, but figured I'd mention it while I was looking at it
2017-10-05T11:46:40.000122
Sirena
pythondev_help_Sirena_2017-10-05T11:46:40.000122
1,507,204,000.000122
95,933
pythondev
help
Wait ...
2017-10-05T11:47:05.000494
Kym
pythondev_help_Kym_2017-10-05T11:47:05.000494
1,507,204,025.000494
95,934
pythondev
help
Can you give us the snippet htat calls `medxml_to_sqlite`?
2017-10-05T11:47:07.000125
Meghan
pythondev_help_Meghan_2017-10-05T11:47:07.000125
1,507,204,027.000125
95,935
pythondev
help
<@Kym> the finally will always execute error or not
2017-10-05T11:47:22.000463
Vada
pythondev_help_Vada_2017-10-05T11:47:22.000463
1,507,204,042.000463
95,936
pythondev
help
Yup!
2017-10-05T11:47:29.000207
Kym
pythondev_help_Kym_2017-10-05T11:47:29.000207
1,507,204,049.000207
95,937
pythondev
help
That you don't receive one is odd
2017-10-05T11:47:29.000693
Vada
pythondev_help_Vada_2017-10-05T11:47:29.000693
1,507,204,049.000693
95,938
pythondev
help
as in receive an error
2017-10-05T11:47:40.000525
Vada
pythondev_help_Vada_2017-10-05T11:47:40.000525
1,507,204,060.000525
95,939
pythondev
help
I'll remove the try/except andsee if it shows me something
2017-10-05T11:47:49.000605
Kym
pythondev_help_Kym_2017-10-05T11:47:49.000605
1,507,204,069.000605
95,940
pythondev
help
I'm not passing it though
2017-10-05T11:47:55.000478
Kym
pythondev_help_Kym_2017-10-05T11:47:55.000478
1,507,204,075.000478
95,941
pythondev
help
Yeah that would be best - not good to except Exception
2017-10-05T11:48:01.000315
Vada
pythondev_help_Vada_2017-10-05T11:48:01.000315
1,507,204,081.000315
95,942
pythondev
help
<@Meghan> medxml_to_sqlite('../data/test.xml','../data/test.sqlite')
2017-10-05T11:48:30.000006
Kym
pythondev_help_Kym_2017-10-05T11:48:30.000006
1,507,204,110.000006
95,943
pythondev
help
Yeah, I'm thinking there is an exception, but the calling function is silently handling it when it is raised.
2017-10-05T11:48:32.000188
Meghan
pythondev_help_Meghan_2017-10-05T11:48:32.000188
1,507,204,112.000188
95,944
pythondev
help
Yeah make sure you set your logging to DEBUG for everything if it isn't already
2017-10-05T11:48:57.000360
Mallie
pythondev_help_Mallie_2017-10-05T11:48:57.000360
1,507,204,137.00036
95,945
pythondev
help
The whole function that calls medxml_to_sqlite, if you can.
2017-10-05T11:48:58.000207
Meghan
pythondev_help_Meghan_2017-10-05T11:48:58.000207
1,507,204,138.000207
95,946
pythondev
help
also on line 201, keywordslist is undefined
2017-10-05T11:49:09.000258
Vada
pythondev_help_Vada_2017-10-05T11:49:09.000258
1,507,204,149.000258
95,947
pythondev
help
<@Kym> what are you using as your IDE?
2017-10-05T11:49:37.000019
Vada
pythondev_help_Vada_2017-10-05T11:49:37.000019
1,507,204,177.000019
95,948
pythondev
help
Jupyter?
2017-10-05T11:49:40.000220
Vada
pythondev_help_Vada_2017-10-05T11:49:40.000220
1,507,204,180.00022
95,949
pythondev
help
Or, throw in a log.exception at line 247
2017-10-05T11:49:41.000071
Meghan
pythondev_help_Meghan_2017-10-05T11:49:41.000071
1,507,204,181.000071
95,950
pythondev
help
Jupyter yup
2017-10-05T11:49:59.000161
Kym
pythondev_help_Kym_2017-10-05T11:49:59.000161
1,507,204,199.000161
95,951
pythondev
help
If the Exception were hitting there though it'd be raised - you are saying Jupyter is suppressing it?
