bulk update: static paths to resources; html directory structure cons…

…istent with pdb-dev website; minor fixes
salilab · Feb 21, 2024 · d21252b · d21252b
1 parent 94c350f
commit d21252b
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Showing 10 changed files with 144 additions and 135 deletions.
diff --git a/ihm_validation/ihm_validator.py b/ihm_validation/ihm_validator.py
@@ -48,7 +48,7 @@
                     help="Path to a directory where the output will be written")
 parser.add_argument('--output-prefix', type=str, default=None,
                     help="Prefix of the output directory. Default is a stem of the mmCIF file")
-parser.add_argument('--html-mode', type=str, default='local',
+parser.add_argument('--html-mode', type=str, default='pdb-dev',
                     choices=['local', 'pdb-dev'],
                     help="HTML mode affects paths to various statis resources")
 parser.add_argument('--html-resources',
@@ -139,8 +139,8 @@
     "model_quality.html",
     "model_composition.html",
     "formodeling.html",
-    "about_validation.html",
-    "validation_help.html",
+#    "about_validation.html",
+#    "validation_help.html",
 ]
 
 # Get the UTC time from ruser
@@ -172,9 +172,9 @@
 
 dirNames.update(
     {
-        'images':  str(Path(dirNames['html'], 'images')),
-        'csv':  str(Path(dirNames['html'], 'csv')),
-        'pdf':  str(Path(dirNames['html'], 'pdf')),
+        'images':  str(Path(dirNames['root_html'], 'images')),
+        'csv':  str(Path(dirNames['root_html'], 'csv')),
+        'pdf':  str(Path(dirNames['root_html'], 'pdf')),
         # 'json': str(Path(output_path, 'json')),
     }
 )
@@ -297,6 +297,7 @@ def write_json(mmcif_file: str, template_dict: dict, dirName: str, dirName_Outpu
     template_dict, molprobity_dict, exv_data = report.run_model_quality(
         template_dict, csvDirName=dirNames['csv'], htmlDirName=dirNames['html'])
 
+    template_dict['enable_sas'] = args.enable_sas
     if args.enable_sas:
         logging.info("SAS validation")
         template_dict, sas_data, sas_fit = report.run_sas_validation(template_dict)
@@ -310,6 +311,7 @@ def write_json(mmcif_file: str, template_dict: dict, dirName: str, dirName_Outpu
         sas_fit = {}
 
     # uncomment below to run CX analysis
+    template_dict['enable_cx'] = args.enable_cx
     if args.enable_cx:
         logging.info("CX validation")
         template_dict, cx_data, cx_ertypes = report.run_cx_validation(template_dict)

