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prance 2022-01-30 22:06:15 +01:00
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22 changed files with 634 additions and 1132 deletions
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1
OpenRefine/.github/FUNDING.yml vendored
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github: OpenRefine

40
OpenRefine/.github/ISSUE_TEMPLATE/bug_report.md vendored
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---
name: Bug report
about: Create a report to help us improve OpenRefine
title: ''
labels: bug, to be reviewed
assignees: ''
---
<!-- Describe the bug - Please add a clear and concise description of the bug above this line. You can delete this line if you want. It will be hidden in the final bug report -->
### To Reproduce
Steps to reproduce the behavior:
1. First, do ...
2. Then, ...
3. Finally, ...
### Current Results
<!-- What results occurred or were shown. -->
### Expected Behavior
<!-- A clear and concise description of what you expected to happen or to show. -->
### Screenshots
<!-- If applicable, add screenshots to help explain your problem. -->
### Versions<!-- (please complete the following information)-->
- Operating System: <!-- e.g. iOS, Windows 10, Linux, Ubuntu 18.04 -->
- Browser Version: <!-- e.g. Chrome 19, Firefox 61, Safari, NOTE: OpenRefine does not support IE but works OK in most cases -->
- JRE or JDK Version: <!-- output of "java -version" e.g. JRE 1.8.0_181 -->
- OpenRefine: <!-- e.g. OpenRefine 3.0 Beta] -->
### Datasets
<!-- If you are allowed and are OK with making your data public, it would be awesome if you can include or attach the data causing the issue or a URL pointing to where the data is.
If you are concerned about keeping your data private, ping us on our [mailing list](https://groups.google.com/forum/#!forum/openrefine) -->
### Additional context
<!-- Add any other context about the problem here. -->

8
OpenRefine/.github/ISSUE_TEMPLATE/config.yml vendored
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blank_issues_enabled: false
contact_links:
- name: Ask a question (mailing list)
url: https://groups.google.com/d/forum/openrefine
about: Please ask and answer questions here.
- name: Gitter chat
url: https://gitter.im/OpenRefine/OpenRefine
about: General and developer discussions

19
OpenRefine/.github/ISSUE_TEMPLATE/feature_request.md vendored
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---
name: Feature request
about: Suggest an idea for OpenRefine
title: ''
labels: enhancement, to be reviewed
assignees: ''
---
<!-- Please provide a clear and concise description of your problem or unsatisfied needs. Ex. I'm always frustrated when [...] or, It would be easier if OpenRefine did [...]. This comment can be deleted, if desired, but it will be hidden in your final submission. Please make sure that your new text is outside the enclosing angle brackets. -->
### Proposed solution
<!-- If you have a proposal for how this need could be met, please provide a clear and concise description of what you want to happen. -->
### Alternatives considered
<!-- If there alternative solutions that you have considered or think should be considered, please list them here -->
### Additional context
<!-- Add any other context or screenshots about the feature request here. -->

5
OpenRefine/.github/SUPPORT.md vendored
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If you are having trouble with OpenRefine we suggest the following steps:
1. Read through our [FAQ (frequently Asked Questions)](https://github.com/OpenRefine/OpenRefine/wiki/FAQ)
2. Search for similar issues in our community email list archives: http://groups.google.com/group/openrefine/
3. Send an email to our community mailing list: openrefine@googlegroups.com

3
OpenRefine/.github/autolabeler.yml vendored
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documentation: ["/docs"]
"current docs": ["/docs/docs"]
"historical docs": ["/docs/versioned_docs"]

45
OpenRefine/.github/dependabot.yml vendored
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# Documentation for all configuration options:
# https://help.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
version: 2
updates:
# For openrefine java deps
- package-ecosystem: maven
directory: "/"
schedule:
interval: daily
open-pull-requests-limit: 10
ignore:
- dependency-name: com.thoughtworks.xstream:xstream
versions:
- "> 1.4.12"
- "< 2"
# Same, on 4.0 branch
- package-ecosystem: maven
directory: "/"
schedule:
interval: daily
open-pull-requests-limit: 10
ignore:
- dependency-name: com.thoughtworks.xstream:xstream
versions:
- "> 1.4.12"
- "< 2"
target-branch: 4.0
# For documentation website
- package-ecosystem: "npm" # For Yarn
directory: "docs/"
schedule:
interval: "monthly"
# For github actions
- package-ecosystem: "github-actions"
directory: "/"
schedule:
interval: "monthly"
# For cypress test_suite
- package-ecosystem: "npm"
directory: "main/tests/cypress"
schedule:
interval: "daily"

