eliminate redundant duplicating IDs

salilab · May 28, 2024 · 07d9af1 · 07d9af1
1 parent 5f0bb76
commit 07d9af1
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Showing 7 changed files with 31 additions and 56 deletions.
diff --git a/ihm_validation/mmcif_io.py b/ihm_validation/mmcif_io.py
@@ -90,27 +90,9 @@ def get_databases(self):
         return dbs
 
     def get_id(self):
-        """ get id from model name, eg: PDBDEV_00XX will be PDBDEV00XX"""
-        # if self.system.id == 'model':
-        #    id = self.get_id_from_entry()
-        # else:
-        #    id = self.system.id.split('_')[0] + self.system.id.split('_')[1]
-        return self.get_id_from_entry()
-
-    def get_id_from_entry(self) -> str:
-        """ get id name from entry for cif files
-            deprecated """
-        sf = open(self.mmcif_file, 'r', encoding='latin1')
-        for ind, ln in enumerate(sf.readlines()):
-            line = ln.strip().split(' ')
-            if '_entry.id' in line[0]:
-                entry_init = line[-1]
-                try:
-                    entry = entry_init.split('_')[0] + \
-                        entry_init.split('_')[1]
-                except:
-                    entry = entry_init.strip()
-        return entry
+        """Return _entry.id; Requires compliant CIF file"""
+        entry_id = self.system.id
+        return entry_id
 
     def get_pdb_id(self) -> str:
         """Check database2 table for PDB ID"""

diff --git a/ihm_validation/report.py b/ihm_validation/report.py
@@ -80,13 +80,6 @@ def run_entry_composition(self, Template_Dict: dict) -> dict:
             utility.dict_to_JSlist_rows(RB, flex))
         entry_id = self.input.get_id()
         Template_Dict['ID'] = entry_id
-        Template_Dict['ID_w'] = entry_id.split()
-        Template_Dict['ID_T'] = entry_id[0:6]+'_' + \
-            entry_id[6:]
-        Template_Dict['ID_MP'] = [str(entry_id[0:6]+'_' +
-                                      entry_id[6:])]
-        Template_Dict['ID_R'] = (
-            entry_id[0:6]+'_'+entry_id[6:]).split()
         Template_Dict['PDB_ID'] = self.input.get_pdb_id()
         Template_Dict['PDBDEV_ID'] = self.input.get_pdb_dev_id()
         Template_Dict['ranked_id_list'] = self.input.get_ranked_id_list()

diff --git a/templates/data_quality.html b/templates/data_quality.html
@@ -60,9 +60,9 @@ <h5 class= ex2 align= center>
               <!-- plots -->
               <div class=row>
                 <!-- log I(q) vs q plot -->
-                {{ insert_sas_plot(ID_w[0], sasdb_code_html[i], "intensities") }}
+                {{ insert_sas_plot(ID, sasdb_code_html[i], "intensities") }}
                 <!-- log I(q) vs log q plot -->
-                {{ insert_sas_plot(ID_w[0], sasdb_code_html[i], "intensities_log") }}
+                {{ insert_sas_plot(ID, sasdb_code_html[i], "intensities_log") }}
               </div>
             </div>
           </div>
@@ -112,9 +112,9 @@ <h5 class= ex2 align= center>
           <!-- plots -->
           <div class=row>
             <!-- Porod-Debye plot -->
-            {{ insert_sas_plot(ID_w[0], sasdb_code_html[i], "porod") }}
+            {{ insert_sas_plot(ID, sasdb_code_html[i], "porod") }}
             <!-- Dimensionless Kratky plot -->
-            {{ insert_sas_plot(ID_w[0], sasdb_code_html[i], "Kratky") }}
+            {{ insert_sas_plot(ID, sasdb_code_html[i], "Kratky") }}
           </div>
         {% endfor %}
       </div>
@@ -142,9 +142,9 @@ <h5 align= center>
           <!-- main plots -->
           <div class=row>
             <!-- Pair distance distribution function -->
-            {{ insert_sas_plot(ID_w[0], sasdb_code_html[i], "pddf") }}
+            {{ insert_sas_plot(ID, sasdb_code_html[i], "pddf") }}
             <!-- P(r) extrapolated fit -->
-            {{ insert_sas_plot(ID_w[0], sasdb_code_html[i], "pddf_int") }}
+            {{ insert_sas_plot(ID, sasdb_code_html[i], "pddf_int") }}
           </div>
         {% endfor %}
       </div>
@@ -183,7 +183,7 @@ <h5 class= ex2 align= center><u><a name=firstG> Guinier analysis </a></u><a clas
             <!-- Guinier plot -->
             <div class=row>
               {% for i in range(sasdb_code_html|length) %}
-                {{ insert_sas_plot(ID_w[0], sasdb_code_html[i], "guinier") }}
+                {{ insert_sas_plot(ID, sasdb_code_html[i], "guinier") }}
               {% endfor %}
             </div>
           </div>

