Running error #9

wangyueyao · 2017-02-22T13:06:23Z

I have already installed the metamap13 and when i run the example under windows 7, i get the following error:

I have also already import the pymetamp and replace the address in the metamap.get_instance method:

I just don't know what to do, please help me ^^

AnthonyMRios · 2017-02-22T13:53:44Z

pymetamap currently does not support Windows because of my use of NamedTemporaryFile in the SubprocessBackend. It will work on Linux and Mac systems.

wangyueyao · 2017-02-23T07:54:08Z

Thank you for answering the question, I will use it in Linux systems.
Thanks! O(∩_∩)O~

Civiano · 2017-08-16T03:31:31Z

I have installed the pymetamap in Mac OS, when I run
>>> sents = ['Heart Attack', 'John had a huge heart attack']
>>> concepts,error = mm.extract_concepts(sents,[1,2])
I get the following errors:
Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Users/changsu/anaconda/lib/python2.7/site-packages/pymetamap-0.1-py2.7.egg/pymetamap/SubprocessBackend.py", line 117, in extract_concepts metamap_process = subprocess.Popen(command, stdout=subprocess.PIPE) File "/Users/changsu/anaconda/lib/python2.7/subprocess.py", line 390, in __init__ errread, errwrite) File "/Users/changsu/anaconda/lib/python2.7/subprocess.py", line 1024, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory

Could you help me please to solve this problem?

AnthonyMRios · 2017-08-16T03:53:26Z

Hi Civiano,

When initializing the api: mm = MetaMap.get_instance('/opt/public_mm/bin/metamap12')
the path must be a full path to where you have installed metamap.

For example, if you installed metamp 16 in your home directory, then you would use the following:

mm = MetaMap.get_instance('/Users/changsu/public_mm/bin/metamap16')

Civiano · 2017-09-01T10:31:46Z

thanks,
but i got another problem when run pymetamap on ubuntu os
concepts,error = mm.extract_concepts(sents,[1,2])
Traceback (most recent call last):
File "", line 1, in
File "pymetamap/SubprocessBackend.py", line 117, in extract_concepts
metamap_process = subprocess.Popen(command, stdout=subprocess.PIPE,shell=True)
File "/usr/lib/python2.7/subprocess.py", line 710, in init
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

Could you help me please to solve this problem? Thanks!

AnthonyMRios · 2017-09-01T12:24:23Z

Hi Civiano,

Can you give me all the code you are trying to run? Assuming the path is correct and everything is installed, then you should check that you started skrmedpostctl and wsdserverctl.

Civiano · 2017-09-02T02:41:58Z

the code:
from pymetamap import MetaMap
mm = MetaMap.get_instance('/media/zhangminhua/205CB4CD5CB49ECA/metamap/public_mm/bin/metamap12')
sents = ['Heart Attack', 'John had a huge heart attack']
concepts,error = mm.extract_concepts(sents,[1,2])
errors:
Traceback (most recent call last):
File "", line 1, in
File "pymetamap/SubprocessBackend.py", line 117, in extract_concepts
metamap_process = subprocess.Popen(command, stdout=subprocess.PIPE)
File "/usr/lib/python2.7/subprocess.py", line 710, in init
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
path:
PATH： /usr/lib/java/jdk180_144/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
JAVA_HOME: /usr/lib/java/jdk180_144
CLASSPATH: /usr/lib/java/jdk180_144/lib
skrmedpostctl and wsdserverctl are started by using:
chmod +x skrmedpostctl\wsdserverctl
sh skrmedpostctl\wsdserverctl start
if not, it will return “insufficient privilege”

thank you very much!

nishalpattan · 2017-11-02T18:14:15Z

I am also facing the same error after executing below line

concepts,error = mm.extract_concepts(sents,[1,2])

concepts,error = mm.extract_concepts(sents,[1,2])Traceback (most recent call last):
File "", line 1, in
File "pymetamap/SubprocessBackend.py", line 124, in extract_concepts
metamap_process = subprocess.Popen(command, stdout=subprocess.PIPE)
File "/usr/lib/python2.7/subprocess.py", line 710, in init
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
raise child_exception
OSError: [Errno 13] Permission denied