6
OpenRefine/.github/pull_request_template.md vendored
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Fixes #{issue number here}
Changes proposed in this pull request:
-
-
-

26
OpenRefine/.github/workflows/label_transfer.yml vendored
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name: Copy labels from issue to pull request
on:
pull_request_target:
types: [opened, edited]
jobs:
transfer_tags:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Set up Python 3.9
uses: actions/setup-python@v2
with:
python-version: 3.9
- name: Install dependencies
run: |
python -m pip install --upgrade pip setuptools
pip install -r .github/workflows/label_transfer/requirements.txt
pip freeze
- name: Run Python label transfer script
run: python .github/workflows/label_transfer/script.py ${{ github.event.number }}
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
GITHUB_REPO: ${{ github.repository }}

2
OpenRefine/.github/workflows/label_transfer/requirements.txt vendored
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requests
lxml

76
OpenRefine/.github/workflows/label_transfer/script.py vendored
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import requests
import os
from lxml import html
import sys
import json
# Config
# list of labels that should not be transferred to PRs
do_not_transfer = [
'good first issue',
'good second issue',
'imported from old code repo',
'help wanted',
'duplicate',
'invalid',
'question',
'to be reviewed',
]
# Internal
repo = os.environ.get('GITHUB_REPO')
github_token = os.environ.get('GITHUB_TOKEN')
headers = {
'Accept': 'application/vnd.github.v3+json',
}
if github_token:
headers['Authorization'] = 'Bearer '+github_token
def get_linked_issues(pr_number):
"""
Given a PR number, extract all the linked issue numbers from it.
Sadly this is not supported by the API yet, so we just scrape the web UI.
"""
url = f'https://github.com/{repo}/pull/{pr_number}'
page = requests.get(url)
page.raise_for_status()
parsed = html.document_fromstring(page.text)
matches = parsed.xpath('//form/div[@class="css-truncate my-1"]/a')
for match in matches:
yield int(match.attrib['href'].split('/')[-1])
def get_issue_labels(issue_number):
"""
Returns all the labels in a given issue / PR
"""
url = f'https://api.github.com/repos/{repo}/issues/{issue_number}/labels'
response = requests.get(url, headers=headers)
response.raise_for_status()
return [ tag['name'] for tag in response.json() ]
def transfer_issue_labels(pr_number):
"""
Transfers labels from all the linked issues to the PR
"""
linked_issues = get_linked_issues(pr_number)
all_labels = [ label for issue in linked_issues for label in get_issue_labels(issue) ]
to_transfer = [ label for label in all_labels if label not in do_not_transfer ]
current_labels = get_issue_labels(pr_number)
missing_labels = [ label for label in to_transfer if label not in current_labels ]
if not missing_labels:
return
new_labels = current_labels + missing_labels
url = f'https://api.github.com/repos/{repo}/issues/{pr_number}/labels'
print(f'adding {missing_labels} to PR #{pr_number}')
if not github_token:
print('no GITHUB_TOKEN, skipping')
else:
resp = requests.put(url, headers=headers, data=json.dumps({'labels':new_labels}))
resp.raise_for_status()
if __name__ == '__main__':
transfer_issue_labels(sys.argv[1])