diff --git a/templates/formodeling.html b/templates/formodeling.html
@@ -56,7 +56,7 @@ <h5 class= ex2 align= center>
                 {% for i in range(sasdb_code_html|length) %}
                   {% for j in range(sasdb_code_fits[i]) %}
                     {% set k = j + 1 %}
-                      {{ insert_sas_plot(ID_w[0], sasdb_code_html[i], j|int ~ 'fit1') }}
+                      {{ insert_sas_plot(ID, sasdb_code_html[i], j|int ~ 'fit1') }}
                   {% endfor %}
                 {% endfor %}
               </div>

diff --git a/templates/full_validation_pdf.html b/templates/full_validation_pdf.html
@@ -237,7 +237,7 @@ <h5 align=center>
 
                 {% for i in range([NumModels, MAXPLOTS] | min) %}
                   <div>
-                    <img src={{ "../images/" ~ ID_w[0] ~ '_' ~ i ~ '_quality_at_glance_MQ.svg'}}>
+                    <img src={{ "../images/" ~ ID ~ '_' ~ i ~ '_quality_at_glance_MQ.svg'}}>
                   </div>
                 {% endfor %}
               {% elif disclaimer == 1 %}
@@ -255,7 +255,7 @@ <h5 align=center>
                     <div class="col-lg-12">
                        <div class="card-header" style="background-color: #FFFFFF ;">
                           <div class="box text-center container-fluid no-padding" align="center">
-                            <img src={{"../images/" ~ ID_w[0] ~ "quality_at_glance_DQ.svg"}}>
+                            <img src={{"../images/" ~ ID ~ "quality_at_glance_DQ.svg"}}>
                           </div>
                        </div>
                     </div>
@@ -271,7 +271,7 @@ <h5 align=center>
                   <div class="col-lg-12">
                     <div class="card-header" style="background-color: #FFFFFF ;">
                       <div class="box text-center container-fluid no-padding" align="center">
-                        <img src={{"../images/" ~ ID_w[0] ~ "quality_at_glance_FQ.svg"}}>
+                        <img src={{"../images/" ~ ID ~ "quality_at_glance_FQ.svg"}}>
                       </div>
                     </div>
                   </div>
@@ -442,12 +442,12 @@ <h5 align=center>
               <div class=row>
                 <div class=col-lg-12>
                   <div class=box text-center container-fluid no-padding align=center>
-                    <img src=../images/{{ ID_w[0] ~ sasdb_code_html[i] }}intensities.svg>
+                    <img src=../images/{{ ID ~ sasdb_code_html[i] }}intensities.svg>
                   </div>
                 </div>
                 <div class=col-lg-12>
                   <div class=box text-center container-fluid no-padding align=center>
-                    <img src=../images/{{ ID_w[0] ~ sasdb_code_html[i] }}intensities_log.svg>
+                    <img src=../images/{{ ID ~ sasdb_code_html[i] }}intensities_log.svg>
                   </div>
                 </div>
               </div>
@@ -481,12 +481,12 @@ <h5 align=center>
               <div class=row>
                 <div class=col-xs-6>
                   <div class=box text-center container-fluid no-padding align=center>
-                    <img src=../images/{{ ID_w[0] ~ sasdb_code_html[i] }}porod.svg>
+                    <img src=../images/{{ ID ~ sasdb_code_html[i] }}porod.svg>
                   </div>
                 </div>
                 <div class=col-xs-6>
                   <div class=box text-center container-fluid no-padding align=center style=height:60vh >
-                    <img src=../images/{{ ID_w[0] ~ sasdb_code_html[i] }}Kratky.svg>
+                    <img src=../images/{{ ID ~ sasdb_code_html[i] }}Kratky.svg>
                   </div>
                 </div>
               </div>
@@ -509,12 +509,12 @@ <h5 align=center>
               <div class=row>
