From 4aed00d2a89144ccd06d5d6f054ea4ba9fa593de Mon Sep 17 00:00:00 2001 From: Martin Burchell Date: Wed, 7 Oct 2026 15:58:14 +0100 Subject: [PATCH 1/5] Bump version to v1.14.0 --- README.md | 25 ++++++++++++------------- intermine/__init__.py | 2 +- 2 files changed, 13 insertions(+), 14 deletions(-) diff --git a/README.md b/README.md index fb5fa4e7..ba1aeda9 100644 --- a/README.md +++ b/README.md @@ -2,9 +2,9 @@ The InterMine Python Webservice Client ===================================== -[![Build Status][badge]][ci] +[![Build Status][badge]][ci] ![Version](http://img.shields.io/badge/version-1.12.0-blue.svg?style=flat) -[![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/intermine/intermine/blob/master/LICENSE) +[![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/intermine/intermine/blob/master/LICENSE) [![Research software impact](http://depsy.org/api/package/pypi/intermine/badge.svg)](http://depsy.org/package/python/intermine) [![Conda](https://anaconda.org/intermine/intermine/badges/installer/conda.svg)](https://anaconda.org/bioconda/intermine) @@ -12,15 +12,15 @@ The InterMine Python Webservice Client [![Downloads](https://anaconda.org/bioconda/intermine/badges/downloads.svg)](https://anaconda.org/bioconda/intermine) -An implementation of a webservice client +An implementation of a webservice client for InterMine webservices, written in Python Who should use this software? ----------------------------- -This software is intended for people who make +This software is intended for people who make use of InterMine datawarehouses (ie. Biologists) -and who want a quicker, more automated way +and who want a quicker, more automated way to perform queries. Some examples of sites that are powered by InterMine software, and thus offer a compatible webservice API, are: @@ -36,9 +36,9 @@ a compatible webservice API, are: See the [InterMine registry](http://registry.intermine.org/) for the full list of available InterMines. -Queries here refer to database queries over the -integrated datawarehouse. Instead of using -SQL, InterMine services use a flexible and +Queries here refer to database queries over the +integrated datawarehouse. Instead of using +SQL, InterMine services use a flexible and powerful sub-set of database query language to enable wide-ranging and arbitrary queries. @@ -67,7 +67,7 @@ the following command: (from the source directory) python setup.py test ``` -If you want to run the suite against a live server (e.g. as deployed by the testmodel/setup.sh in +If you want to run the suite against a live server (e.g. as deployed by the testmodel/setup.sh in the InterMine distribution, then you can run: ``` @@ -122,6 +122,7 @@ For example: Changes: -------- + 1.14.00 Add Python 3.10 support 1.13.00 Added get_template_by_user method Added property view_types to the template 1.12.00 Added organism to list upload @@ -152,7 +153,7 @@ Changes: Ensure lists and queries share the same overloading 0.99.02 Allow sort-orders which are not in the view but are on selected classes 0.99.01 Better representation of multiple sort-orders. - 0.99.00 Fixed bug with subclasses not being included in clones + 0.99.00 Fixed bug with subclasses not being included in clones Added support for new json format for ws versions >= 8. 0.98.16 Fixed bug with XML parsing and subclasses where the subclass is mentioned in the first view. better result format documentation and tests @@ -184,7 +185,5 @@ Please cite [Nucleic Acids Res. 2014 Jul;42(Web Server issue):W468-72](https://academic.oup.com/nar/article/42/W1/W468/2435235) -[![doi](http://img.shields.io/badge/doi-10.1093/nar/gku301-blue.svg?style=flat)](https://doi.org/10.1093/nar/gku301) +[![doi](http://img.shields.io/badge/doi-10.1093/nar/gku301-blue.svg?style=flat)](https://doi.org/10.1093/nar/gku301) [![pubmed](http://img.shields.io/badge/pubmed-24753429-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/24753429) - - diff --git a/intermine/__init__.py b/intermine/__init__.py index cfa2a19a..c1230ddf 100644 --- a/intermine/__init__.py +++ b/intermine/__init__.py @@ -1 +1 @@ -VERSION = "1.13.0" +VERSION = "1.14.0" From 284e415fbd74c18504fbf2afc794edf0ffd705ed Mon Sep 17 00:00:00 2001 From: Martin Burchell Date: Wed, 21 Oct 