From 4c972fa3943f1a99e542b03678c30b5e4b476bd8 Mon Sep 17 00:00:00 2001
From: Arkadii Yakovets <ark@ccdatalab.org>
Date: Wed, 1 Nov 2023 18:31:00 -0700
Subject: [PATCH] Fix difference

---
 api/dockerfiles/Dockerfile.api               |  3 ++-
 api/dockerfiles/Dockerfile.api_base          | 19 +++++++++++++------
 common/dockerfiles/Dockerfile.base           |  8 ++++++--
 common/dockerfiles/Dockerfile.common_tests   |  6 +++---
 common/dockerfiles/Dockerfile.migrations     |  6 +++---
 foreman/dockerfiles/Dockerfile.foreman       | 11 +++++++----
 workers/dockerfiles/Dockerfile.affymetrix    |  7 +++++--
 workers/dockerfiles/Dockerfile.compendia     |  7 +++++--
 workers/dockerfiles/Dockerfile.downloaders   |  5 ++++-
 workers/dockerfiles/Dockerfile.illumina      |  7 +++++--
 workers/dockerfiles/Dockerfile.no_op         |  7 +++++--
 workers/dockerfiles/Dockerfile.salmon        |  7 +++++--
 workers/dockerfiles/Dockerfile.smasher       |  7 +++++--
 workers/dockerfiles/Dockerfile.transcriptome |  7 +++++--
 14 files changed, 73 insertions(+), 34 deletions(-)

diff --git a/api/dockerfiles/Dockerfile.api b/api/dockerfiles/Dockerfile.api
index 292d1149a..3fd03b67b 100644
--- a/api/dockerfiles/Dockerfile.api
+++ b/api/dockerfiles/Dockerfile.api
@@ -8,8 +8,9 @@ SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 RUN <<EOF
 pip install --ignore-installed --no-cache-dir uwsgi
 chmod +x /home/user/collect_and_run_uwsgi.sh
-mkdir -p /tmp/www/static
+mkdir -m 755 -p /tmp/www/static
 chown user /tmp/www/static
+rm -rf /root/.cache/*
 EOF
 
 ENV SYSTEM_VERSION=$SYSTEM_VERSION
diff --git a/api/dockerfiles/Dockerfile.api_base b/api/dockerfiles/Dockerfile.api_base
index 3503db769..53764b60c 100644
--- a/api/dockerfiles/Dockerfile.api_base
+++ b/api/dockerfiles/Dockerfile.api_base
@@ -15,17 +15,24 @@ EOF
 
 WORKDIR /home/user
 
-COPY api/requirements.txt .
+COPY --chmod=644 api/requirements.txt .
 RUN <<EOF
 pip install --upgrade pip
 pip install --ignore-installed --no-cache-dir -r requirements.txt
 EOF
 
-COPY common/dist/data-refinery-common-* common/
-RUN pip install --ignore-installed common/$(ls common -1 | sort --version-sort | tail -1)
+COPY --chmod=644 common/dist/data-refinery-common-* common/
+RUN <<EOF
+pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+rm -r common
+EOF
+
+COPY --chmod=644 api/ .
+COPY --chmod=644 config/ config/
+COPY --chmod=644 setup.cfg .
 
-COPY api/ .
-COPY config/ config/
-COPY setup.cfg .
+RUN <<EOF
+find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
+EOF
 
 ENTRYPOINT []
diff --git a/common/dockerfiles/Dockerfile.base b/common/dockerfiles/Dockerfile.base
index e7b7b703a..f2f4c5633 100644
--- a/common/dockerfiles/Dockerfile.base
+++ b/common/dockerfiles/Dockerfile.base
@@ -65,9 +65,13 @@ useradd --create-home --home-dir /home/user/ -g user user
 chown -R user /home/user/
 EOF
 
-ENV R_LIBS=/usr/local/lib/R/site-library
-
 COPY --chmod=644 config/ config/
 COPY --chmod=644 setup.cfg .
 
+RUN <<EOF
+find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
+EOF
+
+ENV R_LIBS=/usr/local/lib/R/site-library
+
 ENTRYPOINT []
diff --git a/common/dockerfiles/Dockerfile.common_tests b/common/dockerfiles/Dockerfile.common_tests
index 81dd947a4..228b27871 100644
--- a/common/dockerfiles/Dockerfile.common_tests
+++ b/common/dockerfiles/Dockerfile.common_tests
@@ -16,13 +16,13 @@ RUN pip3 install --ignore-installed --no-cache-dir -r requirements.txt
 
 COPY --chmod=644 common/ .
 
