dspinellis / alexandria3k Goto Github PK
View Code? Open in Web Editor NEWLocal relational access to openly-available publication data sets
License: GNU General Public License v3.0
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centaurioun ibalampanis bhagirath20 aggelosmargkas austinjp basverlooy tsoukj dtgupta avoutsas67 jellevlieshout mokhlesurrahman neofob panos-span evgepab adbagioalexandria3k's Issues
CI dependencies installation error
After 5 consequent releases of new versions of pipenv for the month of August, there seems to be something missing from the previous versions. As a result this raises an error on CI when installing the environment dependencies.
The history of releases can be seen here.
One of the missing dependencies is "virtualenv-clone", however the raised error is not based on that specific dependency.
As a workaround
I propose using the last version of pipenv for the month of July (2023.7.23). This way the dependency installation of CI works fine.
I will follow the pipenv releases and test them. If pipenv stops releasing new versions and the a3k CI still has a problem, then I can maybe contact the authors with our error to provide some further information.
GSOC 2023 Proposal
Greeting Mr Diomidis,
I have uploaded my proposal for the GSOC 2023 with regards to the addition of extensions in Alexandria3k. I would love to hear back feedback from you, so to make it better and maybe clarify some parts.
Kind Regards,
Aggelos Margkas.
PubMed Data Set Query Option Missing in PyPI Version of Alexandria3k
Environment:
- OS : Ubuntu 22.04 (Windows Subsystem for Linux 2)
- Python Version : 3.11.5
Alexandria3k Version: 3.1.2
Issue Description:
When attempting to perform a query on the pubmed-data using the alexandria3k CLI, the system returns an error indicating that 'pubmed-data' is not a valid choice for data_name and it doesn't seem like there is a choice for 'pubmed-data' in general. This occurs despite the package documentation suggesting that PubMed data set queries are supported.
Command Attempted:
panaspanakis@hpc:~$ a3k query pubmed-data 'pubmed_data' --query 'SELECT DOI, title FROM pubmed_articles WHERE published_year > 2020 AND title LIKE "%Machine Learning%"'Error Received:
usage: a3k query [-h] [-a ATTACH_DATABASES [ATTACH_DATABASES ...]] [-E OUTPUT_ENCODING] [-F FIELD_SEPARATOR] [-H] [-o OUTPUT] [-P] (-Q QUERY_FILE | -q QUERY) [-s SAMPLE]
{orcid,doaj,asjcs,journal-names,uspto,crossref,ror,funder-names} [data_location]
a3k query: error: argument data_name: invalid choice: 'pubmed-data' (choose from 'orcid', 'doaj', 'asjcs', 'journal-names', 'uspto', 'crossref', 'ror', 'funder-names')Here is also a screenshot of the described issue below:
Possible non-random sampling
Hi there. Firstly, thanks for a3k, I'm finding it very useful.
I noticed a problem when using --sample 'random.random() < 0.0001' to randomly sample from the latest Crossref dataset. It seemed to produce identical samples each time, whereas I was expecting it to produce different samples each time. I've not yet looked through the code, but I wondered if it might be an issue with seeding the random generator? Perhaps this is expected behaviour, so apologies if I missed this in the docs.
An example:
$ a3k populate --sample 'random.random() < 0.0001' /tmp/crossref.db crossref ./data-files/crossref/
$ sqlite3 -batch /tmp/crossref.db 'select id,doi,title from works where id in (select max(id) from works) or id in (select min(id) from works) order by id';
id doi title
----- --------------------------- ------------------------------------------------------------------------------------------
0 10.1007/978-3-658-29701-5_1 Keynote Speech Disruption in mobility – new trends, new concepts and new business models?!
21383 10.18356/98a0368f-en-fr No. 47244 International Bank for Reconstruction and Development and Brazil
$ rm /tmp/crossref.db
$ a3k populate --sample 'random.random() < 0.0001' /tmp/crossref.db crossref ./data-files/crossref/
$ sqlite3 -batch /tmp/crossref.db 'select id,doi,title from works where id in (select max(id) from works) or id in (select min(id) from works) order by id';
id doi title
----- --------------------------- ------------------------------------------------------------------------------------------
0 10.1007/978-3-658-29701-5_1 Keynote Speech Disruption in mobility – new trends, new concepts and new business models?!
21383 10.18356/98a0368f-en-fr No. 47244 International Bank for Reconstruction and Development and BrazilNotice the identical results after deleting and recreating the database with a 'fresh' sample. Perhaps this is expected behaviour, but I was expecting a random sample, and hence different each time.
Some quick sanity checks:
$ sqlite3 -batch /tmp/crossref.db 'select count(*) from works;'
count(*)
--------
10000
$ ls -l data-files/crossref/ | head -n 4
total 185934MB
-rwxrwxrwx 1 austinjp austinjp 8MB 2023-08-10 19:35 0.json.gz
-rwxrwxrwx 1 austinjp austinjp 11MB 2023-08-10 20:10 10000.json.gz
-rwxrwxrwx 1 austinjp austinjp 7MB 2023-08-10 20:11 10001.json.gz
$ ls -1 data-files/crossref/ | wc -l
28702Workaround
As a workaround, I use --sample '( random.seed() ) or random.random() < 0.0001' to re-seed the random generator at every sample decision. It's inefficient, but it gives the results I'd expected:
$ rm /tmp/crossref.db
$ a3k populate --sample '( random.seed() ) or random.random() < 0.0001' /tmp/crossref.db crossref ./data-files/crossref/
$ sqlite3 -batch /tmp/crossref.db 'select id,doi,title from works where id in (select max(id) from works) or id in (select min(id) from works) order by id';
id doi title
----- -------------------------------- -----------------------------------------------------------------------
0 10.1097/00001721-199206000-00004 Protein S negates the activated protein C inhibitory activity of plasma
37767 10.1177/109980040000200201 Summer Camp for Scientists
$ rm /tmp/crossref.db
$ a3k populate --sample '( random.seed() ) or random.random() < 0.0001' /tmp/crossref.db crossref ./data-files/crossref/
$ sqlite3 -batch /tmp/crossref.db 'select id,doi,title from works where id in (select max(id) from works) or id in (select min(id) from works) order by id';
id doi title
----- ----------------------------- --------------------------------------------------------------------------------------------------------------------------
0 10.15296/ijwhr.2017.33 Health Promoting Behaviors and Self-efficacy of Physical Activity During Pregnancy: An Interventional Study
21383 10.1016/s0973-0826(08)60299-9 Risk and uncertainty analysis of natural environmental assets threatened by hydropower projects: case study from Sri LankaBest wishes.
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