Port trail_threshold_variability to flatpages

Also changed generated/ static subdir to g/.

.gitignore

@@ -14,4 +14,4 @@ src/onetime/makepng
 src/onetime/makesvg
 data/networks/xgmml
 .deploy
-django/*/static/*/generated
+django/*/static/*/g

django/hmslincs_server/urls.py

@@ -16,7 +16,11 @@
     url(r'^db/logout/$', logout_page, name='logout'),
     url(r'^db/', include('db.urls')),
 
-    (r'^(?P<url>explore/pathway/)$', 'django.contrib.flatpages.views.flatpage'),
+    (r'^(?P<url>explore/pathway/)$',
+     'django.contrib.flatpages.views.flatpage'),
+
+    (r'^(?P<url>explore/trail-threshold-variability/)$',
+     'django.contrib.flatpages.views.flatpage'),
 
     (r'^explore/responses/$', 'django.views.generic.simple.direct_to_template',
      {'template': 'responses/index.html'}),

django/pathway/management/commands/buildstatic_pathway.py

@@ -174,7 +174,7 @@ def generate_images_and_index(options):
     app_dir = Path(__file__).absolute().ancestor(3)
     data_dir = app_dir.child('resources')
     static_dir = app_dir.child('static', 'pathway')
-    out_dir_image = static_dir.child('generated')
+    out_dir_image = static_dir.child('g')
     out_dir_image.mkdir()
     pathway_image_filename = 'pathway.jpg'
 
@@ -232,7 +232,7 @@ def generate_images_and_index(options):
     # fix up <img> attribs
     del img.attrib['usemap']
     img.attrib['id'] = 'pathway-img'
-    img.attrib['src'] = '%spathway/generated/%s' % (django.conf.settings.STATIC_URL,
+    img.attrib['src'] = '%spathway/g/%s' % (django.conf.settings.STATIC_URL,
                                               pathway_image_filename)
     img.attrib['width'] = str(pathway_image.size[0])
     img.attrib['height'] = str(pathway_image.size[1])

django/pathway/templates/pathway/compound_table.html

@@ -19,7 +19,7 @@
     </td>
     <td class="signature">
       {% if sd.signature %}
-        <img src="{{ STATIC_URL }}pathway/generated/signature-{{ signature.target_name|slugify }}-{{ sd.drug|slugify }}.png"
+        <img src="{{ STATIC_URL }}pathway/g/signature-{{ signature.target_name|slugify }}-{{ sd.drug|slugify }}.png"
              width="250" height="20">
       {% endif %}
     </td>

django/pathway/templates/pathway/signature.html

@@ -42,7 +42,7 @@ <h3>Inhibitors of
     <td colspan="3"></td>
     <td class="signature">
       {% if signature.show_scale %}
-        <img src="{{ STATIC_URL }}pathway/generated/scale-{{ signature.target_name|slugify }}.png" width="250" height="20">
+        <img src="{{ STATIC_URL }}pathway/g/scale-{{ signature.target_name|slugify }}.png" width="250" height="20">
       {% endif %}
     </td>
   </tr>
@@ -57,7 +57,7 @@ <h3>Inhibitors of
             <tr>
               {% for index, cell_line in row %}
                 <td>
-                  <img src="{{ STATIC_URL }}pathway/generated/legend-cell-line-{{ index }}.png" width="14" height="14">
+                  <img src="{{ STATIC_URL }}pathway/g/legend-cell-line-{{ index }}.png" width="14" height="14">
                   <a href="/db/cells/{{ cell_line.cell_id }}/">{{ cell_line.name }}</a>
                 </td>
               {% endfor %}

src/trail_threshold_variability_index.py → django/trail_threshold_variability/management/commands/buildstatic_ttv.py

@@ -11,29 +11,12 @@
 import wand.image
 import django.conf
 from django.template.loader import render_to_string
+from django.core.management.base import BaseCommand, CommandError
+from django.contrib.flatpages.models import FlatPage
+from django.contrib.sites.models import Site
+from optparse import make_option
 
