Merge pull request #30 from Vastra-Gotalandsregionen/AI-844

AI-844: Adds researcher user and renv.lock to R
Vastra-Gotalandsregionen · Mar 17, 2023 · 45712f9 · 45712f9
2 parents d40920f + f6f8716
commit 45712f9
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Showing 7 changed files with 175 additions and 16 deletions.
diff --git a/tests/test_pytorch_env.py b/tests/test_pytorch_env.py
@@ -87,8 +87,8 @@ def test_dockerfile(self):
             lines = list(map(lambda x: x.strip(), fin.readlines()))
         dockerfile_text = Path(dockerfile_path).read_text()
 
-        assert lines[1] == "FROM registry.git.vgregion.se/aiplattform/images/pytorch:0.3.2"
-        assert lines[-1] == 'WORKDIR /workspace'
+        assert lines[0] == "FROM registry.git.vgregion.se/aiplattform/images/pytorch:0.3.2"
+        assert lines[-2] == 'WORKDIR /workspace'
         assert "ADD http://aiav2.vgregion.se/VGC%20Root%20CA%20v2.crt /tmp/vgc_root.der" in lines
         assert "ADD http://aiav2.vgregion.se/VGC%20Issuing%201%20CA%20v2.crt /tmp/vgc_issuing1.der" in lines
         assert "ADD http://aiav2.vgregion.se/VGC%20Issuing%202%20CA%20v2.crt /tmp/vgc_issuing2.der" in lines

diff --git a/tests/test_r_env.py b/tests/test_r_env.py
@@ -51,7 +51,11 @@ def test_dockerfile(self):
             lines = list(map(lambda x: x.strip(), fin.readlines()))
         dockerfile_text = Path(dockerfile_path).read_text()
 
-        assert lines[2] == "FROM registry.git.vgregion.se/aiplattform/images/r:0.2.0"
+        assert lines[0] == "FROM registry.git.vgregion.se/aiplattform/images/r:0.3.0"
+        assert lines[-5] == 'RUN R -e \'renv::activate()\' && R -e \'renv::restore()\''
+        assert lines[-3] == 'USER root'
+        assert lines[-2] == 'EXPOSE 8787'
+
         assert "ADD http://aiav2.vgregion.se/VGC%20Root%20CA%20v2.crt /tmp/vgc_root.der" in lines
         assert "ADD http://aiav2.vgregion.se/VGC%20Issuing%201%20CA%20v2.crt /tmp/vgc_issuing1.der" in lines
         assert "ADD http://aiav2.vgregion.se/VGC%20Issuing%202%20CA%20v2.crt /tmp/vgc_issuing2.der" in lines
@@ -61,6 +65,8 @@ def test_dockerfile(self):
         assert "openssl x509 -inform der -in /tmp/vgc_issuing1_2.der -out /usr/local/share/ca-certificates/vgc_issuing1_2.crt"
         assert "openssl x509 -inform der -in /tmp/vgc_issuing2.der -out /usr/local/share/ca-certificates/vgc_issuing2.crt"
         assert "update-ca-certificates"
+        assert 'echo "setwd(\"/workspace/\")" > /home/rstudio/.Rprofile'
+        assert 'COPY renv.lock /workspace/renv.lock'
 
     def test_folders(self):
         module_name = pytest.param.get("project_name")

diff --git a/tests/test_tensorflow_env.py b/tests/test_tensorflow_env.py
@@ -88,7 +88,7 @@ def test_dockerfile(self):
         dockerfile_text = Path(dockerfile_path).read_text()
 
         assert lines[0] == "FROM registry.git.vgregion.se/aiplattform/images/tensorflow:0.2.1"
-        assert lines[-1] == 'WORKDIR /workspace'
+        assert lines[-2] == 'WORKDIR /workspace'
         assert "ADD http://aiav2.vgregion.se/VGC%20Root%20CA%20v2.crt /tmp/vgc_root.der" in lines
         assert "ADD http://aiav2.vgregion.se/VGC%20Issuing%201%20CA%20v2.crt /tmp/vgc_issuing1.der" in lines
         assert "ADD http://aiav2.vgregion.se/VGC%20Issuing%202%20CA%20v2.crt /tmp/vgc_issuing2.der" in lines