2017-10-05T11:50:05.000684
Mallie
pythondev_help_Mallie_2017-10-05T11:50:05.000684
1,507,204,205.000684
95,952
pythondev
help
Never tried jupyter
2017-10-05T11:50:10.000489
Vada
pythondev_help_Vada_2017-10-05T11:50:10.000489
1,507,204,210.000489
95,953
pythondev
help
But it also behaves in the same way on pycharm
2017-10-05T11:50:21.000362
Kym
pythondev_help_Kym_2017-10-05T11:50:21.000362
1,507,204,221.000362
95,954
pythondev
help
Have both
2017-10-05T11:50:23.000661
Kym
pythondev_help_Kym_2017-10-05T11:50:23.000661
1,507,204,223.000661
95,955
pythondev
help
Is Jupyter calling that function itself, or is another function calling it?
2017-10-05T11:50:27.000258
Meghan
pythondev_help_Meghan_2017-10-05T11:50:27.000258
1,507,204,227.000258
95,956
pythondev
help
But in pycharm the code analysis looks like this:
2017-10-05T11:50:37.000182
Vada
pythondev_help_Vada_2017-10-05T11:50:37.000182
1,507,204,237.000182
95,957
pythondev
help
(I've not used Jupyter, so I'm clueless on how it works.)
2017-10-05T11:50:43.000101
Meghan
pythondev_help_Meghan_2017-10-05T11:50:43.000101
1,507,204,243.000101
95,958
pythondev
help
orange = warning, red = error
2017-10-05T11:50:51.000810
Vada
pythondev_help_Vada_2017-10-05T11:50:51.000810
1,507,204,251.00081
95,959
pythondev
help
Jum ...
2017-10-05T11:50:57.000392
Kym
pythondev_help_Kym_2017-10-05T11:50:57.000392
1,507,204,257.000392
95,960
pythondev
help
and a lot of the warnings are potential errors
2017-10-05T11:51:03.000144
Vada
pythondev_help_Vada_2017-10-05T11:51:03.000144
1,507,204,263.000144
95,961
pythondev
help
Yeah, that red is stuff that will break your code.
2017-10-05T11:51:05.000742
Meghan
pythondev_help_Meghan_2017-10-05T11:51:05.000742
1,507,204,265.000742
95,962
pythondev
help
Mine doesn't show anything.
2017-10-05T11:51:07.000536
Kym
pythondev_help_Kym_2017-10-05T11:51:07.000536
1,507,204,267.000536
95,963
pythondev
help
so might be worth double checking your code
2017-10-05T11:51:09.000756
Vada
pythondev_help_Vada_2017-10-05T11:51:09.000756
1,507,204,269.000756
95,964
pythondev
help
Let me see if I can configure it to show the analysis.
2017-10-05T11:51:19.000179
Kym
pythondev_help_Kym_2017-10-05T11:51:19.000179
1,507,204,279.000179
95,965
pythondev
help
No idea if jupyter does
2017-10-05T11:51:28.000308
Vada
pythondev_help_Vada_2017-10-05T11:51:28.000308
1,507,204,288.000308
95,966
pythondev
help
but I recommend pycharm :wink:
2017-10-05T11:51:32.000067
Vada
pythondev_help_Vada_2017-10-05T11:51:32.000067
1,507,204,292.000067
95,967
pythondev
help
and they support jupyter notebooks
2017-10-05T11:52:02.000240
Vada
pythondev_help_Vada_2017-10-05T11:52:02.000240
1,507,204,322.00024
95,968
pythondev
help
<https://www.jetbrains.com/help/pycharm/using-ipython-jupyter-notebook-with-pycharm.html>
2017-10-05T11:52:02.000647
Vada
pythondev_help_Vada_2017-10-05T11:52:02.000647
1,507,204,322.000647
95,969
pythondev
help
Does Jupyter include an editor? I didn't realize that.
2017-10-05T11:52:13.000736
Mallie
pythondev_help_Mallie_2017-10-05T11:52:13.000736
1,507,204,333.000736
95,970
pythondev
help
I've got to go, but I really think the calling function is ignoring the raised exception, either with suppress or a blanket try/except.
