RHOAIENG-17257: chore(tests): add testcontainers test to check Rmd to PDF rendering in RStudio (#857)

* RHOAIENG-17257: chore(tests): add testcontainers test to check Rmd to PDF rendering in RStudio

* fixup, from review, avoid a copy

Author: jiridanek

tests/containers/docker_utils.py

@@ -66,6 +66,20 @@ def tar_filter(f: tarfile.TarInfo) -> tarfile.TarInfo:
     container.put_archive(dst, fh)
 
 
+def from_container_cp(container: Container, src: str, dst: str) -> None:
+    fh = io.BytesIO()
+    bits, stat = container.get_archive(src, encode_stream=True)
+    for chunk in bits:
+        fh.write(chunk)
+    fh.seek(0)
+    tar = tarfile.open(fileobj=fh, mode="r")
+    try:
+        tar.extractall(path=dst, filter=tarfile.data_filter)
+    finally:
+        tar.close()
+        fh.close()
+
+
 def container_exec(
         container: Container,
         cmd: str | list[str],

tests/containers/workbenches/rstudio/rstudio_tests.py

@@ -0,0 +1,155 @@
+from __future__ import annotations
+
+import json
+import logging
+import pathlib
+import subprocess
+import tempfile
+import textwrap
+from typing import TYPE_CHECKING
+
+import allure
+import pytest
+
+from tests.containers import docker_utils
+from tests.containers.workbenches.workbench_image_test import WorkbenchContainer, skip_if_not_workbench_image
+
+if TYPE_CHECKING:
+    import docker.models.images
+
+
+class TestRStudioImage:
+    """Tests for RStudio Workbench images in this repository."""
+
+    APP_ROOT_HOME = "/opt/app-root/src/"
+
+    @allure.issue("RHOAIENG-17256")
+    def test_rmd_to_pdf_rendering(self, image: str) -> None:
+        """
+        References:
+            https://stackoverflow.com/questions/40563479/relationship-between-r-markdown-knitr-pandoc-and-bookdown
+            https://www.earthdatascience.org/courses/earth-analytics/document-your-science/knit-rmarkdown-document-to-pdf/
+        """
+        skip_if_not_rstudio_image(image)
+
+        container = WorkbenchContainer(image=image, user=1000, group_add=[0])
+        try:
+            container.start(wait_for_readiness=False)
+
+            # language=R
+            script = textwrap.dedent("""
+                library(knitr)
+                library(rmarkdown)
+                render("document.Rmd", output_format = "pdf_document")
+                """)
+            # language=markdown
+            document = textwrap.dedent("""
+                ---
+                title: "Untitled"
+                output: pdf_document
+                date: "2025-01-22"
+                ---
+
+                ```{r setup, include=FALSE}
+                knitr::opts_chunk$set(echo = TRUE)
+                ```
+
+                ## R Markdown
+
+                This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
+
+                When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
+
+                ```{r cars}
+                summary(cars)
+                ```
+
+                ## Including Plots
+
+                You can also embed plots, for example:
+
+                ```{r pressure, echo=FALSE}
+                plot(pressure)
+                ```
+
+                Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
+                """)
+
+            with tempfile.TemporaryDirectory() as tmpdir:
+                tmpdir = pathlib.Path(tmpdir)
+                (tmpdir / "script.R").write_text(script)
+                docker_utils.container_cp(container.get_wrapped_container(), src=str(tmpdir / "script.R"),
+                                          dst=self.APP_ROOT_HOME)
+                (tmpdir / "document.Rmd").write_text(document)
+                docker_utils.container_cp(container.get_wrapped_container(), src=str(tmpdir / "document.Rmd"),
+                                          dst=self.APP_ROOT_HOME)
+
+            # https://stackoverflow.com/questions/28432607/pandoc-version-1-12-3-or-higher-is-required-and-was-not-found-r-shiny
+            check_call(container,
+                       f"bash -c 'RSTUDIO_PANDOC=/usr/lib/rstudio-server/bin/quarto/bin/tools/x86_64 Rscript {self.APP_ROOT_HOME}/script.R'")
+
+            with tempfile.TemporaryDirectory() as tmpdir:
+                docker_utils.from_container_cp(container.get_wrapped_container(), src=self.APP_ROOT_HOME, dst=tmpdir)
+                allure.attach.file(
+                    pathlib.Path(tmpdir) / "src/document.pdf",
+                    name="rendered-pdf",
+                    attachment_type=allure.attachment_type.PDF
+                )
+
+        finally:
+            docker_utils.NotebookContainer(container).stop(timeout=0)
+
+
+def check_call(container: WorkbenchContainer, cmd: str) -> int:
+    """Like subprocess.check_output, but in a container."""
+    logging.debug(_("Running command", cmd=cmd))
+    rc, result = container.exec(cmd)
+    result = result.decode("utf-8")
+    logging.debug(_("Command execution finished", rc=rc, result=result))
+    if rc != 0:
+        raise subprocess.CalledProcessError(rc, cmd, output=result)
+    return rc
+
+
+def check_output(container: WorkbenchContainer, cmd: str) -> str:
+    """Like subprocess.check_output, but in a container."""
+    logging.debug(_("Running command", cmd=cmd))
+    rc, result = container.exec(cmd)
+    result = result.decode("utf-8")
+    logging.debug(_("Command execution finished", rc=rc, result=result))
+    if rc != 0:
+        raise subprocess.CalledProcessError(rc, cmd, output=result)
+    return result
+
+
+def skip_if_not_rstudio_image(image: str) -> docker.models.images.Image:
+    image_metadata = skip_if_not_workbench_image(image)
+    if "-rstudio-" not in image_metadata.labels['name']:
+        pytest.skip(
+            f"Image {image} does not have '-rstudio-' in {image_metadata.labels['name']=}'")
+
+    return image_metadata
+
+
+class StructuredMessage:
+    """https://docs.python.org/3/howto/logging-cookbook.html#implementing-structured-logging"""
+
+    def __init__(self, message, /, **kwargs):
+        self.message = message
+        self.kwargs = kwargs
+
+    def __str__(self):
+        s = Encoder().encode(self.kwargs)
+        return '%s >>> %s' % (self.message, s)
+
+
+class Encoder(json.JSONEncoder):
+    def default(self, o):
+        if isinstance(o, set):
+            return tuple(o)
+        elif isinstance(o, str):
+            return o.encode('unicode_escape').decode('ascii')
+        return super().default(o)
+
+
+_ = StructuredMessage  # optional shortcut, to improve readability