diff --git a/{{ cookiecutter.repo_name }}/Dockerfile b/{{ cookiecutter.repo_name }}/Dockerfile
@@ -1,29 +1,42 @@
-{% if cookiecutter.image == 'Tensorflow' %}FROM registry.git.vgregion.se/aiplattform/images/tensorflow:0.2.1{% endif %}
-{% if cookiecutter.image == 'PyTorch' %}FROM registry.git.vgregion.se/aiplattform/images/pytorch:0.3.2{% endif %}
-{% if cookiecutter.image == 'R' %}FROM registry.git.vgregion.se/aiplattform/images/r:0.2.0{% endif %}
+{% if cookiecutter.image == 'Tensorflow' -%}FROM registry.git.vgregion.se/aiplattform/images/tensorflow:0.2.1
+{% elif cookiecutter.image == 'PyTorch' -%}FROM registry.git.vgregion.se/aiplattform/images/pytorch:0.3.2
+{% elif cookiecutter.image == 'R' -%}FROM registry.git.vgregion.se/aiplattform/images/r:0.3.0{%- endif %}
 ENV GID=1000
 ENV UID=1000
+{% if cookiecutter.image == 'R' %}ENV EDITOR_FOCUS_DIR="/workspace"{% endif %}
 
 RUN apt -y update \
-    && apt install -y --no-install-recommends python3-pip git openssl {% if cookiecutter.image != 'R' %}\
-    && addgroup --gid $GID researcher \
-    && adduser --home /workspace --shell /bin/bash --disabled-password --gecos '' --uid $UID --gid $GID researcher \
+    && apt install -y --no-install-recommends python3-pip git openssl \{% if cookiecutter.image != 'R' %}
+    && addgroup --gid $GID researcher \{% endif %}
+    && useradd --home-dir /workspace --create-home --shell /bin/bash --non-unique --comment '' --uid $UID --gid $GID researcher \
     && chown -R 1000:1000 /workspace
-    {% endif %}
 
 ADD http://aiav2.vgregion.se/VGC%20Root%20CA%20v2.crt /tmp/vgc_root.der
 ADD http://aiav2.vgregion.se/VGC%20Issuing%201%20CA%20v2.crt /tmp/vgc_issuing1.der
 ADD http://aiav2.vgregion.se/VGC%20Issuing%202%20CA%20v2.crt /tmp/vgc_issuing2.der
 ADD http://aiav2.vgregion.se/VGC%20Issuing%201%20CA%20v2(1).crt /tmp/vgc_issuing1_2.der
 
-COPY requirements.txt {% if cookiecutter.image != 'R' %} setup.py {% endif %} ./
+COPY requirements.txt {% if cookiecutter.image != 'R' %} setup.py {% endif %} ./{% if cookiecutter.image == 'R' %}
+COPY renv.lock /workspace/renv.lock
+COPY r-start.sh /usr/local/bin/r-start{% endif %}
+
 RUN pip install -r requirements.txt --no-cache-dir \
     && openssl x509 -inform der -in /tmp/vgc_root.der -out /usr/local/share/ca-certificates/vgc_root.crt \
     && openssl x509 -inform der -in /tmp/vgc_issuing1.der -out /usr/local/share/ca-certificates/vgc_issuing1.crt \
     && openssl x509 -inform der -in /tmp/vgc_issuing1_2.der -out /usr/local/share/ca-certificates/vgc_issuing1_2.crt \
     && openssl x509 -inform der -in /tmp/vgc_issuing2.der -out /usr/local/share/ca-certificates/vgc_issuing2.crt \
     && update-ca-certificates \
-    && rm requirements.txt setup.py
+    {% if cookiecutter.image == 'R' %}&& chown -R 1000:1000 /workspace/ \
+    && echo "setwd(\"/workspace/\")" > /home/rstudio/.Rprofile \
+    && chmod +x /usr/local/bin/r-start \{% endif %}
+    && rm requirements.txt {% if cookiecutter.image != 'R' %} setup.py {% endif %}
 