 
-
-# Read RESOURCE_PATH from environ, or default to something that works for me.
-resource_path_s = os.environ.get(
-    'RESOURCE_PATH',
-    '/home/jmuhlich/Dropbox (HMS-LSP)/Roux Hafner TRAIL_DISC_paper/website/')
-resource_path = unipath.Path(resource_path_s)
-hmslincs_path = unipath.Path(__file__).ancestor(2)
-
-docroot_path = hmslincs_path.child(
-    'temp', 'docroot', 'explore', 'trail-threshold-variability')
-
-img_src_path = resource_path.child('figures')
-img_dest_path = docroot_path.child('img')
-popup_dest_path = img_dest_path.child('popup')
-schematic_dest_path = img_dest_path.child('schematic')
-
-data_src_path = resource_path.child('data')
-data_dest_path = docroot_path.child('data')
-
-base_url = '/explore/trail-threshold-variability/'
-
 table = [{'name': u'Modulation of DISC activity (k)',
           'schematic_page': 1,
           'treatment_map': [('TRAIL', '', 1), ('Mapatumumab', '', 52),
@@ -71,11 +54,50 @@
 schematic_target_width = 230 * 2
 
 
-def main(argv):
+class Command(BaseCommand):
+    help = 'Builds the static assets and html chunks'
+    option_list = BaseCommand.option_list + (
+       make_option('-n', '--no-images', action='store_true', default=False,
+                   help='Skip building images'),
+       make_option('-d', '--no-data', action='store_true', default=False,
+                   help='Skip building data download files'),
+       make_option('-r', '--resource-path',
+                   default=('/home/jmuhlich/Dropbox (HMS-LSP)/'
+                            'Roux Hafner TRAIL_DISC_paper/website/'),
+                   help=('Path to resource files (contains "figures" and '
+                         '"data" directories)'))
+       )
+
+    def handle(self, *args, **options):
+
+        url = '/explore/trail-threshold-variability/'
+        content = build_static(options)
+
+        page, created = FlatPage.objects.get_or_create(url=url)
+        page.title = ('Fractional killing arises from cell-to-cell '
+                      'variability in overcoming a caspase activity threshold')
+        page.content = content
+        page.template_name = 'trail_threshold_variability/base.html'
+        page.sites.clear()
+        page.sites.add(Site.objects.get_current())
+        page.save()
+
 
-    argparser = argparse.ArgumentParser(
-        description='Build trail_threshold_variability app resources.')
-    args = argparser.parse_args()
+def build_static(options):
+
+    app_path = unipath.Path(__file__).absolute().ancestor(3)
+    static_path = app_path.child('static', 'trail_threshold_variability')
+    generated_path = static_path.child('g')
+    generated_path.mkdir()
+
+    resource_path = unipath.Path(options['resource_path'])
+
+    img_src_path = resource_path.child('figures')
+    popup_dest_path = generated_path.child('popup')
+    schematic_dest_path = generated_path.child('schematic')
+
+    data_src_path = resource_path.child('data')
+    data_dest_path = generated_path.child('data')
 
     treatment_reverse_map = {}
     for s_idx, section in enumerate(table):
@@ -131,54 +153,52 @@ def main(argv):
 