AnthonyMRios · 2017-11-02T18:19:04Z

Hi Nishal,

The issue you are having is different. Can you create a new issue specific to your problem? Anyways, did you install metamap? Also, do you have read permissions to use metamap assuming it is installed?

nishalpattan · 2017-11-02T18:50:31Z

yes , I have installed metamap. will try again and let you know

nishalpattan · 2017-11-02T23:59:42Z

I had tried again after reinstalling java in my Linux machine. I made sure that metamap is working correctly. Now it is working fine. Thanks

kaushikacharya · 2018-07-20T14:38:03Z

@AnthonyMRios
I was also struggling with the same issue as mentioned by Civiano on Sep 2, 2017 in Linux environment.
But it got resolved based on your suggestion on Aug 16, 2017:

the path must be a full path to where you have installed metamap.

I think in the README file under the Example Usage section, you should mention this in bold.

Also I feel in the code its better to check if the MetaMap path is absolute or not.
In MetaMap.py, inside both the functions a) init and (b) get_instance
you can check if the path is absolute or not using os.path.isabs
According to python documentation, it will check:

On Unix, that means it begins with a slash

If its not absolute, just exit with appropriate message.

AnthonyMRios · 2018-07-20T14:48:37Z

Hi @kaushikacharya, I'm sorry for the issues you had running the code.

I agree with your suggestions. I'm currently working on other projects. I have noted the suggestion and I will try to add them sometime within the next couple weeks.

kaushikacharya · 2018-07-20T16:31:52Z

Hi Anthony, If you are ok then I can also make changes and create a pull request. Regards, Kaushik

…

On Fri, Jul 20, 2018 at 8:18 PM, Anthony Rios ***@***.***> wrote: Hi @kaushikacharya <https://github.com/kaushikacharya>, I'm sorry for the issues you had running the code. I agree with your suggestions. I'm currently working on other projects. I have noted the suggestion and I will try to add them sometime within the next couple weeks. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#9 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AEWfs_JFxUCpz2j3L7LtFmk_KfUsxnczks5uIe3FgaJpZM4MIno9> .

AnthonyMRios · 2018-07-20T16:32:51Z

Sure. That would be great.

…nthonyMRios#9

* 1. Mentioned in bold that Metamap binary path should be absolute. 2. spelling correction * asserting if Metamap binary path is not absolute. This handles issue #9 * Update MetaMap.py modify error message

kibamin · 2019-04-27T16:52:44Z

thanks,
but i got another problem when run pymetamap on ubuntu os
concepts,error = mm.extract_concepts(sents,[1,2])
Traceback (most recent call last):
File "", line 1, in
File "pymetamap/SubprocessBackend.py", line 117, in extract_concepts
metamap_process = subprocess.Popen(command, stdout=subprocess.PIPE,shell=True)
File "/usr/lib/python2.7/subprocess.py", line 710, in init
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

Could you help me please to solve this problem? Thanks!

how you fixed this problem ?
please help me

AnthonyMRios · 2019-04-27T17:25:38Z

Hi @kibamin,

Do you have MetaMap installed on the Ubuntu machine? If not, you will need to get it from here: https://metamap.nlm.nih.gov/MetaMap.shtml

kibamin · 2019-04-28T08:14:52Z

Hi @kibamin,

Do you have MetaMap installed on the Ubuntu machine? If not, you will need to get it from here: https://metamap.nlm.nih.gov/MetaMap.shtml

Yes, i installed that on ubuntu and run WSD server and work with that without problem.
But when run your code in line >>> concepts,error = mm.extract_concepts(sents,[1,2])
i get this (same) error :

File "pymetamap/SubprocessBackend.py", line 117, in extract_concepts
metamap_process = subprocess.Popen(command, stdout=subprocess.PIPE,shell=True)
File "/usr/lib/python2.7/subprocess.py", line 710, in init
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

how to fix this ?

thank you

AnthonyMRios · 2019-04-28T16:43:25Z

Hi kibamin,

from the looks of things, it looks like you are not pointing to the location where you installed everything. I will need to see more of your code and know the file path to help more.

kibamin · 2019-04-29T05:55:11Z

Hi kibamin,

from the looks of things, it looks like you are not pointing to the location where you installed everything. I will need to see more of your code and know the file path to help more.