171
OpenRefine/.github/workflows/pull_request.yml vendored
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name: Continuous Integration
on:
pull_request_target:
paths-ignore:
- 'docs/**'
branches:
- master
- '4.0'
permissions: read-all
jobs:
server_tests:
strategy:
matrix:
java: [ 11, 17 ]
runs-on: ubuntu-latest
services:
postgres:
image: postgres
ports:
- 5432
env:
POSTGRES_USER: postgres
POSTGRES_PASSWORD: 'postgres'
POSTGRES_DB: test_db
options: >-
--health-cmd pg_isready
--health-interval 10s
--health-timeout 5s
--health-retries 5
mysql:
image: mysql:8
ports:
- 3306
env:
MYSQL_ROOT_PASSWORD: root
options: >-
--health-cmd "mysqladmin ping"
--health-interval 5s
--health-timeout 2s
--health-retries 3
steps:
- uses: actions/checkout@v2.3.4
with:
ref: ${{ github.event.pull_request.head.ref }}
repository: ${{ github.event.pull_request.head.repo.full_name }}
- name: Restore dependency cache
uses: actions/cache@v2.1.7
with:
path: ~/.m2/repository
key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
restore-keys: |
${{ runner.os }}-maven-
- name: Set up Java ${{ matrix.java }}
uses: actions/setup-java@v2
with:
distribution: 'adopt'
java-version: ${{ matrix.java }}
- name: Check Java linting
id: java_linting
run: |
mvn formatter:validate
- name: Configure connections to databases
id: configure_db_connections
run: cat extensions/database/tests/conf/github_actions_tests.xml | sed -e "s/MYSQL_PORT/${{ job.services.mysql.ports[3306] }}/g" | sed -e "s/POSTGRES_PORT/${{ job.services.postgres.ports[5432] }}/g" > extensions/database/tests/conf/tests.xml
- name: Populate databases with test data
id: populate_databases_with_test_data
run: |
mysql -u root -h 127.0.0.1 -P ${{ job.services.mysql.ports[3306] }} -proot -e 'CREATE DATABASE test_db;'
mysql -u root -h 127.0.0.1 -P ${{ job.services.mysql.ports[3306] }} -proot < extensions/database/tests/conf/test-mysql.sql
psql -U postgres test_db -h 127.0.0.1 -p ${{ job.services.postgres.ports[5432] }} < extensions/database/tests/conf/test-pgsql.sql
env:
PGPASSWORD: postgres
- name: Build and test with Maven
run: mvn jacoco:prepare-agent test
- name: Submit test coverage to Coveralls
run: |
mvn prepare-package -DskipTests=true
mvn jacoco:report coveralls:report -DrepoToken=${{ secrets.COVERALLS_TOKEN }} -DpullRequest=${{ github.event.number }}
prepare_ui_test_matrix:
runs-on: ubuntu-latest
outputs:
matrix: ${{ steps.set-matrix.outputs.matrix }}
steps:
- uses: actions/checkout@v2.3.4
with:
ref: ${{ github.event.pull_request.head.ref }}
repository: ${{ github.event.pull_request.head.repo.full_name }}
- name: Setup Node
uses: actions/setup-node@v2
with:
node-version: '12'
- id: set-matrix
run: npm install --save glob && node main/tests/cypress/build-test-matrix.js
env:
browsers: chrome
ui_test:
needs: prepare_ui_test_matrix
runs-on: ubuntu-latest
strategy:
matrix: ${{fromJSON(needs.prepare_ui_test_matrix.outputs.matrix)}}
steps:
- uses: actions/checkout@v2.3.4
with:
ref: ${{ github.event.pull_request.head.ref }}
repository: ${{ github.event.pull_request.head.repo.full_name }}
- name: Restore dependency cache
uses: actions/cache@v2.1.7
with:
path: ~/.m2/repository
key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
restore-keys: |
${{ runner.os }}-maven-
- name: Set up Java 11
uses: actions/setup-java@v2
with:
distribution: 'adopt'
java-version: 11
- name: Build OpenRefine
run: ./refine build
- name: Setup Node
uses: actions/setup-node@v2
with:
node-version: '12'
- name: Restore Tests dependency cache
uses: actions/cache@v2.1.7
with:
path: |
~/cache
~/.cache
**/node_modules
!~/cache/exclude
key: ${{ runner.os }}-modules-${{ hashFiles('**/yarn.lock') }}
restore-keys: |
${{ runner.os }}-yarn
- name: Install test dependencies
run: |
cd ./main/tests/cypress
npm i -g yarn
yarn install
- name: Test with Cypress on ${{ matrix.browser }}
run: |
echo REFINE_MIN_MEMORY=1400M >> ./refine.ini
echo REFINE_MEMORY=4096M >> ./refine.ini
./refine ui_tests
env:
CYPRESS_BROWSER: ${{ matrix.browser }}
CYPRESS_RECORD_KEY: ${{ secrets.CYPRESS_RECORD_KEY }}
CYPRESS_PROJECT_ID: ${{ secrets.CYPRESS_PROJECT_ID }}
CYPRESS_CI_BUILD_ID: '${{ github.run_id }}'
CYPRESS_SPECS: ${{ matrix.specs }}