     # Assemble data for template and render html.
     data = {'table': table,
-            'data_rel_url': docroot_path.rel_path_to(data_dest_path),
             'STATIC_URL': django.conf.settings.STATIC_URL,
-            'BASE_URL': base_url,
             }
-    docroot_path.mkdir(parents=True)
-    render_template('trail_threshold_variability/index.html', data,
-                    docroot_path, 'index.html')
-
-    # Resize and copy popup images.
-    popup_dest_path.mkdir(parents=True)
-    for dose in doses:
-        dest_path = popup_dest_path.child(dose['img_filename'])
-        with wand.image.Image(filename=dose['img_path']) as img, \
-                open(dest_path, 'w') as f:
-            scale = float(popup_target_width) / img.width
-            target_size = [int(round(d * scale)) for d in img.size]
-            img.resize(*target_size, blur=1.5)
-            img.compression_quality = 20
-            img.format = 'JPEG'
-            img.save(file=f)
-            dest_path.chmod(0o644)
-    # Extract and copy schematic images.
-    schematic_dest_path.mkdir(parents=True)
-    schematic_path = img_src_path.child('schematics', 'Trajectories_schematics.pdf')
-    with wand.image.Image(filename=schematic_path, resolution=500) as img:
-        for section in table:
-            page_number = section['schematic_page']
-            page = wand.image.Image(image=img.sequence[page_number])
-            page.alpha_channel = False
-            scale = float(schematic_target_width) / page.width
-            target_size = [int(round(d * scale)) for d in page.size]
-            page.resize(*target_size)
-            page.compression_quality = 100
-            page.format = 'JPEG'
-            filename = '{}.jpg'.format(page_number)
-            dest_path = schematic_dest_path.child(filename)
-            page.save(filename=dest_path)
+    content = render_to_string('trail_threshold_variability/index.html', data)
+
+    if not options['no_images']:
+        # Resize and copy popup images.
+        popup_dest_path.mkdir()
+        for dose in doses:
+            dest_path = popup_dest_path.child(dose['img_filename'])
+            with wand.image.Image(filename=dose['img_path']) as img, \
+                    open(dest_path, 'w') as f:
+                scale = float(popup_target_width) / img.width
+                target_size = [int(round(d * scale)) for d in img.size]
+                img.resize(*target_size, blur=1.5)
+                img.compression_quality = 20
+                img.format = 'JPEG'
+                img.save(file=f)
+                dest_path.chmod(0o644)
+        # Extract and copy schematic images.
+        schematic_dest_path.mkdir()
+        schematic_path = img_src_path.child('schematics', 'Trajectories_schematics.pdf')
+        with wand.image.Image(filename=schematic_path, resolution=500) as img:
+            for section in table:
+                page_number = section['schematic_page']
+                page = wand.image.Image(image=img.sequence[page_number])
+                page.alpha_channel = False
+                scale = float(schematic_target_width) / page.width
+                target_size = [int(round(d * scale)) for d in page.size]
+                page.resize(*target_size)
+                page.compression_quality = 100
+                page.format = 'JPEG'
+                filename = '{}.jpg'.format(page_number)
+                dest_path = schematic_dest_path.child(filename)
+                page.save(filename=dest_path)
+                dest_path.chmod(0o644)
+
+    if not options['no_data']:
+        # Copy data download files.
+        data_dest_path.mkdir(parents=True)
+        for filename in data_filenames:
+            src_path = data_src_path.child(filename)
+            dest_path = data_dest_path.child(filename)
+            src_path.copy(dest_path)
             dest_path.chmod(0o644)
-    # Copy data download files.
-    data_dest_path.mkdir(parents=True)
-    for filename in data_filenames:
-        src_path = data_src_path.child(filename)
-        dest_path = data_dest_path.child(filename)
-        src_path.copy(dest_path)
-        dest_path.chmod(0o644)
 
-    globals().update(locals())
-    return 0
+    return content
 
 
 def as_css_identifier(s):
@@ -190,15 +210,3 @@ def as_css_identifier(s):
     the values returned from this function to sidestep the issue entirely.
     """
     return re.sub(r'[^a-z0-9-]', '-', s, flags=re.IGNORECASE)
-
-
-def render_template(template_name, data, dirname, basename):
-    "Render a template with data to a file specified by dirname and basename."
-    out_filename = unipath.Path(dirname, basename)
-    content = render_to_string(template_name, data)
-    with codecs.open(out_filename, 'w', 'utf-8') as out_file:
-        out_file.write(content)
-
-
-if __name__ == '__main__':
-    sys.exit(main(sys.argv[1:]))

django/trail_threshold_variability/templates/trail_threshold_variability/base.html

@@ -0,0 +1,19 @@
+{% extends "base_flatpage.html" %}
+
+{% block requirejs %}
+    <script>
+     require.config({
+         paths: {
+             ttv: 'trail_threshold_variability/js',
+         },
+     });
+     require( [ 'ttv/main' ] );
+    </script>
+{% endblock %}
+
+{% block head_extra %}
+  <link rel="stylesheet" type="text/css" href="{{ STATIC_URL }}ext/jquery-ui/1.11.4/jquery-ui.min.css"/>
+  <link rel="stylesheet" type="text/css" href="{{ STATIC_URL }}trail_threshold_variability/css/style.css"/>
+{% endblock %}
+
+{% block contentclass %}fullwidth{% endblock %}

django/trail_threshold_variability/templates/trail_threshold_variability/index.html

@@ -1,32 +1,5 @@
-{% extends "base.html" %}
-
 {% load trail_threshold_variability %}
 