Hi Anthony

thank you for everything.
I found my mistake, i made a mistake in pulbic_mm file path.

thank you

kaushikacharya · 2019-04-29T12:01:45Z

@AnthonyMRios, We should probably put a check for existence of MetaMap path just after assigning self.metamap_filename https://github.com/AnthonyMRios/pymetamap/blob/master/pymetamap/MetaMap.py#L30 something like this:

assert os.path.exists(mm.metamap_filename), "Incorrect MetaMap filename path"

Regards, Kaushik

…

On Mon, Apr 29, 2019 at 11:25 AM Amin Abbasi ***@***.***> wrote: Hi kibamin, from the looks of things, it looks like you are not pointing to the location where you installed everything. I will need to see more of your code and know the file path to help more. Hi Anthony thank you for everything. I found my mistake, i made a mistake in pulbic_mm file path. thank you — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#9 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABCZ7M4QU5ZH7WJMXTW2PY3PS2EUFANCNFSM4DBCPI6Q> .

AnthonyMRios · 2019-05-01T17:52:11Z

Yeah, I agree. That would help clear up many of the issues posted here.

lediona · 2019-11-22T04:46:14Z

Hi,
I am running :
mm = MetaMap.get_instance('/Users/ledionanishani/Documents/public_mm/bin/metamap18')
sents = ['Heart Attack', 'John had a huge heart attack']
concepts,error = mm.extract_concepts(sents,[1,2])

And the concepts are empty.
Could you please what I am doing wrong? thanks in advance

kaushikacharya · 2019-11-22T05:12:03Z

Hi,
I am running :
mm = MetaMap.get_instance('/Users/ledionanishani/Documents/public_mm/bin/metamap18')
sents = ['Heart Attack', 'John had a huge heart attack']
concepts,error = mm.extract_concepts(sents,[1,2])

And the concepts are empty.
Could you please what I am doing wrong? thanks in advance

@lediona
Have a look at the suggestion by Anthony on a similar issue: #19

https://metamap.nlm.nih.gov/Docs/README.html#Starting%20the%20MetaMap%20Servers
This shows how to run the part of speech tagger and WSD servers. Most likely you haven't started these servers.

lediona · 2019-11-22T05:27:25Z

@kaushikacharya thank you so much for your prompt reply. It is working like a charm now !!!

lediona · 2019-11-28T02:53:18Z

Hi, I am using pymetamap but seems like its output is not that accurate:
sentence='Its like its stuck Sinus pain and pressure Amoxicillin has worked in the past'
concepts, error =mm.extract_concepts(sentence, [1,2])

it does not make sense. I getting the same output from different sentences: preferred name: Iodides or Blood group antibody . In the sentence it is not mentioned any blood or antibody.
I have used the pymetamap last year and it worked really good in terms of extracting medical terms.
I am noticing that it captures the first letter of the sentence instead of the word
Do you have any idea why is this happening?
thanks in advance!

kaushikacharya · 2019-11-28T05:00:43Z

@lediona
Your input isn't correct.

Note the difference between your and mine input.
It should be list of string.
What you have given is string.
Your input is considered as list of characters. And the 2nd input parameter of extract_concepts i.e. [1,2]
suggests to use the 1st two elements i.e. 1st two characters of the string.