 USER researcher
-WORKDIR /workspace
+WORKDIR /workspace
+
+{% if cookiecutter.image == 'R' %}RUN R -e 'renv::activate()' && R -e 'renv::restore()'
+
+USER root
+EXPOSE 8787
+
+{% endif %}
diff --git a/{{ cookiecutter.repo_name }}/README.md b/{{ cookiecutter.repo_name }}/README.md
@@ -83,6 +83,9 @@ Project Organization
     ├── renv.lock          <- R packages for reproducing the analysis environment, e.g.
     |                         generated with `renv::restore()`
     |
+    ├── r-start.sh         <- An R start script that will be available in your Docker image as
+    |                         /usr/local/bin/r-start
+    |
     ├── requirements.txt   <- Python requirements file for reproducing the analysis environment. 
     |                         Used in **addition** to R for things like documentation and DVC.
     │

diff --git a/{{ cookiecutter.repo_name }}/r-start.sh b/{{ cookiecutter.repo_name }}/r-start.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+su - researcher
+R -e 'renv::activate()'
+
+# Insert additional code here
diff --git a/{{ cookiecutter.repo_name }}/renv.lock b/{{ cookiecutter.repo_name }}/renv.lock
@@ -1,6 +1,6 @@
 {
   "R": {
-    "Version": "4.1.2",
+    "Version": "4.2.1",
     "Repositories": [
       {
         "Name": "CRAN",
@@ -9,6 +9,117 @@
     ]
   },
   "Packages": {
+    "DBI": {
+      "Package": "DBI",
+      "Version": "1.1.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "dcd1743af4336156873e3ce3c950b8b9",
+      "Requirements": []
+    },
+    "Rcpp": {
+      "Package": "Rcpp",
+      "Version": "1.0.8.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "32e79b908fda56ee57fe518a8d37b864",
+      "Requirements": []
+    },
+    "bit": {
+      "Package": "bit",
+      "Version": "4.0.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "f36715f14d94678eea9933af927bc15d",
+      "Requirements": []
+    },
+    "bit64": {
+      "Package": "bit64",
+      "Version": "4.0.5",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "9fe98599ca456d6552421db0d6772d8f",
+      "Requirements": [
+        "bit"
+      ]
+    },
+    "blob": {
+      "Package": "blob",
+      "Version": "1.2.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "dc5f7a6598bb025d20d66bb758f12879",
+      "Requirements": [
+        "rlang",
+        "vctrs"
+      ]
+    },
+    "ellipsis": {
+      "Package": "ellipsis",
+      "Version": "0.3.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077",
+      "Requirements": [
+        "rlang"
+      ]
+    },
+    "glue": {
+      "Package": "glue",
+      "Version": "1.6.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "4f2596dfb05dac67b9dc558e5c6fba2e",
+      "Requirements": []
+    },
+    "hms": {
+      "Package": "hms",
+      "Version": "1.1.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "5b8a2dd0fdbe2ab4f6081e6c7be6dfca",
+      "Requirements": [
+        "ellipsis",
+        "lifecycle",
+        "pkgconfig",
+        "rlang",
+        "vctrs"
+      ]
+    },
+    "lifecycle": {
+      "Package": "lifecycle",
+      "Version": "1.0.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "a6b6d352e3ed897373ab19d8395c98d0",
+      "Requirements": [
+        "glue",
+        "rlang"
+      ]
+    },
+    "odbc": {
+      "Package": "odbc",
+      "Version": "1.3.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "3f9efc29c48dca3aebf00b61a472d543",
+      "Requirements": [
+        "DBI",
+        "Rcpp",
+        "bit64",
+        "blob",
+        "hms",
+        "rlang"
+      ]
+    },
+    "pkgconfig": {
+      "Package": "pkgconfig",
+      "Version": "2.0.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "01f28d4278f15c76cddbea05899c5d6f",
+      "Requirements": []
+    },
     "renv": {
       "Package": "renv",
       "Version": "0.15.2-2",
@@ -21,6 +132,26 @@
       "RemoteSha": "4a12af7cd16e5d4120d2515a2318bd5315dca8b4",
       "Hash": "93afeb9fb3a032439684997363b7423a",
       "Requirements": []
+    },
+    "rlang": {
+      "Package": "rlang",
+      "Version": "1.0.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "04884d9a75d778aca22c7154b8333ec9",
+      "Requirements": []
+    },
+    "vctrs": {
+      "Package": "vctrs",
+      "Version": "0.3.8",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "ecf749a1b39ea72bd9b51b76292261f1",
+      "Requirements": [
+        "ellipsis",
+        "glue",
+        "rlang"
+      ]
     }
   }
-}
+}