-{% block requirejs %}
-    <script>
-     require.config({
-         paths: {
-             ttv: 'trail_threshold_variability/js',
-         },
-     });
-     require( [ 'ttv/main' ] );
-    </script>
-{% endblock %}
-
-{% block head_extra %}
-  <link rel="stylesheet" type="text/css" href="{{ STATIC_URL }}ext/jquery-ui/1.11.4/jquery-ui.min.css"/>
-  <link rel="stylesheet" type="text/css" href="{{ STATIC_URL }}trail_threshold_variability/css/style.css"/>
-{% endblock %}
-
-{% block title %}
-  Fractional killing arises from cell-to-cell variability in overcoming a
-  caspase activity threshold - {{ block.super }}
-{% endblock %}
-
-{% block contentclass %}fullwidth{% endblock %}
-
-{% block body %}
-
   <h1>Fractional killing arises from cell-to-cell variability in overcoming a
   caspase activity threshold</h1>
 
@@ -100,15 +73,15 @@ <h2>Treatment/dose lookup table</h2>
           </td>
           {% for dose in treatment.doses %}
             <td class="lookup-table-hotspot cell-{{ dose.id }}">
-              <a href="img/popup/{{ dose.img_filename }}">{{ dose.amount }}</a>
+              <a href="{{ STATIC_URL }}trail_threshold_variability/g/popup/{{ dose.img_filename }}">{{ dose.amount }}</a>
             </td>
           {% endfor %}
           {% if forloop.first %}
             {% if section.num_padding_columns %}
               <td class="padding" colspan="{{ section.num_padding_columns }}"></td>
             {% endif %}
             <td>
-              <img src="img/schematic/{{ section.schematic_page }}.jpg"
+              <img src="{{ STATIC_URL }}trail_threshold_variability/g/schematic/{{ section.schematic_page }}.jpg"
                    class="schematic" width="250">
             </td>
           {% endif %}
@@ -139,7 +112,7 @@ <h2 id="downloads">Available data, signatures and software</h2>
       <td>Data and signatures</td>
       <td>All single-cell raw data, smoothed trajectories, and fitted parameters
       for each replicate for each treatment condition in HeLa cells.</td>
-      <td><a href="{{ data_rel_url}}/All_SingleCell_data.zip">Download (.zip)</a></td>
+      <td><a href="{{ STATIC_URL }}trail_threshold_variability/g/data/All_SingleCell_data.zip">Download (.zip)</a></td>
     </tr>
     <tr>
       <td>Signatures</td>
@@ -148,21 +121,19 @@ <h2 id="downloads">Available data, signatures and software</h2>
       for download through the
       <a href="http://lincs.hms.harvard.edu/db/datasets/20232/">HMS LINCS Database</a>.
       </em></td>
-      <td><a href="{{ data_rel_url}}/Aggregate_SingleCell_results.tsv">Download (.tsv)</a></td>
+      <td><a href="{{ STATIC_URL }}trail_threshold_variability/g/data/Aggregate_SingleCell_results.tsv">Download (.tsv)</a></td>
     </tr>
     <tr>
       <td>Data and signatures</td>
       <td>Population-based viability and C8 activity results for Apomab, Apomab
       + anti-Fc, and TRAIL treatments in several other cancer cell lines with
       varying sensitivities to TRAIL.</td>
-      <td><a href="{{ data_rel_url}}/Results_other_lines.zip">Download (.zip)</a></td>
+      <td><a href="{{ STATIC_URL }}trail_threshold_variability/g/data/Results_other_lines.zip">Download (.zip)</a></td>
     </tr>
     <tr>
       <td>Software</td>
       <td>The MATLAB code for the image processing routines developed for this
       project.</td>
-      <td><a href="{{ data_rel_url}}/scripts.zip">Download (.zip)</a></td>
+      <td><a href="{{ STATIC_URL }}trail_threshold_variability/g/data/scripts.zip">Download (.zip)</a></td>
     </tr>
   </table>
-
-{% endblock %}

django/trail_threshold_variability/templates/trail_threshold_variability/popup.html

@@ -1,5 +1,5 @@
 <div class="lookup-table-popup cell-{{ dose.id }}">
-  <a class="media-ondemand" href="img/popup/{{ dose.img_filename }}">Single-cell
+  <a class="media-ondemand" href="{{ STATIC_URL }}trail_threshold_variability/g/popup/{{ dose.img_filename }}">Single-cell
     data summary for {{ treatment.name_main }}
     @ {{ dose.amount }} {{ treatment.unit }}
     {% if treatment.name_other %}