diff --git a/templates/data_quality.html b/templates/data_quality.html
@@ -9,7 +9,7 @@
     <div class="card-header" style="background-color: #FFF;">    
       <div class="row">
         <div class="col-lg-12">
-          <h4 class="ex2" align="center"><u><a name='first'>Data quality</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='validation_help.html#dataquality'>?</a>
+          <h4 class="ex2" align="center"><u><a name='first'>Data quality</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='https://pdb-dev.wwpdb.org/validation_help.html#dataquality'>?</a>
           </h4>
         </div>
       </div>
@@ -43,7 +43,7 @@ <h5 class= ex2 align= center>
           <div class="col-lg-12">
             <!-- potential nesting inconsistency -->
             <h5 class= ex2 align= center>
-              <u><a name=firstI>SAS:Scattering profile</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='validation_help.html#scattering'>?</a>
+              <u><a name=firstI>SAS:Scattering profile</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='https://pdb-dev.wwpdb.org/validation_help.html#scattering'>?</a>
             </h5>
             <p align=justify>
               SAS data used in this integrative model was obtained from {{sasdb_code_html|length|int}} deposited SASBDB entry (entries).
@@ -76,7 +76,7 @@ <h5 class= ex2 align= center>
         <div class="col-lg-12">
           <div class="card-header" style="background-color: #FFF;">
             <h5 class= ex2 align= center>
-              <u><a name=firstE>Key experimental estimates</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='validation_help.html#expt'>?</a>
+              <u><a name=firstE>Key experimental estimates</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='https://pdb-dev.wwpdb.org/validation_help.html#expt'>?</a>
             </h5>
             <p class=ex2 align='justify'>
               <u>Molecular weight (MW) estimates from experiments and analysis</u>: true molecular weight can be compared to the Porod estimate from scattering profiles.
@@ -99,7 +99,7 @@ <h5 class= ex2 align= center>
           <div class="col-lg-12">
             {% if sas|length > 0 and sasdb_sascif|length > 0 %}
               <h5 class= ex2 align= center>
-                <u><a name=firstF>Flexibility analysis</a> </u><a class='help'  title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='validation_help.html#flexibility'>?</a>
+                <u><a name=firstF>Flexibility analysis</a> </u><a class='help'  title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='https://pdb-dev.wwpdb.org/validation_help.html#flexibility'>?</a>
               </h5>
             {% endif %}
           </div>
@@ -127,7 +127,7 @@ <h5 class= ex2 align= center>
           <!-- header -->
           <div class="col-lg-12">
             <h5 align= center>
-              <u><a name=firstP>Pair-distance distribution analysis</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='validation_help.html#pofr'>?</a>
+              <u><a name=firstP>Pair-distance distribution analysis</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='https://pdb-dev.wwpdb.org/validation_help.html#pofr'>?</a>
             </h5>
             <p class=ex2 align='justify'>
               <u>P(r) analysis:</u> P(r) represents the distribution of distances between all pairs of atoms within the particle weighted by the respective electron densities. P(r) is the Fourier transform of I(s) (and vice versa). R<sub>g</sub> can be estimated from integrating the P(r) function. Agreement between the P(r) and Guinier-determined R<sub>g</sub> (table below) is a good measure of the self-consistency of the SAS profile. R<sub>g</sub> is a measure for the overall size of a macromolecule; e.g. a protein with a smaller R<sub>g</sub> is more compact than a protein with a larger R<sub>g</sub>, provided both have the same molecular weight (MW). The point where P(r) is decaying to zero is called D<sub>max</sub> and represents the maximum size of the particle.
@@ -156,7 +156,7 @@ <h5 align= center>
         <div class="row">
           <!-- description -->
           <div class="col-lg-12">
-            <h5 class= ex2 align= center><u><a name=firstG> Guinier analysis </a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='validation_help.html#guinier'>?</a>
+            <h5 class= ex2 align= center><u><a name=firstG> Guinier analysis </a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='https://pdb-dev.wwpdb.org/validation_help.html#guinier'>?</a>
             </h5>
             <p class=ex2 align='justify'>
               <u> Guinier analysis:</u> agreement between the P(r) and Guinier-determined R<sub>g</sub> (table below) is a good measure of the self-consistency of the SAS profile. Molecular weight estimates can also be compared to Porod and sample molecular weights for consistency.

diff --git a/templates/formodeling.html b/templates/formodeling.html
@@ -10,7 +10,7 @@
       <div class="row">
         <div class="col-lg-12">
           <h4 class="ex2" align="center">
-            <u><a name='first'>Fit of model to data used for modeling</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='validation_help.html#fittodata'>?</a>
+            <u><a name='first'>Fit of model to data used for modeling</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='https://pdb-dev.wwpdb.org/validation_help.html#fittodata'>?</a>
           </h4>
         </div>
       </div>
@@ -35,7 +35,7 @@ <h5 class= ex2 align= center><u> Fit of model(s) to SAS data</u></h5>
           <div class="row">
             <div class="col-lg-6">
               <h5 class= ex2 align= center>
-                <u><a name='second'>Cormap p-value analysis of fits </a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='validation_help.html#cormap'>?</a>
+                <u><a name='second'>Cormap p-value analysis of fits </a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='https://pdb-dev.wwpdb.org/validation_help.html#cormap'>?</a>
               </h5>
               {% if number_of_fits > 0 %}
                 <p class =ex2>

diff --git a/templates/full_validation_pdf.html b/templates/full_validation_pdf.html
@@ -600,18 +600,18 @@ <h5 align=center>
                 </h5>
 
                 {% if molp_b|length > 1 %}
-                  <i>There are {{ bond }} bond outliers in this entry. A summary is provided below, and a detailed list of outliers can be found <a href=https://pdb-dev.wwpdb.org/{{ ID_MP }}/html/bond_outliers.html>here</a>.</i>
+                  <i>There are {{ bond }} bond outliers in this entry. A summary is provided below, and a detailed list of outliers can be found <a href=https://pdb-dev.wwpdb.org/Validation/{{ ID_MP[0] }}/htmls/bond_outliers.html>here</a>.</i>
                   {{ write_table(molp_b) }}
                 {% else %}
                   <i> Bond length outliers can not be evaluated for this model</i>
                 {% endif %}
 
                 <!-- Angle outliers -->
                 <h5 align=center>
-                  <u><a name='geometry2'>Standard geometry: angle outliers</a></u><a class='help1' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=12px' href='../../../validation_help.html#molprobity'>?</a></h5>
+                  <u><a name='geometry2'>Standard geometry: angle outliers</a></u><a class='help1' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=12px' href='https://pdb-dev.wwpdb.org/validation_help.html#molprobity'>?</a></h5>
 