Have a look at the function:
https://github.com/AnthonyMRios/pymetamap/blob/master/pymetamap/SubprocessBackend.py#L27
def extract_concepts(self, sentences=None, ids=None,

More details are available here:
https://github.com/AnthonyMRios/pymetamap/blob/master/pymetamap/SubprocessBackend.py#L95
for identifier, sentence in zip(ids, sentences):

Also note the trigger, pos_info fields in the output. (Read https://metamap.nlm.nih.gov/Docs/MMI_Output.pdf for detail). They show which part of the text is used to create the UMLS concept.
In your case its only the 1st character of the string that's creating the concepts.

itSammycodethngy · 2019-12-05T19:15:00Z

TypeError Traceback (most recent call last)
in
1 sents = ['Heart Attack']
----> 2 concepts,error = mm.extract_concepts(sents,[1])
3 concepts

~/pyte/pymetamap/SubprocessBackend.py in extract_concepts(self, sentences, ids, composite_phrase, filename, file_format, allow_acronym_variants, word_sense_disambiguation, allow_large_n, strict_model, relaxed_model, allow_overmatches, allow_concept_gaps, term_processing, no_derivational_variants, derivational_variants, ignore_word_order, unique_acronym_variants, prefer_multiple_concepts, ignore_stop_phrases, compute_all_mappings, mm_data_version, exclude_sources, restrict_to_sources, restrict_to_sts, exclude_sts)
152 if ids is not None:
153 for identifier, sentence in zip(ids, sentences):
--> 154 input_text += '{0!r}|{1!r}\n'.format(identifier, sentence).encode('utf8')
155 else:
156 for sentence in sentences:

TypeError: can only concatenate str (not "bytes") to str

I tried running the example and this is what I get

kaushikacharya · 2019-12-06T08:29:01Z

@itSammycodethngy
Ii seems you are running in Python 3.

https://stackoverflow.com/questions/55033372/can-only-concatenate-str-not-bytes-to-str
chepner's answer explains the difference between Python 2 and Python 3:

Python 3 made the distinction between the two very clear and does not allow you to combine them implicitly.

In python 3:

whereas in python 2 it works smoothly:

Solution:
https://github.com/AnthonyMRios/pymetamap/blob/master/pymetamap/SubprocessBackend.py#L151
Replace input_text = ""
by input_text = bytes()
Hopefully this change will work. In case you get similar error elsewhere, try making similar changes.

Edit: input_text = "".encode('utf8') should make it consistent for both python 2 and 3.

itSammycodethngy · 2019-12-06T13:31:25Z

thanks

…

On Fri, Dec 6, 2019 at 4:29 PM Kaushik Acharya ***@***.***> wrote: @itSammycodethngy <https://github.com/itSammycodethngy> Ii seems you are running in Python 3. https://stackoverflow.com/questions/55033372/can-only-concatenate-str-not-bytes-to-str chepner's answer explains the difference between Python 2 and Python 3: Python 3 made the distinction between the two very clear and does not allow you to combine them implicitly. In python 3: [image: image] <https://user-images.githubusercontent.com/4562867/70307767-e7d13b00-182f-11ea-8c2b-803a1b15ad08.png> whereas in python 2 it works smoothly: [image: image] <https://user-images.githubusercontent.com/4562867/70307844-0800fa00-1830-11ea-9d05-3aa1a995589c.png> Solution: https://github.com/AnthonyMRios/pymetamap/blob/master/pymetamap/SubprocessBackend.py#L151 Replace input_text = "" by input_text = bytes() Hopefully this change will work. In case you get similar error elsewhere, try making similar changes. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#9?email_source=notifications&email_token=AHDPLR72W724Q3HGMP573TTQXIEM5A5CNFSM4DBCPI62YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGDMNKY#issuecomment-562480811>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHDPLR42YVKLG2NYFPD5URLQXIEM5ANCNFSM4DBCPI6Q> .

AnthonyMRios · 2019-12-06T14:28:48Z

I made a quick update. I believe it should be consistent now.

itSammycodethngy · 2019-12-06T16:02:47Z

will pull the latest then

…

On Fri, Dec 6, 2019 at 10:28 PM Anthony Rios ***@***.***> wrote: I made a quick update. I believe it should be consistent now. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#9?email_source=notifications&email_token=AHDPLR4ZYHFPZG3Z6FUWZG3QXJOSDA5CNFSM4DBCPI62YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGEHVCY#issuecomment-562592395>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHDPLRYGSM7RIGLJVBSDWK3QXJOSDANCNFSM4DBCPI6Q> .

itSammycodethngy · 2019-12-11T16:42:03Z

TypeError Traceback (most recent call last)
in
1 sents = ['Heart Attack']
----> 2 concepts,error = mm.extract_concepts(sents,[1])
3 concepts
4

