From 8dff37789a7845fdbde992d1c82d18265101f7b7 Mon Sep 17 00:00:00 2001 From: Tim Dudgeon Date: Mon, 9 Mar 2026 12:12:06 +0000 Subject: [PATCH 1/4] minValue -> minimum --- data-manager/im-virtual-screening.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/data-manager/im-virtual-screening.yaml b/data-manager/im-virtual-screening.yaml index ac4cf98..bb0eddf 100644 --- a/data-manager/im-virtual-screening.yaml +++ b/data-manager/im-virtual-screening.yaml @@ -524,7 +524,7 @@ jobs: top: title: Keep best n records type: integer - minValue: 1 + minimum: 1 tests: simple-sort: inputs: @@ -634,7 +634,7 @@ jobs: top: title: Keep best n records type: integer - minValue: 1 + minimum: 1 tests: group-and-sort: inputs: @@ -1922,7 +1922,7 @@ jobs: title: Size of chunks to split type: integer default: 1000 - minValue: 100 + minimum: 100 tests: simple-execution: inputs: From c25f712dfdba36bb7bf15090db82411a6299af5c Mon Sep 17 00:00:00 2001 From: Tim Dudgeon Date: Mon, 9 Mar 2026 12:14:11 +0000 Subject: [PATCH 2/4] minValue -> minimum --- data-manager/rdkit.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data-manager/rdkit.yaml b/data-manager/rdkit.yaml index 0debff4..4298c96 100644 --- a/data-manager/rdkit.yaml +++ b/data-manager/rdkit.yaml @@ -1963,7 +1963,7 @@ jobs: title: Size of chunks to split type: integer default: 1000 - minValue: 100 + minimum: 100 tests: simple-execution: inputs: From 168a6201a4ac42976cf28548225dd5745d25bf46 Mon Sep 17 00:00:00 2001 From: Tim Dudgeon Date: Mon, 9 Mar 2026 12:31:49 +0000 Subject: [PATCH 3/4] schema error corrected --- data-manager/rdkit.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/data-manager/rdkit.yaml b/data-manager/rdkit.yaml index 4298c96..52ae48e 100644 --- a/data-manager/rdkit.yaml +++ b/data-manager/rdkit.yaml @@ -918,8 +918,7 @@ jobs: - pipe idColumn: title: Index (text) or name (SDF) to use for the ID field - type: - - string + type: string pattern: "^[A-Za-z0-9_\\.\\- ]+$" readRecords: title: Number of records to read field names From fe0aec21b39adb1bbaffb0a3285bf9571882e03d Mon Sep 17 00:00:00 2001 From: Tim Dudgeon Date: Mon, 9 Mar 2026 12:58:23 +0000 Subject: [PATCH 4/4] various docker build fixes --- Dockerfile-mordred | 2 +- Dockerfile-nextflow | 2 +- Dockerfile-oddt | 3 ++- Dockerfile-rdock | 4 ++++ 4 files changed, 8 insertions(+), 3 deletions(-) diff --git a/Dockerfile-mordred b/Dockerfile-mordred index 067e35b..4ecd8b1 100644 --- a/Dockerfile-mordred +++ b/Dockerfile-mordred @@ -11,7 +11,7 @@ ENV HOME=/code WORKDIR ${HOME} # install our requirements. RDKit is present in base container -RUN pip install pip install mordredcommunity==2.0.4 \ +RUN pip install mordredcommunity==2.0.4 \ im-standardize-molecule==0.1.0 \ im-data-manager-job-utilities==1.1.1 diff --git a/Dockerfile-nextflow b/Dockerfile-nextflow index 58f8778..89ee1e5 100644 --- a/Dockerfile-nextflow +++ b/Dockerfile-nextflow @@ -1,4 +1,4 @@ -FROM debian:buster +FROM debian:bullseye LABEL maintainer="Tim Dudgeon" # Note: When run by the Data Manager the uid and gid # will be set according to the Project we're running against. diff --git a/Dockerfile-oddt b/Dockerfile-oddt index 9decfb6..9907a6f 100644 --- a/Dockerfile-oddt +++ b/Dockerfile-oddt @@ -6,7 +6,8 @@ FROM informaticsmatters/vs-rdkit-base:latest # for execution, and so we must ensure the code runs # as any user. -RUN apt-get -y install git &&\ +RUN apt-get -y update &&\ + apt-get -y install git &&\ apt-get clean ENV PYTHONPATH=/code diff --git a/Dockerfile-rdock b/Dockerfile-rdock index e4232d6..89cbeca 100644 --- a/Dockerfile-rdock +++ b/Dockerfile-rdock @@ -1,6 +1,8 @@ FROM informaticsmatters/rdock:2013.1 LABEL maintainer="Tim Dudgeon" +USER 0 + RUN yum -y update &&\ yum -y install python-jinja2 &&\ yum clean all @@ -9,3 +11,5 @@ RUN pip install im-data-manager-job-utilities==1.0.1 COPY prepare_rdock.py rdock_*.sh /code/ RUN chmod 755 /code/prepare_rdock.py + +USER rdock