Problems with Installation

[zuphilip]

I tried to install bcite but didn't succeed. The online app shows for any input

<class 'IndexError'> at /
list index out of range

and points to

bcite/script/web/app.py

Line 104 in 63d87e6

idCitingRef = response[0]['id']

but I guess that the problem here is that response=[]. Any idea what could be the problem?

---

Then I looked into python3 script/api/test/bciteapi.py but couldn't get this working. What I faced so far with this call:

• ImportError: No module named script.api.bciteapi --> Fixed by export PYTHONPATH="${PYTHONPATH}:/main/directory/of/the/repository" but maybe you can fix that also in the code...
• rdflib.plugin.PluginException: No plugin registered for (json-ld,... --> Fixed by pip install rdflib-jsonld
• Tests are now running but showing me TypeError: the JSON object must be str, not 'bytes' and AssertionError: Subject None must be an rdflib term. --> How to fix that? Are tests working for you?

[marilenadaquino]

ATM bcite is a prototype and is supposed to run locally, hence I guess the problem is related to the absolute path of the API that you call twice in app.py

line 102:
request = requests.get('http://localhost:8000/api/citing/'+str(ts)+'/'+urllib.parse.quote(str(citingEntityEncoded)))

line 119:
request = requests.get('http://localhost:8000/api/reference/'+str(web.input().time)+'/'+web.input().idRef+'/'+web.input().style+'/'+urllib.parse.quote(referenceText) )

there is a third call in main.js
request.open('GET', 'http://localhost:8000/api/store/'+timestamp+'/'+$(this).attr('data-update')+'/'+citing+'/'+$(this).attr('id')+'/'+encodeURIComponent($(this).text()), true);

I see you have problems with all the paths actually in your online instance (I can't see the graphics). We'll fix it soon to run everywhere with a local path. In the meantime try to modify your absolute paths.

[zuphilip]

Thank you for your response. I tried to change all paths but the result is still the same. Maybe also note that on the server the API is running on localhost:8000 but this port is not exposed to the outside world but rather proxyfied to a subdirectory. Thus, something like curl localhost:8000 works fine on the server and I guess that also Python can access it as well.

Is there an easy way to test that the API is working as expected? Maybe a short example request?

[marilenadaquino]

Hi,
I tried to reproduce the errors you found, and I got an error because a rdflib plugin (json-ld serialiser) was missing. I updated the readme with suggestions (including the suggested python version) and the requirements.txt file. Plus, I removed some mandatory fields in the form.

Second, script/api/bciteapi.py is the file you should look at.

A complete workflow requires the API to be called three times, and works only if you input:

• metadata of a citing article (now almost all the fields are optional). These are processed and stored as RDF. The call returns an ID you use in the second call
• a list of references, together with the ID you got in the first call, creates the RDF citation data and returns the list of matched references.

The last call is to confirm input data are correct and verified by the user.

Hence I cannot paste here a short example request.
Hope it works for you now. Let us know!

[zuphilip]

Thank you. I switched to the new version and updated the python libraries. I don't see any error now, but the result is simply None. I guess that I need to have something in the triplestore before? I don't understand how the API works...

[marilenadaquino]

Did the triplestore start correctly?
Can you please paste here the output in the shell?

[zuphilip]

Which output? (The webservice outputs for me just with None.)

[marilenadaquino]

Just to double-check.

• You started the triplestore and the app from the shell.
• You opened the app at localhost:8000
• You input the metadata of your citing article and a list of references.
• you click submit
• a new page appears with only none written there

what the shell says at this point?

[zuphilip]

Ah, I see. I run it on a server where I only have ssh access, therefore I start the app with nohup python3 -m script.web.app 8000 & in the background. Here is the output of python for the action:

...:~/bcite$ python3 -m script.web.app 8000
http://0.0.0.0:8000/
127.0.0.1:55974 - - [02/Oct/2018 10:59:54] "HTTP/1.1 GET /" - 200 OK
127.0.0.1:55976 - - [02/Oct/2018 10:59:55] "HTTP/1.1 GET /static/js/main.js" - 200
127.0.0.1:55976 - - [02/Oct/2018 10:59:55] "HTTP/1.1 GET /static/js/Blob.min.js" - 200
127.0.0.1:55974 - - [02/Oct/2018 10:59:55] "HTTP/1.1 GET /static/js/FileSaver.js" - 200
127.0.0.1:55974 - - [02/Oct/2018 10:59:55] "HTTP/1.1 GET /static/js/mark.min.js" - 200
127.0.0.1:55978 - - [02/Oct/2018 10:59:55] "HTTP/1.1 GET /static/js/xlsx.core.min.js" - 200
127.0.0.1:55978 - - [02/Oct/2018 10:59:55] "HTTP/1.1 GET /static/css/tableexport.css" - 200
127.0.0.1:55978 - - [02/Oct/2018 10:59:57] "HTTP/1.1 GET /static/favicon.ico" - 200
127.0.0.1:55980 - - [02/Oct/2018 11:00:19] "HTTP/1.1 POST /" - 200 OK

However, I see that the java process outputs that the service url is my web adress and not localhost. There are also two warnings:

WARN : NanoSparqlServer.java:517: Starting NSS
WARN : ServiceProviderHook.java:171: Running.
serviceURL: http://134.155.108.51:9999

How should that look like?