2017-10-05T11:52:33.000009
Meghan
pythondev_help_Meghan_2017-10-05T11:52:33.000009
1,507,204,353.000009
95,971
pythondev
help
Yup, is not very good but I like it to scratch stuff and then I try to refactor it in Pycharm
2017-10-05T11:52:37.000267
Kym
pythondev_help_Kym_2017-10-05T11:52:37.000267
1,507,204,357.000267
95,972
pythondev
help
I think this is it:
2017-10-05T11:52:44.000518
Kym
pythondev_help_Kym_2017-10-05T11:52:44.000518
1,507,204,364.000518
95,973
pythondev
help
Does it have a hook for like pyflakes or anything? Any kind of syntax checking?
2017-10-05T11:53:11.000823
Mallie
pythondev_help_Mallie_2017-10-05T11:53:11.000823
1,507,204,391.000823
95,974
pythondev
help
Even if it's not it it's still an issue
2017-10-05T11:54:21.000802
Vada
pythondev_help_Vada_2017-10-05T11:54:21.000802
1,507,204,461.000802
95,975
pythondev
help
So I'll test two things:
2017-10-05T11:54:31.000562
Kym
pythondev_help_Kym_2017-10-05T11:54:31.000562
1,507,204,471.000562
95,976
pythondev
help
exception being swallowed somehow
2017-10-05T11:54:39.000454
Kym
pythondev_help_Kym_2017-10-05T11:54:39.000454
1,507,204,479.000454
95,977
pythondev
help
perhaps those lines trigger the exception
2017-10-05T11:54:53.000573
Kym
pythondev_help_Kym_2017-10-05T11:54:53.000573
1,507,204,493.000573
95,978
pythondev
help
that's why when I remove set year, day, month execution continues until next assignment
2017-10-05T11:55:15.000601
Kym
pythondev_help_Kym_2017-10-05T11:55:15.000601
1,507,204,515.000601
95,979
pythondev
help
IIRC you don't re-set `datetime` atttributes, you use replace: <https://docs.python.org/2/library/datetime.html#datetime.date.replace>
2017-10-05T11:55:36.000131
Mallie
pythondev_help_Mallie_2017-10-05T11:55:36.000131
1,507,204,536.000131
95,980
pythondev
help
So it seems like it is catching your Exceptions and logging them
2017-10-05T11:55:56.000532
Mallie
pythondev_help_Mallie_2017-10-05T11:55:56.000532
1,507,204,556.000532
95,981
pythondev
help
``` In [14]: from datetime import datetime as dt In [15]: today = dt.today() In [16]: today Out[16]: datetime.datetime(2017, 10, 5, 8, 57, 30, 530237) In [17]: today.year = 2018 --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) &lt;ipython-input-17-92aaf2ec95dc&gt; in &lt;module&gt;() ----&gt; 1 today.year = 2018 AttributeError: attribute 'year' of 'datetime.date' objects is not writable In [19]: today.replace(year=2018) Out[19]: datetime.datetime(2018, 10, 5, 8, 57, 30, 530237) ```
2017-10-05T11:58:16.000091
Mallie
pythondev_help_Mallie_2017-10-05T11:58:16.000091
1,507,204,696.000091
95,982
pythondev
help
<@Marcie> Did you ever figure it out?
2017-10-05T12:01:34.000834
Seema
pythondev_help_Seema_2017-10-05T12:01:34.000834
1,507,204,894.000834
95,983
pythondev
help
I'm on it! :slightly_smiling_face:
2017-10-05T12:03:29.000810
Kym
pythondev_help_Kym_2017-10-05T12:03:29.000810
1,507,205,009.00081
95,984
pythondev
help
I can't bring the damn thing to generate <@Mallie>'s exception.
2017-10-05T12:03:57.000044
Kym
pythondev_help_Kym_2017-10-05T12:03:57.000044
1,507,205,037.000044
95,985
pythondev
help
But I think that's it problem with setting the date+exception getting lost somehow
2017-10-05T12:04:25.000809
Kym
pythondev_help_Kym_2017-10-05T12:04:25.000809
1,507,205,065.000809
95,986
pythondev
help
<@Kym> What is the output of `import sys; sys.excepthook`?