-ENV SYSTEM_VERSION=$SYSTEM_VERSION
-
 RUN <<EOF
-rm -rf /root/.cache/*
 find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
+rm -rf /root/.cache/*
 EOF
 
+ENV SYSTEM_VERSION=$SYSTEM_VERSION
+
 USER user
 
 ENTRYPOINT []
diff --git a/common/dockerfiles/Dockerfile.migrations b/common/dockerfiles/Dockerfile.migrations
index 603997c72..9edaa2bd1 100644
--- a/common/dockerfiles/Dockerfile.migrations
+++ b/common/dockerfiles/Dockerfile.migrations
@@ -12,13 +12,13 @@ RUN pip install --ignore-installed --no-cache-dir -r requirements.txt
 
 COPY --chmod=644 common/ .
 
-ENV SYSTEM_VERSION=$SYSTEM_VERSION
-
 RUN <<EOF
-rm -rf /root/.cache/*
 find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
+rm -rf /root/.cache/*
 EOF
 
+ENV SYSTEM_VERSION=$SYSTEM_VERSION
+
 USER user
 
 ENTRYPOINT []
diff --git a/foreman/dockerfiles/Dockerfile.foreman b/foreman/dockerfiles/Dockerfile.foreman
index 24cea88ae..357d24e91 100644
--- a/foreman/dockerfiles/Dockerfile.foreman
+++ b/foreman/dockerfiles/Dockerfile.foreman
@@ -18,18 +18,21 @@ EOF
 
 # Get the latest version from the dist directory.
 COPY --chmod=644 common/dist/data-refinery-common-* common/
-RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+RUN <<EOF
+pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+rm -r common
+EOF
 
 COPY --chmod=644 .boto .boto
 COPY --chmod=644 foreman/ .
 
-ENV SYSTEM_VERSION=$SYSTEM_VERSION
-
 RUN <<EOF
-rm -rf /root/.cache/*
 find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
+rm -rf /root/.cache/*
 EOF
 
+ENV SYSTEM_VERSION=$SYSTEM_VERSION
+
 USER user
 
 ENTRYPOINT []
diff --git a/workers/dockerfiles/Dockerfile.affymetrix b/workers/dockerfiles/Dockerfile.affymetrix
index 979dc15d8..e2a07e37a 100644
--- a/workers/dockerfiles/Dockerfile.affymetrix
+++ b/workers/dockerfiles/Dockerfile.affymetrix
@@ -19,14 +19,17 @@ RUN pip3 install --ignore-installed --no-cache-dir -r requirements.txt
 
 # Get the latest version from the dist directory.
 COPY --chmod=644 common/dist/data-refinery-common-* common/
-RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+RUN <<EOF
+pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+rm -r common
+EOF
 
 COPY --chmod=644 .boto .boto
 COPY --chmod=644 workers/ .
 
 RUN <<EOF
-rm -rf /root/.cache/*
 find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
+rm -rf /root/.cache/*
 EOF
 
 ENV SYSTEM_VERSION=$SYSTEM_VERSION
diff --git a/workers/dockerfiles/Dockerfile.compendia b/workers/dockerfiles/Dockerfile.compendia
index 23fb06903..fe6eface1 100644
--- a/workers/dockerfiles/Dockerfile.compendia
+++ b/workers/dockerfiles/Dockerfile.compendia
@@ -88,7 +88,10 @@ EOF
 
 # Get the latest version from the dist directory.
 COPY --chmod=644 common/dist/data-refinery-common-* common/
-RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+RUN <<EOF
+pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+rm -r common
+EOF
 
 COPY --chmod=644 .boto .boto
 COPY --chmod=644 config/ config/
@@ -96,8 +99,8 @@ COPY --chmod=644 setup.cfg .
 COPY --chmod=644 workers/ .
 
 RUN <<EOF
-rm -rf /root/.cache/*
 find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
+rm -rf /root/.cache/*
 EOF
 
 ARG SYSTEM_VERSION
diff --git a/workers/dockerfiles/Dockerfile.downloaders b/workers/dockerfiles/Dockerfile.downloaders
index a7788acbc..af7030e4e 100644
--- a/workers/dockerfiles/Dockerfile.downloaders
+++ b/workers/dockerfiles/Dockerfile.downloaders
@@ -37,7 +37,10 @@ USER root
 
 # Get the latest version from the dist directory.
 COPY --chmod=644 common/dist/data-refinery-common-* common/
-RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+RUN <<EOF
+pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+rm -r common
+EOF
 