[zuphilip]

I give it another attempt with docker, see zuphilip@fe77b9f but this leads me to the same problem(s)...

[zuphilip]

Okay, I have never filled out the ORCID field and this is currently a problem, but can be fixed with #7. But now I see again the error from the beginning. The console shows then:

<web.form.Form object at 0x7fa82ed48198>
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): localhost:8000
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): api.crossref.org
:443
DEBUG:urllib3.connectionpool:https://api.crossref.org:443 "GET /works/10.1017/S0
018246X06005966 HTTP/1.1" 200 1634
[SPACIN CrossrefProcessor - INFO] Data retrieved from 'https://api.crossref.org/
works/10.1017/S0018246X06005966'.
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): localhost:9999
DEBUG:urllib3.connectionpool:http://localhost:9999 "GET /blazegraph/sparql?query
=PREFIX%20fabio%3A%20%3Chttp%3A//purl.org/spar/fabio/%3E%0ASELECT%20%3Fid%0AWHER
E%20%7B%0A%20%20%20%20BIND%20%28%3Chttp%3A//localhost%3A8000/corpus/br/17%3E%20A
S%20%3Fbr%29%20.%0A%20%20%20%20%3Fbr%20a%20fabio%3AExpression%20.%0A%20%20%20%20
BIND%20%28strafter%28str%28%3Fbr%29%2C%20%22/corpus/%22%29%20AS%20%3Fid%29%20.%0
A%7D%0ALIMIT%201 HTTP/1.1" 200 None
127.0.0.1:38606 - - [04/Oct/2018 16:48:38] "HTTP/1.1 GET /api/citing/1538671713.
103041/{"author": ["Berners-Lee, Tim"], "title": "Title", "journal": "Journal",
"volume": "18", "issue": "1", "year": "2009", "publisher": "Wiley", "doi": "10.1
017/S0018246X06005966"}" - 200 OK
DEBUG:urllib3.connectionpool:http://localhost:8000 "GET /api/citing/1538671713.1
03041/%7B%22author%22%3A%20%5B%22Berners-Lee%2C%20Tim%22%5D%2C%20%22title%22%3A%
20%22Title%22%2C%20%22journal%22%3A%20%22Journal%22%2C%20%22volume%22%3A%20%2218
%22%2C%20%22issue%22%3A%20%221%22%2C%20%22year%22%3A%20%222009%22%2C%20%22publis
her%22%3A%20%22Wiley%22%2C%20%22doi%22%3A%20%2210.1017/S0018246X06005966%22%7D H
TTP/1.1" 200 None
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/site-packages/web/application.py", line 257, in
 process
    return self.handle()
  File "/usr/local/lib/python3.6/site-packages/web/application.py", line 248, in
 handle
    return self._delegate(fn, self.fvars, args)
  File "/usr/local/lib/python3.6/site-packages/web/application.py", line 488, in
 _delegate
    return handle_class(cls)
  File "/usr/local/lib/python3.6/site-packages/web/application.py", line 466, in
 handle_class
    return tocall(*args)
  File "/usr/src/app/script/web/app.py", line 87, in POST
    idCitingRef = response[0]['id']
IndexError: list index out of range

192.168.99.1:55885 - - [04/Oct/2018 16:48:38] "HTTP/1.1 POST /" - 500 Internal Server Error
192.168.99.1:55885 - - [04/Oct/2018 16:48:39] "HTTP/1.1 GET /favicon.ico" - 404 Not Found

[atomotic]

same behaviour for me. to avoid data entry with the form i can reproduce the post this way

pip3 install httpie

cat data.txt
author=Not,Exists
&title=NO
&ORCID=0000-0001-8770-4972
&references=Gibby,+R.,+and+Brazier,+C.+2012.+Observations+on+the+development+of+non-print+legal+deposit+in+the+UK.+Library+Review+61,+5+(2012),+362-377.+DOI=https://doi.org/10.1108/00242531211280487
&style=MLA
&form_action=search

http --form POST http://localhost:8000/ < data.txt
HTTP/1.1 200 OK
Date: Fri, 05 Oct 2018 09:51:55 GMT
Server: localhost
Transfer-Encoding: chunked

None

[marilenadaquino]

I see, I tried again and everything works fine. I get that error only when I do not include the DOI of the citing article, which is a required field for creating the KG.

[marilenadaquino]

I committed a change in app.py. ORCID is removed (we do not need it at this stage), and the rendering of the page works correctly now - so you won't see None anymore, but the form fields missing required values highlighted.

[zuphilip]

Validation works for me now, but i see the same error as in the very beginning of this issue. It seems that the API request in line 81 is empty:

bcite/script/web/app.py

Line 81 in 3611deb

request = requests.get('http://localhost:8000/api/citing/'+str(ts)+'/'+urllib.parse.quote( citingEntityEncoded ))

i.e. after this line I have request=[], which then leads to the error some lines later.