177
OpenRefine/.github/workflows/snapshot_release.yml vendored
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name: Snapshot release
on:
push:
branches:
- 'master'
- '4.0'
paths-ignore:
- 'docs/**'
jobs:
prepare_ui_test_matrix:
runs-on: ubuntu-latest
outputs:
matrix: ${{ steps.set-matrix.outputs.matrix }}
steps:
- uses: actions/checkout@v2.3.4
with:
ref: ${{ github.event.pull_request.head.ref }}
repository: ${{ github.event.pull_request.head.repo.full_name }}
- name: Setup Node
uses: actions/setup-node@v2
with:
node-version: '12'
- id: set-matrix
run: npm install --save glob && node main/tests/cypress/build-test-matrix.js
env:
browsers: chrome
ui_test:
needs: prepare_ui_test_matrix
runs-on: ubuntu-latest
strategy:
matrix: ${{fromJSON(needs.prepare_ui_test_matrix.outputs.matrix)}}
steps:
- uses: actions/checkout@v2.3.4
with:
ref: ${{ github.event.pull_request.head.ref }}
repository: ${{ github.event.pull_request.head.repo.full_name }}
- name: Restore dependency cache
uses: actions/cache@v2.1.7
with:
path: ~/.m2/repository
key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
restore-keys: |
${{ runner.os }}-maven-
- name: Set up Java 11
uses: actions/setup-java@v2
with:
distribution: 'adopt'
java-version: 11
- name: Build OpenRefine
run: ./refine build
- name: Setup Node
uses: actions/setup-node@v2
with:
node-version: '12'
- name: Restore Tests dependency cache
uses: actions/cache@v2.1.7
with:
path: |
~/cache
~/.cache
**/node_modules
!~/cache/exclude
key: ${{ runner.os }}-modules-${{ hashFiles('**/yarn.lock') }}
restore-keys: |
${{ runner.os }}-yarn
- name: Install test dependencies
run: |
cd ./main/tests/cypress
npm i -g yarn
yarn install
- name: Test with Cypress on ${{ matrix.browser }}
run: |
echo REFINE_MIN_MEMORY=1400M >> ./refine.ini
echo REFINE_MEMORY=4096M >> ./refine.ini
./refine ui_tests
env:
CYPRESS_BROWSER: ${{ matrix.browser }}
CYPRESS_RECORD_KEY: ${{ secrets.CYPRESS_RECORD_KEY }}
CYPRESS_PROJECT_ID: ${{ secrets.CYPRESS_PROJECT_ID }}
CYPRESS_CI_BUILD_ID: '${{ github.run_id }}'
CYPRESS_SPECS: ${{ matrix.specs }}
build:
services:
postgres:
image: postgres
ports:
- 5432
env:
POSTGRES_USER: postgres
POSTGRES_PASSWORD: 'postgres'
POSTGRES_DB: test_db
options: >-
--health-cmd pg_isready
--health-interval 10s
--health-timeout 5s
--health-retries 5
mysql:
image: mysql:8
ports:
- 3306
env:
MYSQL_ROOT_PASSWORD: root
options: >-
--health-cmd "mysqladmin ping"
--health-interval 5s
--health-timeout 2s
--health-retries 3
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2.3.4
with:
fetch-depth: 0 # This is wasteful, but needed for git describe
- name: Restore dependency cache
uses: actions/cache@v2.1.7
with:
path: ~/.m2/repository
key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
restore-keys: |
${{ runner.os }}-maven-
- name: Set up Java 11
uses: actions/setup-java@v2
with:
distribution: 'adopt'
java-version: 11
server-id: ossrh
server-username: OSSRH_USER
server-password: OSSRH_PASS
- name: Install genisoimage and jq
run: sudo apt-get install genisoimage jq
- name: Configure connections to databases
id: configure_db_connections
run: cat extensions/database/tests/conf/github_actions_tests.xml | sed -e "s/MYSQL_PORT/${{ job.services.mysql.ports[3306] }}/g" | sed -e "s/POSTGRES_PORT/${{ job.services.postgres.ports[5432] }}/g" > extensions/database/tests/conf/tests.xml
- name: Populate databases with test data
id: populate_databases_with_test_data
run: |
mysql -u root -h 127.0.0.1 -P ${{ job.services.mysql.ports[3306] }} -proot -e 'CREATE DATABASE test_db;'
mysql -u root -h 127.0.0.1 -P ${{ job.services.mysql.ports[3306] }} -proot < extensions/database/tests/conf/test-mysql.sql
psql -U postgres test_db -h 127.0.0.1 -p ${{ job.services.postgres.ports[5432] }} < extensions/database/tests/conf/test-pgsql.sql
env:
PGPASSWORD: postgres
- name: Build and test with Maven
run: mvn jacoco:prepare-agent test
- name: Submit test coverage to Coveralls
run: |
mvn prepare-package -DskipTests=true
mvn jacoco:report coveralls:report -DrepoToken=${{ secrets.COVERALLS_TOKEN }} -DpullRequest=${{ github.event.number }} -DserviceName="GitHub Actions" -DserviceBuildNumber=${{ env.GITHUB_RUN_ID }} -Dbranch=master
- name: Generate dist files
run: mvn package -DskipTests=true
- name: Upload snapshot releases to OSSRH
run: mvn deploy -DskipTests=true
env:
OSSRH_USER: ${{ secrets.OSSRH_USER }}
OSSRH_PASS: ${{ secrets.OSSRH_PASS }}

