ami search: 'OutOfMemoryError' #73
Comments
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Using the dictionary |
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I am assuming that you are running something like: try : `ls - |
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The new logger from Remko may help on this. |
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@petermr, I was running |
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Thanks!
On Fri, Jul 3, 2020 at 5:07 PM VAISHALI ARORA ***@***.***> wrote:
@petermr <https://github.com/petermr>, I was running ami -p
miniprojectfunders search --dictionary funders. I don't have logs/ami.log
file in my CProject directory named miniprojectfunders.
Yes, I did got a list of 952 items in my directory.
OS: Windows 10
C:\Users\me>miniprojectfunders 1s -1 . PMC*/scholarly.html | wc
'miniprojectfunders' is not recognized as an internal or external command,
operable program or batch file.
You have an unwanted word in the command.
and also two of your "els" are "ones"
1s -1 . PMC*/scholarly.html | wc
should be
ls -l . PMC*/scholarly.html | wc
We all make this mistake!! It's very difficult to distinguish "el" from
"one" in some fonts
Should be:
1s -1 . PMC*/scholarly.html | wc
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Peter Murray-Rust
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and
Reader Emeritus in Molecular Informatics
Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK
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In command prompt, I gave the command So I tried the same commands in Git Bash and got the following some numbers as output. @petermr Is the above output correct? I also tried setting the environment variable
and gave the command @petermr Is there any change should I do in the environment variable? |
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Thanks @petermr, I got no search tables for dictionary funders, so next, I deleted this large file PMC6824115 from the directory and again run the same command:
This time I got full data tables in my directory with complete search for dictionary funders. https://photos.google.com/search/_tra_/photo/AF1QipPM1Mytn-__zViXjfugVKIslmzYWMYp9RPEHv-2 |
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Thanks - this is very clear.
We'll take it in bits:
In command prompt, I gave the command cd mpc (mpc is the directory where my
950 files are) and then I tried the command
ls -l . PMC*/scholarly.html | wc
The output was
'ls' is not recognized as an internal or external command, operable program
or batch file.
PMR> maybe something is wrong with your PATH
Try
ls
or
which ls
("which" tells you where the ls program is).
If you get "ls" working you probably want:
either
ls .
(list all files in current directory)
OR
ls PMC*/scholarly.html
list the scholarly.html childrens of PMC* files.
Let's try to solve that and then move to the OOM error.
…--
Peter Murray-Rust
Founder ContentMine.org
and
Reader Emeritus in Molecular Informatics
Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK
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Well done.
I'll create an FAQ and you can answer it!
…On Sat, Jul 4, 2020 at 9:49 AM VAISHALI ARORA ***@***.***> wrote:
Thanks @petermr <https://github.com/petermr>,
I first entered this in the Command prompt : set MAVEN_OPTS=-Xmx512m
-XX:MaxPermSize=128m
I again ran this : C:\Users\me>ami -p miniprojectfunders search
--dictionary funders
and got :
+++++++++++++++++++running: search; search([funders])[]
279807 [main] DEBUG org.contentmine.ami.plugins.CommandProcessor -
+++++++++++++++++++running: search; search([funders])[]
..............................................
large document (1507) for PMC6824115 truncated to 500 sections
.......................................................................................................
I got no search tables for dictionary funders, so next, I deleted this
large file PMC6824115 from the directory and again run the same command:
C:\Users\me>ami -p miniprojectfunders search --dictionary funders
This time I got full data tables in my directory with complete search for
dictionary funders.
https://photos.google.com/search/_tra_/photo/AF1QipPM1Mytn-__zViXjfugVKIslmzYWMYp9RPEHv-2
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--
Peter Murray-Rust
Founder ContentMine.org
and
Reader Emeritus in Molecular Informatics
Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK
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Thanks @petermr |
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@petermr I gave the command But for using in command prompt, I found an equivalent command DIR for For my corpus containing 950 articles, I gave the command Next, when I gave the command Is there any change, I could do? |
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Well done.
On Sat, Jul 4, 2020 at 5:18 PM Lakshmi Devi Priya ***@***.***> wrote:
@petermr <https://github.com/petermr> I gave the command which ls in
command prompt and the output was :
'which' is not recognized as an internal or external command, operable
program or batch file.
So I tried in git and successfully got the path of ls.
I forgot you were on Windows! `which` does not exist there. (We are going
to remind each other which Operating system we are on).
But for using in command prompt, I found an equivalent command *DIR* for
ls from
https://skimfeed.com/blog/windows-command-prompt-ls-equivalent-dir/#:~:text=Answer%3A%20Type%20DIR%20to%20show,commands%20and%20their%20Windows%20equivalents
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Well done.
I used DIR in command prompt and the following output was obtained for a
small directory
[image: lsdir]
<https://user-images.githubusercontent.com/65600695/86516249-a7c14d80-be3c-11ea-9f31-423b5edb0968.PNG>
For my corpus containing 950 articles, I gave the command DIR mpc in
command prompt and the output was
[...]
01/07/2020 03:44 PM <DIR> PMC7310742
01/07/2020 03:44 PM <DIR> PMC7312578
01/07/2020 03:44 PM <DIR> PMC7314749
01/07/2020 03:44 PM <DIR> PMC7316228
[...]
Good
Next, when I gave the command DIR PMC*/scholarly.html , the output was
Parameter format not correct - "scholarly.html".
Is there any change, I could do?
This is another difference between Windows and Unix - they use backslash.
try
```
DIR PMC*\scholarly.html
```
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Peter Murray-Rust
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and
Reader Emeritus in Molecular Informatics
Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK
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For viewing the html files, first I gave the command @petermr I checked the filename and directory name. Is there anything I should do about the volume label? |
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I don't run windows. So I forget it doesn't expand the *.
Maybe you can run powershell. Clyde Davies knows how.
…On Sun, Jul 5, 2020 at 5:17 AM Lakshmi Devi Priya ***@***.***> wrote:
For viewing the html files, first I gave the command cd mpc (mpc is the
950 articles directory) in command prompt and then I gave the command DIR
PMC*\scholarly.html and the output was
The filename, directory name, or volume label syntax is incorrect,
@petermr <https://github.com/petermr> I checked the filename and
directory name. Is there anything I should do about the volume label?
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Peter Murray-Rust
Founder ContentMine.org
and
Reader Emeritus in Molecular Informatics
Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK
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@petermr I tried the command |
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Well done.
…On Sun, Jul 5, 2020 at 11:55 AM Lakshmi Devi Priya ***@***.***> wrote:
@petermr <https://github.com/petermr> I tried the command DIR
PMC*\scholarly.html, in Windows PowerShell. It worked and showed the
following output :
Directory: C:\Users\Admin\Desktop\mpc\PMC5764404
Mode LastWriteTime Length Name
---- -------------- ------ -----
-a---- 04/07/2020 11:11 AM 124852 scholarly.html
[...]
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Peter Murray-Rust
Founder ContentMine.org
and
Reader Emeritus in Molecular Informatics
Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK
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Closed as part of the learning process |
Using
Amisearchfor a corpus of 950 articles showing anOutOfMemoryErrorwhen searched for the dictionary, shoeed the following error:....
The text was updated successfully, but these errors were encountered: