Add docker build #528

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czyszCTDS wants to merge 4 commits into develop from acollet/docker-build

.dockerignore

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@@ -0,0 +1,7 @@
+    logs/
+    .git
+    *.md
+    .cache
+    *Dockerfile*
+    .dockerignore
+    .dive-ci

.gitignore

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@@ Expand Up / @@ -4,3 +4,5 @@ site/ @@
     venv*/
     .vscode/
     docs/*/PDF/*.pdf
+    .python-version
+    .idea/

Dockerfile

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@@ -0,0 +1,51 @@
+    # syntax=docker/dockerfile:1
+    ARG BASE_VERSION=3.2.4
+    ARG REGISTRY=docker.osdc.io/ncigdc
+    ARG SERVICE_NAME=gene-expression
+    ARG PYTHON_VERSION=python3.9
+    FROM ${REGISTRY}/${PYTHON_VERSION}-builder:${BASE_VERSION} as build
+    ARG SERVICE_NAME
+    ARG PIP_INDEX_URL
+    ENV PIP_INDEX_URL=$PIP_INDEX_URL
+    WORKDIR /build
+    # Install dependencies first so Docker can reuse the cached layer as
+    # long as we don't update any pins.
+    COPY epel.repo /etc/yum.repos.d/
+    RUN dnf install -y pandoc --enablerepo=epel && \
+        dnf install -y sed texlive texlive-xetex pango-devel
+    COPY requirements.txt .
+    RUN pip install -r requirements.txt
+    #RUN pip install git+https://github.com/jgrassler/mkdocs-pandoc
+    #COPY pandoc_converter.patch .
+    #COPY tables.patch .
+    #RUN patch -u /venv/lib/python3.9/site-packages/mkdocs_pandoc/pandoc_converter.py -i pandoc_converter.patch && \
+    #    patch -u /venv/lib/python3.9/site-packages/mkdocs_pandoc/filters/tables.py -i tables.patch
+    COPY . /apps
+    WORKDIR /apps
+    RUN rm -rf docs/Data/Release_Notes/*.gz &&  \
+        bash build.sh
+    FROM ${REGISTRY}/nginx:${BASE_VERSION}
+    ARG NAME
+    ARG PYTHON_VERSION
+    ARG SERVICE_NAME
+    ARG GIT_BRANCH
+    ARG COMMIT
+    ARG BUILD_DATE
+    LABEL org.opencontainers.image.title="${SERVICE_NAME}" \
+          org.opencontainers.image.description="${SERVICE_NAME} container image" \
+          org.opencontainers.image.source="https://github.com/NCI-GDC/${SERVICE_NAME}" \
+          org.opencontainers.image.vendor="NCI GDC" \
+          org.opencontainers.image.ref.name="${SERVICE_NAME}:${GIT_BRANCH}" \
+          org.opencontainers.image.revision="${COMMIT}" \
+          org.opencontainers.image.created="${BUILD_DATE}"
+    COPY --chown=app:app nginx.conf /etc/nginx/conf.d/default.conf
+    COPY --chown=app:app --from=build /app /app
+    EXPOSE 80 443

build.sh

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+    #!/bin/bash
+    # Generating PDFs from *_UG.yml files.
+    echo "$(date +'%d %B %Y - %k:%M'): ${ENVIRONMENT}: Looking for User Guides"
+    userGuides=()
+    for i in $( ls *_UG.yml ); do
+       userGuides+=(${i::${#i}-7})
+    done
+    echo "$(date +'%d %B %Y - %k:%M'): ${ENVIRONMENT}: Number of User Guides found: ${#userGuides[@]}"
+    for userGuide in "${userGuides[@]}"; do
+       echo "$(date +'%d %B %Y - %k:%M'): ${ENVIRONMENT}: ${userGuide}: Starting creation"
+       if [ ! -d "docs/Data_Portal/PDF/" ]; then
+          echo "$(date +'%d %B %Y - %k:%M'): ${ENVIRONMENT}: ${userGuide}: PDF Directory does not exists, creating ..."
+          mkdir docs/${userGuide}/PDF/
+       fi
+       echo "$(date +'%d %B %Y - %k:%M'): ${ENVIRONMENT}: ${userGuide}: Building PDF documents"
+       ENABLE_PDF_EXPORT=1 /venv/bin/mkdocs build -f ${userGuide}_UG.yml
+    done
+    echo "$(date +'%d %B %Y - %k:%M'): ${ENVIRONMENT}: Deploying new version to /app"
+    /venv/bin/mkdocs build -v --site-dir /app/

epel9.repo

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@@ -0,0 +1,7 @@
+    [epel9]
+    baseurl=https://nexus.osdc.io/repository/rpm-epel/9/Everything/x86_64
+    gpgcheck=0
+    metadata_expire=1d
+    mode=0640
+    name=Extra Packages for Enterprise Linux 9
+    enabled=0

nginx.conf

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@@ -0,0 +1,19 @@
+    server {
+      listen 80 default_server;
+      listen 443 ssl default_server;
+      listen [::]:80 default_server;
+      listen [::]:443 ssl default_server;
+      server_name _;
+      set $empty "";
+      ssl_ciphers aNULL;
+      ssl_certificate data:$empty;
+      ssl_certificate_key data:$empty;
+      location / {
+        root /app;
+        index index.html;
+      }
+    }

pandoc_converter.patch

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@@ -0,0 +1,11 @@
+    --- /venv/lib/python3.9/site-packages/mkdocs_pandoc/pandoc_converter.py	2025-04-10 13:54:36.348159540 +0000
+    +++ /venv/lib/python3.9/site-packages/mkdocs_pandoc/pandoc_converter.py	2025-04-10 13:55:01.268162893 +0000
+    @@ -34,7 +34,7 @@
+                 raise FatalError("Couldn't open %s for reading: %s" % (self.config_file,
+                     e.strerror), 1)
+    -        self.config = yaml.load(cfg)
+    +        self.config = yaml.full_load(cfg)
+             if not 'docs_dir' in self.config:
+                 self.config['docs_dir'] = 'docs'

requirements.in

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@@ Expand Up / @@ -3,4 +3,12 @@ mkdocs-material>=9.5.26 @@
     pyyaml>=6.0.1
     mkdocs-with-pdf>=0.9.3
     # an init method changed it's signature. version 44 works. newer versions may too. untested.
-    weasyprint==44
+    weasyprint==44
+    # mkdocs~=0.17.5
+    #  mkdocs-bootstrap~=0.1.1
+    #  mkdocs-bootswatch~=0.4
+    #  BSCodeTabs
+    #  Markdown~=2.6.11
+    #  MarkupSafe~=1.0
+    #  mkdocs-pandoc
+    #  mkdocs-pandoc-plugin

tables.patch

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@@ -0,0 +1,20 @@
+    --- /venv/lib/python3.9/site-packages/mkdocs_pandoc/filters/tables.py	2025-04-10 09:11:33
+    +++ /venv/lib/python3.9/site-packages/mkdocs_pandoc/filters/tables.py	2025-04-10 11:18:15
+    @@ -88,7 +88,7 @@
+             # Initialize width arrays
+    -        for i in range(0, len(self._split_row(lines_orig[0], has_border))):
+    +        for i in range(0, len(self._split_row(lines_orig[0]))):
+                 widest_cell.append(0)
+                 widest_word.append(0)
+                 widths.append(0)
+    @@ -96,7 +96,7 @@
+             # Parse lines into array of cells and record width of widest cell/word
+             for line in lines_orig:
+    -            row = self._split_row(line, has_border)
+    +            row = self._split_row(line)
+                 # pad widest_cell to account for under length first row
+                 for i in range(0, len(row) - len(widest_cell)):
+                     widest_cell.append(0)

theme/404.html

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@@ Expand Up / @@ -19,7 +19,7 @@ @@
             {% if page_description %}<meta name="description" content="{{ page_description }}">{% endif %}
             {% if site_author %}<meta name="author" content="{{ site_author }}">{% endif %}
-            {% if canonical_url %}<link rel="canonical" href="{{ canonical_url }}">{% endif %}
+            {% if page.canonical_url %}<link rel="canonical" href="{{ page.canonical_url }}">{% endif %}
             {% if favicon %}<link rel="shortcut icon" href="{{ favicon }}">
             {% else %}<link rel="shortcut icon" href="/img/favicon.ico">{% endif %}
@@ Expand Down @@

theme/base.html

            
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    @@ -5,20 +5,20 @@
  
        <head>

            <meta charset="utf-8">

            <meta http-equiv="X-UA-Compatible" content="IE=edge">

            {% if current_page.title == config.extra.gdcmvs_viewer_page_id %}

            {% if page.title == config.extra.gdcmvs_viewer_page_id %}

            <meta name="viewport" content="width=1024">

            {% else %}

            <meta name="viewport" content="width=device-width, initial-scale=1.0">

            {% endif %}

             {% if page_description %}<meta name="description" content="{{ page_description }}">{% endif %}

            {% if site_author %}<meta name="author" content="{{ site_author }}">{% endif %}

            {% if canonical_url %}<link rel="canonical" href="{{ canonical_url }}">{% endif %}

            {% if page.canonical_url %}<link rel="canonical" href="{{ page.canonical_url }}">{% endif %}

            {% if favicon %}<link rel="shortcut icon" href="{{ favicon }}">

            {% else %}<link rel="shortcut icon" href="/img/favicon.ico">{% endif %}

            <link rel="apple-touch-icon" href="/img/apple-touch-icon.png">

            <title>{% if page_title %}{{ page_title }} - {% endif %}{{ site_name }}</title>

            <title>{% if page.title %}{{ page.title }} - {% endif %}{{ site_name }}</title>

            <script src="https://assets.adobedtm.com/6a4249cd0a2c/073fd0859f8f/launch-39d47c17b228.min.js"></script>

    @@ -43,14 +43,14 @@
  
                {% endif %}

            {% endfor %}

            {% if current_page.title == config.extra.gdcmvs_viewer_page_id %}

            {% if page.title == config.extra.gdcmvs_viewer_page_id %}

            <!-- GDCMVS CSS-->

            <link rel="stylesheet" type="text/css" href="{{ config.extra.gdcmvs_app_root }}/lib/css/jquery-ui.min.css" />

            <link rel="stylesheet" type="text/css" href="{{ config.extra.gdcmvs_app_root }}/lib/css/pagination.min.css" />

            <link rel="stylesheet" type="text/css" href="{{ config.extra.gdcmvs_app_root }}/dist/styles.css" />

            {% endif %}

            {% if current_page.title == "Home" %}

            {% if page.title == "Home" %}

            <link href="/css/homepage.css" rel="stylesheet">

            {% endif %}

    @@ -72,7 +72,7 @@
  
            </script>

            {% endif %}

            {% if current_page.title == config.extra.dictionary_viewer_page_id %}

            {% if page.title == config.extra.dictionary_viewer_page_id %}

            {% include "apps/dictionary/html-shards/dictionary-deps.html" %}

            <script src="/js/dictionary-init.js"></script>

            {% endif %}

    @@ -86,7 +86,7 @@
  
            <!-- div id="sliding-drawer-container" class="sliding-drawer-container">

            </div -->

            <div class="parent-container">

              {% if current_page.title != config.extra.dictionary_viewer_page_id and current_page.title != config.extra.gdcmvs_viewer_page_id %}

              {% if page.title != config.extra.dictionary_viewer_page_id and page.title != config.extra.gdcmvs_viewer_page_id %}

                <div class="spinParticle">

                    <div class="particle red"></div>

                    <div class="particle grey other-particle"></div>

    @@ -96,44 +96,44 @@
  
                {% include "nav.html" %}

                <div id="docs-container" class="container">

                    <div data-current-page="{{current_page.title}}" id="body">

                    <div data-current-page="{{page.title}}" id="body">

                    {% if current_page.title == "Home" %}

                    {% if page.title == "Home" %}

                        {% include "homepage.html" %}

                    {% else %}

                    <!-- {% if toc and ((toc | first) is defined) and current_page.title != config.extra.dictionary_viewer_page_id %}

                    <div class="col-md-3 toc-container" role="navigation" aria-label="In-Page Navigation">{% include "toc.html" %}</div>

                    {% endif %} -->

                    {% if "/Encyclopedia" in current_page.abs_url %}

                    {% if "/Encyclopedia" in page.abs_url %}

                      {% include "encyclopedia/menu.html" %}

                    {% elif current_page.title != config.extra.dictionary_viewer_page_id and current_page.title != 'Home' and current_page.title != config.extra.gdcmvs_viewer_page_id %}

                    {% elif page.title != config.extra.dictionary_viewer_page_id and page.title != 'Home' and page.title != config.extra.gdcmvs_viewer_page_id %}

                      {% include "nav-section-map.html" %}

                    {% elif current_page.title == 'Home' %}

                      {% if toc and ((toc | first) is defined) %}

                    {% elif page.title == 'Home' %}

                      {% if page.toc and ((page.toc | first) is defined) %}

                        <div class="col-md-3 toc-container" role="navigation" aria-label="In-Page Navigation">{% include "toc.html" %}</div>

                      {% endif %}

                    {% endif %}

                    {% if current_page.title == config.extra.dictionary_viewer_page_id or current_page.title == config.extra.gdcmvs_viewer_page_id %}

                    {% if page.title == config.extra.dictionary_viewer_page_id or page.title == config.extra.gdcmvs_viewer_page_id %}

                    <div class="col-md-12 main-container" role="main" id="main" tabindex="-1">

                    {% else %}

                    <div class="col-md-9 main-container fadeInBlurIntroOld loading-content-old" role="main" id="main" tabindex="-1">

                    {% endif %}

                    {% if current_page.title == config.extra.encyclopedia_page_title%}

                    {% if page.title == config.extra.encyclopedia_page_title%}

                        {% include "encyclopedia/index.html" %}

                    {% else %}

                        {% include "content.html" %}    

                    {% endif %}

                    </div>

                        {% if next_page or previous_page %}

                        <div class="history-nav-control-container clearfix" role="navigation" aria-label="footer navigation">

                            {% if next_page.ancestors and next_page.ancestors[0].active and current_page.title != config.extra.dictionary_viewer_page_id and current_page.title != config.extra.gdcmvs_viewer_page_id %}

                            {% if next_page.ancestors and next_page.ancestors[0].active and page.title != config.extra.dictionary_viewer_page_id and page.title != config.extra.gdcmvs_viewer_page_id %}

                            <a href="{{ next_page.url }}" class="btn pull-right indicate-right" title="Click to go to the Next Page: {{ next_page.title }}">

                                <span class="btn-nav-text">Next:</span> {{next_page.title}} <span class="fa fa-chevron-right"></span>

                            </a>

                            {% endif %}

                            {% if previous_page.ancestors and previous_page.ancestors[0].active and current_page.title != config.extra.dictionary_viewer_page_id and current_page.title != config.extra.gdcmvs_viewer_page_id %}

                            {% if previous_page.ancestors and previous_page.ancestors[0].active and page.title != config.extra.dictionary_viewer_page_id and page.title != config.extra.gdcmvs_viewer_page_id %}

                            <a href="{{ previous_page.url }}" class="btn pull-left indicate-left" title="Click to go to the Previous Page: {{ previous_page.title }}">

                                <span class="fa fa-chevron-left"></span> <span class="btn-nav-text">Previous:</span> {{previous_page.title}}</a>

                            {% endif %}

    @@ -191,17 +191,17 @@
  
                <script src="{{ path }}"></script>

                {%- endfor %}

                {% if current_page.title == config.extra.encyclopedia_page_title %}

                {% if page.title == config.extra.encyclopedia_page_title %}

                    <script src="/js/encyclopedia.js"></script>

                {% endif %}

                {% if current_page.title == config.extra.gdcmvs_viewer_page_id %}

                {% if page.title == config.extra.gdcmvs_viewer_page_id %}

                <!-- GDCMVS JS-->

                <script type="text/javascript" src="{{ config.extra.gdcmvs_app_root }}/lib/js/jquery-ui.min.js"></script>

                <script type="text/javascript" src="{{ config.extra.gdcmvs_app_root }}/lib/js/pagination.min.js"></script>

                <script type="text/javascript" src="{{ config.extra.gdcmvs_app_root }}/lib/js/jsrender.min.js"></script>

                <script type="text/javascript" src="{{ config.extra.gdcmvs_app_root }}/dist/bundle.js"></script>

                {% endif %}

                {% if current_page.title == "Home" %}

                {% if page.title == "Home" %}

                <script src="/js/homepage.js"></script>

                {% endif %}

            </div>

theme/content.html

            
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    @@ -1,9 +1,9 @@
  
    {% if meta.source %}

    {% if page.meta.source %}

    <div class="source-links">

    {% for filename in meta.source %}

    {% for filename in page.meta.source %}

        <span class="label label-primary">{{ filename }}</span>

    {% endfor %}

    </div>

    {% endif %}

    {{ content }}

    {{ page.content }}

theme/nav-section-map-toc.html

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+Diff line change
@@ -1,5 +1,5 @@
     <ul class="nav bs-sidenav">
-      {% for toc_nav_item in toc %}
+      {% for toc_nav_item in page.toc %}
             {% for toc_item in toc_nav_item.children %}
             <li class="{% if toc_item.active %}active{% endif %}"><a href="{{ toc_item.url }}">{{ toc_item.title }}</a>
               {% if toc_item.children %}
@@ Expand Down @@

theme/nav-section-map.html

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+Diff line change
@@ Expand Up / @@ -10,7 +10,7 @@ @@
                   <a href="{{ sub_nav_item.url }}">
                     {{ sub_nav_item.title }}
                   </a>
-                    {% if toc and ((toc | first) is defined) and sub_nav_item.active %}
+                    {% if page.toc and ((page.toc | first) is defined) and sub_nav_item.active %}
                         {% include "nav-section-map-toc.html" %}
                     {% endif %}
                 </li>
@@ Expand Down @@

theme/nav.html

            
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    @@ -103,13 +103,13 @@
  
                {% if false %}

                <ul class="nav navbar-nav navbar-right">

                    <li {% if not previous_page %}class="disabled"{% endif %}>

                        <a rel="next" {% if previous_page %}href="{{ previous_page.url }}"{% endif %}>

                    <li {% if not page.previous_page %}class="disabled"{% endif %}>

                        <a rel="next" {% if page.previous_page %}href="{{ previous_page.url }}"{% endif %}>

                            <i class="fa fa-arrow-left"></i> Previous

                        </a>

                    </li>

                    <li {% if not next_page %}class="disabled"{% endif %}>

                        <a rel="prev" {% if next_page %}href="{{ next_page.url }}"{% endif %}>

                    <li {% if not page.next_page %}class="disabled"{% endif %}>

                        <a rel="prev" {% if page.next_page %}href="{{ next_page.url }}"{% endif %}>

                            Next <i class="fa fa-arrow-right"></i>

                        </a>

                    </li>

theme/toc.html

-Original file line number
+Diff line change
@@ -1,6 +1,6 @@
     <div class="bs-sidebar hidden-print affix well animated fadeIn">
         <ul class="nav bs-sidenav">
-        {% for nav_item in toc %}
+        {% for nav_item in page.toc %}
             <li class="main {% if nav_item.active %}active{% endif %}"><a href="{{ nav_item.url }}">{{ nav_item.title }}</a>
                <ul class="nav">
                {% for toc_item in nav_item.children %}
@@ Expand Down @@

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