19
OpenRefine/Dockerfile Normal file
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FROM maven:3-jdk-11 as build
WORKDIR /usr/src/app
COPY OpenRefine .
WORKDIR /usr/src/app/OpenRefine
RUN ./refine clean
RUN ./refine build
FROM openjdk:11
WORKDIR /usr/app
COPY --from=build /usr/src/app/OpenRefine .
VOLUME /data
EXPOSE 3333
ENTRYPOINT ["/usr/app/refine"]
CMD ["-i", "0.0.0.0", "-d", "/data", "-m", "3G"]

29
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razem 164
drwxr-xr-x 13 prance prance 4096 01-30 20:46 .
drwxr-xr-x 4 prance prance 4096 01-30 20:41 ..
-rw-r--r-- 1 prance prance 1603 01-30 20:42 appveyor.yml
drwxr-xr-x 3 prance prance 4096 01-30 20:42 benchmark
-rw-r--r-- 1 prance prance 3483 01-30 20:42 CODE_OF_CONDUCT.md
drwxr-xr-x 2 prance prance 4096 01-30 20:42 conf
-rw-r--r-- 1 prance prance 6438 01-30 20:42 CONTRIBUTING.md
drwxr-xr-x 7 prance prance 4096 01-30 20:42 docs
drwxr-xr-x 9 prance prance 4096 01-30 20:42 extensions
drwxr-xr-x 8 prance prance 4096 01-30 20:42 .git
-rw-r--r-- 1 prance prance 482 01-30 20:42 .gitattributes
drwxr-xr-x 4 prance prance 4096 01-30 20:42 .github
-rw-r--r-- 1 prance prance 1254 01-30 20:42 .gitignore
-rw-r--r-- 1 prance prance 8613 01-30 20:42 GOVERNANCE.md
drwxr-xr-x 4 prance prance 4096 01-30 20:42 graphics
drwxr-xr-x 3 prance prance 4096 01-30 20:42 IDEs
-rw-r--r-- 1 prance prance 1478 01-30 20:42 LICENSE.txt
-rw-r--r-- 1 prance prance 0 01-30 20:46 ls1.txt
drwxr-xr-x 6 prance prance 4096 01-30 20:42 main
drwxr-xr-x 2 prance prance 4096 01-30 20:42 packaging
-rw-r--r-- 1 prance prance 13518 01-30 20:42 pom.xml
-rw-r--r-- 1 prance prance 3523 01-30 20:42 README.md
-rwxr-xr-x 1 prance prance 29532 01-30 20:42 refine
-rw-r--r-- 1 prance prance 7680 01-30 20:42 refine.bat
-rw-r--r-- 1 prance prance 1549 01-30 20:42 refine.ini
-rw-r--r-- 1 prance prance 729 01-30 20:42 SECURITY.md
drwxr-xr-x 5 prance prance 4096 01-30 20:42 server
-rw-r--r-- 1 prance prance 1099 01-30 20:42 settings.xml