                 {% if molp_a|length > 1 %}
-                  <i>There are {{ angle }} angle outliers in this entry. A summary is provided below, and a detailed list of outliers can be found <a href=https://pdb-dev.wwpdb.org/{{ ID_MP }}/html/angle_outliers.html>here</a>.</i>
+                  <i>There are {{ angle }} angle outliers in this entry. A summary is provided below, and a detailed list of outliers can be found <a href=https://pdb-dev.wwpdb.org/Validation/{{ ID_MP[0] }}/htmls/angle_outliers.html>here</a>.</i>
                   {{ write_table(molp_a) }}
                 {% else %}
                   <i>Bond angle outliers do not exist or can not be evaluated for this model</i>
@@ -795,7 +795,7 @@ <h4 align="center">
               <p align="justify"><em>Implementation of validation methods for SAS data and SAS-based models are funded by <a href='https://www.rcsb.org/'>RCSB PDB</a> (grant number DBI-1832184). Dr. Stephen Burley, Dr. John Westbrook, and Dr. Jasmine Young from <a href='https://www.rcsb.org/'>RCSB PDB</a>,  Dr. Jill Trewhella, Dr. Dina Schneidman, and members of the <a href='https://www.sasbdb.org/'>SASBDB</a> repository are acknowledged for their advice and support in implementing SAS validation methods.</em></p>
             </li>
             <li>
-              <p align="justify"><em>Members of the <a href='http://www.wwpdb.org/task/hybrid'>wwPDB Integrative/Hybrid Methods Task Force</a> provided recommendations and community support for the project. </em> </p>
+              <p align="justify"><em>Members of the <a href='https://www.wwpdb.org/task/hybrid'>wwPDB Integrative/Hybrid Methods Task Force</a> provided recommendations and community support for the project. </em> </p>
             </li>
           </ul>
         </div>

diff --git a/templates/layout.html b/templates/layout.html
@@ -10,8 +10,8 @@
       <link rel="stylesheet" href="static/css/main.css">
       <link rel="stylesheet" href="static/css/layout.css">
     {% else %}
-      <link rel="stylesheet" href="/css/main.css">
-      <link rel="stylesheet" href="/css/layout.css">
+      <link rel="stylesheet" href="https://pdb-dev.wwpdb.org/css/main.css">
+      <link rel="stylesheet" href="https://pdb-dev.wwpdb.org/css/layout.css">
     {% endif %}
 
     <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.5.1/jquery.min.js"></script>
@@ -41,7 +41,7 @@
                 {% if html_mode == 'local' %}
                   <img src="static/images/logon.png" class="float-left" alt="PDBDEV.org" height="100" width="110" style="margin-top: 0px; margin-bottom: 0px" />
                 {% else %}
-                  <img src="/images/logon.png" class="float-left" alt="PDBDEV.org" height="100" width="110" style="margin-top: 0px; margin-bottom: 0px" />
+                  <img src="https://pdb-dev.wwpdb.org/images/logon.png" class="float-left" alt="PDBDEV.org" height="100" width="110" style="margin-top: 0px; margin-bottom: 0px" />
                 {% endif %}
                 <p>
                   <h1 style="margin-left: 0px; color: #003366;">PDB-Dev</h1>
@@ -83,7 +83,7 @@ <h5>
 
               <!-- About validation -->
               <li class="nav-item mr-4 dropdown">
-                <a class="btn btn-primary " href="about_validation.html"><span class="overview">About <br> Validation</span></a>
+                <a class="btn btn-primary " href="https://pdb-dev.wwpdb.org/about_validation.html"><span class="overview">About <br> Validation</span></a>
               </li>
               <li class="nav-item mr-4 dropdown">
                 <a class="dropdown-toggle"  data-toggle="dropdown"><button type="button" class="btn btn-primary" onclick=window.location='main.html';>Validation <br> Overview</button></a>
@@ -107,18 +107,18 @@ <h5>
 
               <!-- Model details -->
               <li class="nav-item mr-4 dropdown">
-                {% if 'SAS DATA' in Data %}
+                {% if ('SAS DATA' in Data) and enable_sas %}
                   <a class="dropdown-toggle"  data-toggle="dropdown"><button type="button" class="btn btn-primary" onclick=window.location="data_quality.html";>Data <br> Quality </button></a>
 
-                {% elif 'SAS DATA' not in Data and Unique_dataset|length > 0 %}
+                {% elif (('SAS DATA' not in Data) or not enable_sas) and Unique_dataset|length > 0 %}
                   <a class="dropdown-toggle"  data-toggle="dropdown"><button type="button" class="btn btn-primary">Data <br> Quality </button></a>
 
                 {% else %}
                   <a class="btn btn-success dropdown-toggle button4" value="Disabled" disabled background-color: #555555 ><span >Data <br>Quality</span></a>
                 {% endif %}
 