~/pyte/pymetamap/SubprocessBackend.py in extract_concepts(self, sentences, ids, composite_phrase, filename, file_format, allow_acronym_variants, word_sense_disambiguation, allow_large_n, strict_model, relaxed_model, allow_overmatches, allow_concept_gaps, term_processing, no_derivational_variants, derivational_variants, ignore_word_order, unique_acronym_variants, prefer_multiple_concepts, ignore_stop_phrases, compute_all_mappings, mm_data_version, exclude_sources, restrict_to_sources, restrict_to_sts, exclude_sts)
180 prev_new_line = -1
181 while (prev_new_line + 1) < len(output):
--> 182 next_new_line = output.find('\n', prev_new_line + 1)
183 if next_new_line < 0:
184 next_new_line = len(output)

TypeError: argument should be integer or bytes-like object, not 'str'

…g of python 2 and python 3. Resolves issue AnthonyMRios#9 raised on 11th Dec 2019.

…g of python 2 and python 3. Resolves issue #9 raised on 11th Dec 2019. (#44)

fatemehshmd · 2020-10-06T18:45:33Z

I ran your code on my Mac laptop and it worked perfectly. But I need to set the whole thing on my station with Windows 10 operating system too. I would really appreciate it if you provide us a setup code which works well on windows too.

kaushikacharya · 2020-10-16T10:46:01Z

@fatemehshmd

But I need to set the whole thing on my station with Windows 10 operating system too.
Have a look at the changes done in #39

Though haven't tested on Windows, but I feel pymetamap should now run in Windows too if you have passed input parameter: "sentences" as its not using NamedTemporaryFile.

If you are still facing any issue, we can discuss on the thread: #10

But first do check if you are able to run the commands as mentioned in https://metamap.nlm.nih.gov/Installation.shtml
e.g. echo "lung cancer" | ./bin/metamap -I

FayZ676 · 2022-07-30T20:23:01Z

@AnthonyMRios the pymetamap wrapper works like a charm, much appreciated. I am using it to analyze large amounts of medical related data and have noticed that execution halts after 100 calls, I am unable to get passed article 99 in my dataset. Is there a way around this?

dax-westerman · 2023-12-14T21:44:12Z

I have metamap 2014 running on Windows, and I hit similar issues. I hit an update where the input and output files couldn't be opened for read/write. I made the following updates to resolve on my end:

Changed the tempFiles to open 'r+b' (likely overkill)
Closed both files after the input_file.flush() to close the file handles
Reopened the output_file with mode='r' before output = str(output_file.read()) to open a new file handle
in the finally, closed both, then removed.

AnthonyMRios mentioned this issue Feb 22, 2017

Add Windows Support #10

Open

AnthonyMRios added the enhancement label Jul 20, 2018

kaushikacharya mentioned this issue Jul 20, 2018

Highlighting need for giving META_MAP_HOME as absolute path ncbi-nlp/NegBio#7

Closed

kaushikacharya added a commit to kaushikacharya/pymetamap that referenced this issue Jul 21, 2018

asserting if Metamap binary path is not absolute. This handles issue A…

4910df4

…nthonyMRios#9

This was referenced May 2, 2019

Check added for MetaMap file existence and executable access for the user #38

Merged

Avoiding creating temporary input and output files when input is list of sentences #39

Merged

kaushikacharya added a commit to kaushikacharya/pymetamap that referenced this issue Dec 13, 2019

converting MetaMap returned output in bytes to str for common handlin…

a5715b5

…g of python 2 and python 3. Resolves issue AnthonyMRios#9 raised on 11th Dec 2019.

kaushikacharya mentioned this issue Dec 13, 2019

converting MetaMap returned output in bytes to str for common handlin… #44

Merged

AnthonyMRios pushed a commit that referenced this issue Jan 27, 2020

converting MetaMap returned output in bytes to str for common handlin…

2c9490f

…g of python 2 and python 3. Resolves issue #9 raised on 11th Dec 2019. (#44)

Running error #9

Running error #9

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