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razem 172
drwxr-xr-x 14 prance prance 4096 01-30 20:47 .
drwxr-xr-x 4 prance prance 4096 01-30 20:41 ..
-rw-r--r-- 1 prance prance 1603 01-30 20:42 appveyor.yml
drwxr-xr-x 3 prance prance 4096 01-30 20:42 benchmark
-rw-r--r-- 1 prance prance 3483 01-30 20:42 CODE_OF_CONDUCT.md
drwxr-xr-x 2 prance prance 4096 01-30 20:42 conf
-rw-r--r-- 1 prance prance 6438 01-30 20:42 CONTRIBUTING.md
drwxr-xr-x 7 prance prance 4096 01-30 20:42 docs
drwxr-xr-x 9 prance prance 4096 01-30 20:42 extensions
drwxr-xr-x 8 prance prance 4096 01-30 20:42 .git
-rw-r--r-- 1 prance prance 482 01-30 20:42 .gitattributes
drwxr-xr-x 4 prance prance 4096 01-30 20:42 .github
-rw-r--r-- 1 prance prance 1254 01-30 20:42 .gitignore
-rw-r--r-- 1 prance prance 8613 01-30 20:42 GOVERNANCE.md
drwxr-xr-x 4 prance prance 4096 01-30 20:42 graphics
drwxr-xr-x 3 prance prance 4096 01-30 20:42 IDEs
-rw-r--r-- 1 prance prance 1478 01-30 20:42 LICENSE.txt
-rw-r--r-- 1 prance prance 1563 01-30 20:46 ls1.txt
-rw-r--r-- 1 prance prance 0 01-30 20:47 ls2.txt
drwxr-xr-x 6 prance prance 4096 01-30 20:42 main
drwxr-xr-x 2 prance prance 4096 01-30 20:42 packaging
-rw-r--r-- 1 prance prance 13518 01-30 20:42 pom.xml
-rw-r--r-- 1 prance prance 3523 01-30 20:42 README.md
-rwxr-xr-x 1 prance prance 29532 01-30 20:42 refine
-rw-r--r-- 1 prance prance 7680 01-30 20:42 refine.bat
-rw-r--r-- 1 prance prance 1549 01-30 20:42 refine.ini
-rw-r--r-- 1 prance prance 729 01-30 20:42 SECURITY.md
drwxr-xr-x 5 prance prance 4096 01-30 20:42 server
-rw-r--r-- 1 prance prance 1099 01-30 20:42 settings.xml
drwxr-xr-x 2 prance prance 4096 01-30 20:46 tools

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drwxr-xr-x 2 prance prance 4096 01-30 20:47 build
drwxr-xr-x 2 prance prance 4096 01-30 20:46 tools

2
OpenRefine/main/webapp/modules/core/styles/index.less
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@ -47,7 +47,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
font-size: 110%;
color: @near_black;
white-space: nowrap;
}
}
#left-panel-body {
margin-left: @padding_tight;