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TMMA-506: Bug fix parsing OVID abstracts with a HTML tag at the start of a line #295

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merged 7 commits into from
Jun 20, 2024
Merged

TMMA-506: Bug fix parsing OVID abstracts with a HTML tag at the start of a line #295

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e322c38
Replace source of django-clamd egg from github to pypi
asset-web Jun 20, 2024
bd0b076
Ignore more files
asset-web Jun 20, 2024
ec9cba6
Update cypress
asset-web Jun 20, 2024
fddaa7f
Add better checks around parsing start of a citation to resolve bug T…
asset-web Jun 20, 2024
01d2f82
[skip-ci] Update CHANGELOG
asset-web Jun 20, 2024
6276b62
Add missing test file; Bug fix determining if contents of byte are al…
asset-web Jun 20, 2024
1b84ed3
Bug fix test for reading all citations after bug fix
asset-web Jun 20, 2024
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5 changes: 4 additions & 1 deletion .gitignore
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Expand Up @@ -82,4 +82,7 @@ cypress/screenshots
cypress/videos
cypress.env.json

google-chrome-stable_current_amd64.deb
google-chrome-stable_current_amd64.deb

.env
secret.txt
4 changes: 4 additions & 0 deletions CHANGELOG
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@@ -1,3 +1,7 @@
9.3.0 Make use of pypi index for django-clamd
Update Cypress
TMMA-506: Bug fix parsing OVID abstracts that include HTML tags at the start of a line.

9.2.0 Apply Python dependencies security related updates

9.1.0 Apply Python dependency updates
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2 changes: 1 addition & 1 deletion Jenkinsfile.dc2.demo
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Expand Up @@ -16,7 +16,7 @@ pipeline {
stage('Demo: Cypress tests') {
agent {
docker {
image 'cypress/included:13.10.0'
image 'cypress/included:13.12.0'
args '--add-host app-dc2-tmpo-d0.epi.bris.ac.uk:172.26.10.141 --entrypoint=""'
}
}
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2 changes: 1 addition & 1 deletion Jenkinsfile.dc2.prod
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Expand Up @@ -17,7 +17,7 @@ pipeline {
stage('Production: Cypress tests') {
agent {
docker {
image 'cypress/included:13.10.0'
image 'cypress/included:13.12.0'
args '--add-host www.temmpo.org.uk:172.26.10.142 --entrypoint=""'
}
}
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2 changes: 1 addition & 1 deletion Jenkinsfile.dc2.test
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Expand Up @@ -16,7 +16,7 @@ pipeline {
stage('Test: Cypress tests') {
agent {
docker {
image 'cypress/included:13.10.0'
image 'cypress/included:13.12.0'
args '--add-host app-dc2-tmpo-t0.epi.bris.ac.uk:172.26.10.143 --entrypoint=""'
}
}
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -212,7 +212,7 @@ NB: Some tests require these environment variables `CREDENTIALS_USR` and `CREDEN

Using docker and electron browser

docker run --rm -it -v $PWD:/e2e -w /e2e cypress/included:13.10.0
docker run --rm -it -v $PWD:/e2e -w /e2e cypress/included:13.12.0

## Warnings

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2 changes: 1 addition & 1 deletion browser/matching.py
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Expand Up @@ -200,7 +200,7 @@ def _ovid_medline_read_citations(abstract_file_path):
line = line.strip(b"\r\n")
if len(line) == 0:
pass
elif line[0:1] == b"<":
elif line[0:1] == b"<" and line[-1:] == b">" and (line.strip(b"<").strip(b">")).decode("utf-8").isdecimal():
# Starting a new citation, yield if one has already been set up
if citation:
yield citation
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5 changes: 3 additions & 2 deletions requirements/dev.txt
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Expand Up @@ -279,8 +279,9 @@ django==4.2.13 \
django-autocomplete-light==3.11.0 \
--hash=sha256:212576a17e3308ef7ca77e280b86684167916d2091d4b73640f38845d9516328
# via -r requirements/test.txt
django-clamd @ https://github.com/vstoykov/django-clamd/releases/download/1.0.0/django_clamd-1.0.0-py3-none-any.whl \
--hash=sha256:9a5c2a4215da20772fd37e617d75b57e253779dccd49d149b911cfd9be1e1748
django-clamd==1.0.0 \
--hash=sha256:106429a71db571b570c88493115891a5472623263d25ebe7f92bead6c2f04e81 \
--hash=sha256:ee2d46ed535355aa0840f93dd8468bf9e2236e2a54ea2affa956e5c9326e328a
# via -r requirements/test.txt
django-debug-toolbar==4.4.2 \
--hash=sha256:5d7afb2ea5f8730241e5b0735396e16cd1fd8c6b53a2f3e1e30bbab9abb23728 \
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3 changes: 1 addition & 2 deletions requirements/requirements.in
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@@ -1,8 +1,7 @@
# This is an implicit value, here for clarity
--index-url https://pypi.python.org/simple/
Bottleneck>=1.3.6
# django-clamd==1.0.0 currently not available on pypi
https://github.com/vstoykov/django-clamd/releases/download/1.0.0/django_clamd-1.0.0-py3-none-any.whl
django-clamd>=1.0.0
django-mptt>=0.14.0
django-redis-cache>=3.0.1
django-registration-redux>=2.12
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5 changes: 3 additions & 2 deletions requirements/requirements.txt
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Expand Up @@ -93,8 +93,9 @@ django==4.2.13 \
django-autocomplete-light==3.11.0 \
--hash=sha256:212576a17e3308ef7ca77e280b86684167916d2091d4b73640f38845d9516328
# via -r requirements/requirements.in
django-clamd @ https://github.com/vstoykov/django-clamd/releases/download/1.0.0/django_clamd-1.0.0-py3-none-any.whl \
--hash=sha256:9a5c2a4215da20772fd37e617d75b57e253779dccd49d149b911cfd9be1e1748
django-clamd==1.0.0 \
--hash=sha256:106429a71db571b570c88493115891a5472623263d25ebe7f92bead6c2f04e81 \
--hash=sha256:ee2d46ed535355aa0840f93dd8468bf9e2236e2a54ea2affa956e5c9326e328a
# via -r requirements/requirements.in
django-hcaptcha-field==1.4.0 \
--hash=sha256:36001030f53af709db3be01bf1d25023706b701bb7130f67f2aa58900b20df42 \
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5 changes: 3 additions & 2 deletions requirements/test.txt
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Expand Up @@ -262,8 +262,9 @@ django==4.2.13 \
django-autocomplete-light==3.11.0 \
--hash=sha256:212576a17e3308ef7ca77e280b86684167916d2091d4b73640f38845d9516328
# via -r requirements/requirements.txt
django-clamd @ https://github.com/vstoykov/django-clamd/releases/download/1.0.0/django_clamd-1.0.0-py3-none-any.whl \
--hash=sha256:9a5c2a4215da20772fd37e617d75b57e253779dccd49d149b911cfd9be1e1748
django-clamd==1.0.0 \
--hash=sha256:106429a71db571b570c88493115891a5472623263d25ebe7f92bead6c2f04e81 \
--hash=sha256:ee2d46ed535355aa0840f93dd8468bf9e2236e2a54ea2affa956e5c9326e328a
# via -r requirements/requirements.txt
django-hcaptcha-field==1.4.0 \
--hash=sha256:36001030f53af709db3be01bf1d25023706b701bb7130f67f2aa58900b20df42 \
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