2026 09:18:22 +0100 Subject: [PATCH 2/5] Attempt to fix the build workflow Need to run the install_intermine.py script now to set up the properties files --- .github/workflows/im-build.yml | 2 +- config/ci/init.sh | 4 +++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/im-build.yml b/.github/workflows/im-build.yml index d0220b7f..710560c6 100644 --- a/.github/workflows/im-build.yml +++ b/.github/workflows/im-build.yml @@ -58,6 +58,6 @@ jobs: run: | set -euo pipefail ./config/ci/init-solr.sh ${GITHUB_WORKSPACE} - ./config/ci/init.sh ${GITHUB_WORKSPACE} http://localhost:8080/intermine-demo + ./config/ci/init.sh ${GITHUB_WORKSPACE} $(which python3) http://localhost:8080/intermine-demo python setup.py test python setup.py livetest diff --git a/config/ci/init.sh b/config/ci/init.sh index 8afafceb..cd921d7e 100755 --- a/config/ci/init.sh +++ b/config/ci/init.sh @@ -8,7 +8,8 @@ if [ "$#" != "2" ]; then fi WORKSPACE_DIR=$1 -TESTMODEL_URL=$2 +PYTHON=$2 +TESTMODEL_URL=$3 INTERMINE_DIR=${WORKSPACE_DIR}/server TESTMINE_DIR=${INTERMINE_DIR}/testmine @@ -48,6 +49,7 @@ sed -i -e "s/PSQL_HOST/${PSQL_HOST}/" "$TESTMODEL_PROPS" sed -i -e "s/PSQL_USER/${PSQL_USER}/" "$TESTMODEL_PROPS" sed -i -e "s/PSQL_PWD/${PSQL_PWD}/" "$TESTMODEL_PROPS" +${PYTHON} "${INTERMINE_DIR}"/config/lib/install_intermine.py # We will need a fully operational web-application echo '#---> Building and releasing web application to test against' From 4b1da0011bd17f6abe976a3a510b2137b5efb1e5 Mon Sep 17 00:00:00 2001 From: Martin Burchell Date: Wed, 21 Oct 2026 11:48:40 +0100 Subject: [PATCH 3/5] Speed up Solr in GitHub workflow --- .github/workflows/im-build.yml | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/.github/workflows/im-build.yml b/.github/workflows/im-build.yml index 710560c6..b56be204 100644 --- a/.github/workflows/im-build.yml +++ b/.github/workflows/im-build.yml @@ -4,6 +4,8 @@ on: push: pull_request: +env: + SOLR_VERSION: 8.6.2 jobs: build: @@ -34,6 +36,11 @@ jobs: uses: actions/setup-python@v5 with: python-version: '3.10' + - name: Setup Apache Solr + uses: DhavalGojiya/setup-solr-action@v1.2.0 + with: + solr-version: ${{ env.SOLR_VERSION }} + solr-core-name: 'intermine-search' - name: Change apt mirror run: | set -euo pipefail @@ -44,7 +51,7 @@ jobs: - name: Install dependencies run: | set -euo pipefail - sudo apt-get install libxml2-dev libxslt-dev python3-dev + sudo apt-get install -y libxml2-dev libxslt-dev python3-dev wait-for-it python -m pip install --upgrade pip pip install -U setuptools pip install -r requirements.txt @@ -54,10 +61,16 @@ jobs: sudo apt-get update -y sudo apt-get install -y libpq-dev postgresql-client sudo service postgresql start + - name: Create additional Solr core + run: | + set -euo pipefail + wait-for-it localhost:8983 + docker ps + SOLR_CONTAINER=$(docker ps -f ancestor=solr:"$SOLR_VERSION" --format '{{.ID}}' | head -n1) + docker exec "$SOLR_CONTAINER" /opt/solr/bin/solr create -c intermine-autocomplete - name: Run unit tests run: | set -euo pipefail - ./config/ci/init-solr.sh ${GITHUB_WORKSPACE} ./config/ci/init.sh ${GITHUB_WORKSPACE} $(which python3) http://localhost:8080/intermine-demo python setup.py test python setup.py livetest From 555f187355cff5ed15bffb1b90b2b85d2e613690 Mon Sep 17 00:00:00 2001 From: Martin Burchell Date: Wed, 21 Oct 2026 11:50:27 +0100 Subject: [PATCH 4/5] Stop running workflow on pull request --- .github/workflows/im-build.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/im-build.yml b/.github/workflows/im-build.yml index b56be204..0e923d7f 100644 --- a/.github/workflows/im-build.yml +++ b/.github/workflows/im-build.yml @@ -2,7 +2,6 @@ name: InterMine WS Python CI on: push: - pull_request: env: SOLR_VERSION: 8.6.2 From 289b23ba3d7755aef7a71764c52067b5eabdcfec Mon Sep 17 00:00:00 2001 From: Martin Burchell Date: Wed, 21 Oct 2026 11:54:01 +0100 Subject: [PATCH 5/5] Fix arguments to CI init script --- config/ci/init.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/config/ci/init.sh b/config/ci/init.sh index cd921d7e..d176f7fd 100755 --- a/config/ci/init.sh +++ b/config/ci/init.sh @@ -2,8 +2,8 @@ set -euo pipefail -if [ "$#" != "2" ]; then - echo "Usage: $0 " +if [ "$#" != "3" ]; then + echo "Usage: $0 " exit 2 fi