2017-10-05T12:06:52.000415
Mallie
pythondev_help_Mallie_2017-10-05T12:06:52.000415
1,507,205,212.000415
95,987
pythondev
help
In the interpreter where this is happening of course, so however you make that happen in a Jupyter notebook.
2017-10-05T12:08:53.000655
Mallie
pythondev_help_Mallie_2017-10-05T12:08:53.000655
1,507,205,333.000655
95,988
pythondev
help
OK: 1. the exception <@Mallie> pointed out was indeed one of the problems. The fact that I tried to set pubdate.year and month triggered the exception "AttributeError: attribute 'month' of 'datetime.date' objects is not writable" 2. Now, the interesting part is why the exception was being "swallowed." It was because I put the return clause in the finally block! finally: curs.connection.commit() curs.connection.close() return len(root.getchildren()) vs. finally: curs.connection.commit() curs.connection.close() return len(root.getchildren())
2017-10-05T12:26:45.000431
Kym
pythondev_help_Kym_2017-10-05T12:26:45.000431
1,507,206,405.000431
95,989
pythondev
help
Does it make sense that the exception is hidden just because I put the return clause in the finally block? ... I broke Python? heh
2017-10-05T12:27:28.000061
Kym
pythondev_help_Kym_2017-10-05T12:27:28.000061
1,507,206,448.000061
95,990
pythondev
help
&gt;If finally is present, it specifies a ‘cleanup’ handler. The try clause is executed, including any except and else clauses. If an exception occurs in any of the clauses and is not handled, the exception is temporarily saved. The finally clause is executed. If there is a saved exception, it is re-raised at the end of the finally clause. If the finally clause raises another exception or executes a return or break statement, the saved exception is discarded
2017-10-05T12:28:36.000009
Mallie
pythondev_help_Mallie_2017-10-05T12:28:36.000009
1,507,206,516.000009
95,991
pythondev
help
Nice one!
2017-10-05T12:28:39.000354
Mallie
pythondev_help_Mallie_2017-10-05T12:28:39.000354
1,507,206,519.000354
95,992
pythondev
help
<https://docs.python.org/2/reference/compound_stmts.html#the-try-statement>
2017-10-05T12:28:50.000019
Mallie
pythondev_help_Mallie_2017-10-05T12:28:50.000019
1,507,206,530.000019
95,993
pythondev
help
HOLY CRAP!
2017-10-05T12:29:08.000310
Kym
pythondev_help_Kym_2017-10-05T12:29:08.000310
1,507,206,548.00031
95,994
pythondev
help
That makes no sense ... I'll read it, give me a sec
2017-10-05T12:29:28.000684
Kym
pythondev_help_Kym_2017-10-05T12:29:28.000684
1,507,206,568.000684
95,995
pythondev
help
interesting find
2017-10-05T12:30:10.000224
Ciera
pythondev_help_Ciera_2017-10-05T12:30:10.000224
1,507,206,610.000224
95,996
pythondev
help
Now the interesting part ... print(sys.version): 3.5.3
2017-10-05T12:31:44.000222
Kym
pythondev_help_Kym_2017-10-05T12:31:44.000222
1,507,206,704.000222
95,997
pythondev
help
seems like return inside of finally should be discouraged pretty broadly
2017-10-05T12:31:56.000242
Sirena
pythondev_help_Sirena_2017-10-05T12:31:56.000242
1,507,206,716.000242
95,998
pythondev
help
Yes, but the docu doesn't say anything.
2017-10-05T12:32:09.000118
Kym
pythondev_help_Kym_2017-10-05T12:32:09.000118
1,507,206,729.000118
95,999
pythondev
help
I'm using python2
2017-10-05T12:32:14.000817
Kym
pythondev_help_Kym_2017-10-05T12:32:14.000817
1,507,206,734.000817
96,000
pythondev
help
<https://docs.python.org/3/tutorial/errors.html>
2017-10-05T12:32:17.000128
Kym
pythondev_help_Kym_2017-10-05T12:32:17.000128
1,507,206,737.000128
96,001
pythondev
help
the only mention of return is the following:
2017-10-05T12:32:25.000511
Kym
pythondev_help_Kym_2017-10-05T12:32:25.000511
1,507,206,745.000511
96,002