                 <div class="dropdown-menu">
-                  {% if 'SAS DATA' in Data and sasdb_sascif|length > 0 %}
+                  {% if ('SAS DATA' in Data) and (sasdb_sascif|length > 0) and enable_sas %}
                     <a class="dropdown-item colorclass" dropdown-toggle  href=data_quality.html#first>SAS</a>
                     <ul class=dropdown-submenu>                  
                       <li>
@@ -141,7 +141,7 @@ <h5>
                         <a class=dropdown-item2 href=data_quality.html#firstG>Guinier analysis </a>
                       </li>
                     </ul>
-                  {% elif 'SAS DATA' in Data and sasdb_sascif|length < 1 %}
+                  {% elif ('SAS DATA' in Data) and (sasdb_sascif|length < 1) and enable_sas %}
                     <a class="dropdown-item colorclass" dropdown-toggle type=button href=data_quality.html#first>SAS</a>
                   {% endif %}
 
@@ -169,7 +169,7 @@ <h5>
 
               <!-- Fit to data used for modeling -->
               <li class="nav-item mr-4 dropdown">
-                {% if 'SAS DATA' in Data or 'CX-MS DATA' in Data%}
+                {% if (('SAS DATA' in Data) and enable_sas) or (('CX-MS DATA' in Data) and enable_cx) %}
                   <a class="dropdown-toggle"  data-toggle="dropdown"><button type="button" class="btn btn-primary" onclick=window.location="formodeling.html";>Fit to Data <br> Used for Modeling </button></a>
 
                 {% elif Unique_dataset|length > 0 %}
@@ -180,7 +180,7 @@ <h5>
                 {% endif %}
 
 								<div class="dropdown-menu">
-                  {% if 'SAS DATA' in Data and sasdb_sascif|length > 0 %}
+                  {% if ('SAS DATA' in Data) and (sasdb_sascif|length > 0) and enable_sas %}
                     <a class="dropdown-item colorclass" dropdown-toggle href=formodeling.html>SAS</a>
                     <ul class=dropdown-submenu>
                       <li>
@@ -190,11 +190,11 @@ <h5>
                         <a  class=dropdown-item2 href=formodeling.html#second>Cormap analysis </a>
                       </li>
                     </ul>
-                  {% elif 'SAS DATA' in Data and sasdb_sascif|length < 1 %}
+                  {% elif ('SAS DATA' in Data) and (sasdb_sascif|length < 1) and enable_sas%}
                     <a class=dropdown-item dropdown-toggle type=button href=data_quality.html#first>SAS</a>
                   {% endif %}
 
-									{% if 'CX-MS DATA' in Data %}
+									{% if ('CX-MS DATA' in Data) and enable_cx %}
                     <a class="dropdown-item colorclass" dropdown-toggle href=formodeling.html#cxms>
                       CX-MS
                     </a>
@@ -227,7 +227,7 @@ <h5>
                 </div>
               </li>
               <li class="nav-item mr-4 dropdown">
-                <a class="btn btn-primary " href="validation_help.html"><span class="overview">Validation <br> Help</span></a>
+                <a class="btn btn-primary " href="https://pdb-dev.wwpdb.org/validation_help.html"><span class="overview">Validation <br> Help</span></a>
               </li>
             </ul>
           </div>
@@ -241,11 +241,11 @@ <h5>
           <div class="container-fluid">
             <div class="row" style="/color:#FFF; background-color: rgba(102,153,102, 0.5); padding-top: 10px; padding-bottom: 2px;">
               <div class="col-sm-6" style="padding-top: 10px; padding-bottom: 10px;">
-                <a href="http://www.wwpdb.org/" target="_blank">
+                <a href="https://www.wwpdb.org/" target="_blank">
                 {% if html_mode == 'local' %}
                   <img src="static/images/wwpdb-logo11.png" alt="wwpdb" height="35px" width="160px"></a>
                 {% else %}
-                  <img src="/images/wwpdb-logo11.png" alt="wwpdb" height="35px" width="160px"></a>
+                  <img src="https://pdb-dev.wwpdb.org/images/wwpdb-logo11.png" alt="wwpdb" height="35px" width="160px"></a>
                 {% endif %}
               </div>
               <div class="col-sm-6">

diff --git a/templates/macro.html b/templates/macro.html
@@ -45,7 +45,7 @@
 {% macro insert_sas_plot(id, sasdb_id, plot_name) %}
   <div class=col-lg-6>
     <div class=box text-center container-fluid no-padding style=height:60vh>
-      <iframe src=images/{{id}}{{sasdb_id}}{{plot_name}}.html frameborder=0 scrolling=yes width=100% height=550vh  style=position:relative>
+      <iframe src=../images/{{id}}{{sasdb_id}}{{plot_name}}.html frameborder=0 scrolling=yes width=100% height=600vh  style=position:relative>
       </iframe>
     </div>
   </div>