 COPY --chmod=644 .boto .boto
 COPY --chmod=644 workers/ .
diff --git a/workers/dockerfiles/Dockerfile.illumina b/workers/dockerfiles/Dockerfile.illumina
index 63ea79189..50885503c 100644
--- a/workers/dockerfiles/Dockerfile.illumina
+++ b/workers/dockerfiles/Dockerfile.illumina
@@ -16,7 +16,10 @@ RUN pip3 install --ignore-installed --no-cache-dir -r requirements.txt
 
 # Get the latest version from the dist directory.
 COPY --chmod=644 common/dist/data-refinery-common-* common/
-RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+RUN <<EOF
+pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+rm -r common
+EOF
 
 COPY --chmod=644 .boto .boto
 COPY --chmod=644 workers/ .
@@ -24,8 +27,8 @@ COPY --chmod=644 workers/data_refinery_workers/processors/detect_database.R .
 COPY --chmod=644 workers/illumina_probe_maps/ probe_maps/
 
 RUN <<EOF
-rm -rf /root/.cache/*
 find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
+rm -rf /root/.cache/*
 EOF
 
 ENV SYSTEM_VERSION=$SYSTEM_VERSION
diff --git a/workers/dockerfiles/Dockerfile.no_op b/workers/dockerfiles/Dockerfile.no_op
index 5719e59c8..3f3bb35c4 100644
--- a/workers/dockerfiles/Dockerfile.no_op
+++ b/workers/dockerfiles/Dockerfile.no_op
@@ -30,14 +30,17 @@ WORKDIR /home/user
 
 # Get the latest version from the dist directory.
 COPY --chmod=644 common/dist/data-refinery-common-* common/
-RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+RUN <<EOF
+pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+rm -r common
+EOF
 
 COPY --chmod=644 .boto .boto
 COPY --chmod=644 workers/ .
 
 RUN <<EOF
-rm -rf /root/.cache/*
 find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
+rm -rf /root/.cache/*
 EOF
 
 ENV SYSTEM_VERSION=$SYSTEM_VERSION
diff --git a/workers/dockerfiles/Dockerfile.salmon b/workers/dockerfiles/Dockerfile.salmon
index 6ad2247fe..7e4ab49f5 100644
--- a/workers/dockerfiles/Dockerfile.salmon
+++ b/workers/dockerfiles/Dockerfile.salmon
@@ -51,14 +51,17 @@ EOF
 
 # Get the latest version from the dist directory.
 COPY --chmod=644 common/dist/data-refinery-common-* common/
-RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+RUN <<EOF
+pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+rm -r common
+EOF
 
 COPY --chmod=644 .boto .boto
 COPY --chmod=644 workers/ .
 
 RUN <<EOF
-rm -rf /root/.cache/*
 find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
+rm -rf /root/.cache/*
 EOF
 
 ENV SYSTEM_VERSION=$SYSTEM_VERSION
diff --git a/workers/dockerfiles/Dockerfile.smasher b/workers/dockerfiles/Dockerfile.smasher
index d0cbd2525..939c3d6f1 100644
--- a/workers/dockerfiles/Dockerfile.smasher
+++ b/workers/dockerfiles/Dockerfile.smasher
@@ -16,14 +16,17 @@ RUN pip3 install --ignore-installed --no-cache-dir -r requirements.txt
 
 # Get the latest version from the dist directory.
 COPY --chmod=644 common/dist/data-refinery-common-* common/
-RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+RUN <<EOF
+pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+rm -r common
+EOF
 
 COPY --chmod=644 .boto .boto
 COPY --chmod=644 workers/ .
 
 RUN <<EOF
-rm -rf /root/.cache/*
 find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
+rm -rf /root/.cache/*
 EOF
 
 ENV SYSTEM_VERSION=$SYSTEM_VERSION
diff --git a/workers/dockerfiles/Dockerfile.transcriptome b/workers/dockerfiles/Dockerfile.transcriptome
index 3721234da..89c32a6b4 100644
--- a/workers/dockerfiles/Dockerfile.transcriptome
+++ b/workers/dockerfiles/Dockerfile.transcriptome
@@ -34,14 +34,17 @@ rm -rf RSEM
 EOF
 
 COPY --chmod=644 common/dist/data-refinery-common-* common/
-RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+RUN <<EOF
+pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+rm -r common
+EOF
 
 COPY --chmod=644 .boto .boto
 COPY --chmod=644 workers/ .
 
 RUN <<EOF
-rm -rf /root/.cache/*
 find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
+rm -rf /root/.cache/*
 EOF
 
 ENV SYSTEM_VERSION=$SYSTEM_VERSION