                 <div class=col-xs-6>
                   <div class=box text-center container-fluid no-padding align=center>
-                    <img src=../images/{{ ID_w[0] ~ sasdb_code_html[i] }}pddf.svg>
+                    <img src=../images/{{ ID ~ sasdb_code_html[i] }}pddf.svg>
                   </div>
                 </div>
                 <div class=col-xs-6>
                   <div class=box text-center container-fluid no-padding align=center>
-                    <img src=../images/{{ ID_w[0] ~ sasdb_code_html[i] }}pddf_int.svg>
+                    <img src=../images/{{ ID ~ sasdb_code_html[i] }}pddf_int.svg>
                   </div>
                 </div>
               </div>
@@ -538,7 +538,7 @@ <h5 align= center>
               <div class=row>
                 <div class=col-lg-12>
                   <div class=box text-center container-fluid no-padding align=center>
-                    <img src=../images/{{ ID_w[0] ~ sasdb_code_html[i] }}guinier.svg>
+                    <img src=../images/{{ ID ~ sasdb_code_html[i] }}guinier.svg>
                   </div>
                 </div>
               </div>
@@ -602,7 +602,7 @@ <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/Validation/{{ ID_MP[0] }}/htmls/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 }}/htmls/bond_outliers.html>here</a>.</i>
                   {{ write_table(molp_b) }}
                 {% else %}
                   <i> Bond length outliers can not be evaluated for this model</i>
@@ -613,7 +613,7 @@ <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='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/Validation/{{ ID_MP[0] }}/htmls/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 }}/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>
@@ -728,7 +728,7 @@ <h5 align=center>
                       <div class=row>
                         <div class=col-lg-12>
                           <div class=box text-center container-fluid no-padding align=center>
-                            <img src=../images/{{ ID_w[0] ~ sasdb_code_html[i] ~ j|int }}fit1.svg>
+                            <img src=../images/{{ ID ~ sasdb_code_html[i] ~ j|int }}fit1.svg>
                           </div>
                         </div>
                       </div>

diff --git a/templates/main.html b/templates/main.html
@@ -7,8 +7,8 @@
     <div class="col-lg-4">
       <div class="card-header" style="background-color: #FFFFFF; border-color:#003366; height: 29rem;">
         <h3 align=center>
-          <a href=/entry.html?{{ID_R[0]}}>
-            {{ID_R[0]}}
+          <a href=/entry.html?{{ ID }}>
+            {{ ID }}
           </a>
         </h3>
         <div class="box text-center no-padding float-left" style="text-align: center" >
@@ -26,7 +26,7 @@ <h5 align="center" style="text-align: center";>Download Summary Table</h5>
           </a>
         </div>
         <div class="box text-center container-fluid no-padding">
-          <img src=/images/{{ID_R[0]}}_resize_1.png class=image-fluid alt=Model Image style=width:300px align=center>
+          <img src=/images/{{ ID }}_resize_1.png class=image-fluid alt=Model Image style=width:300px align=center>
         </div>
       </div>
       <!-- end card header -->
@@ -144,20 +144,20 @@ <h3 align="center">
             <div id="home" class="tab-pane active">
               <div class="box text-center container-fluid no-padding" align='center'>
                 {% if not disclaimer %}
-                  <iframe src=../images/{{ID_w[0]}}quality_at_glance_MQ.html frameborder=0 scrolling=yes width=90% align=center text-align: center style="position:relative; min-height:470px; max-height:2048px;">
+                  <iframe src=../images/{{ ID }}quality_at_glance_MQ.html frameborder=0 scrolling=yes width=90% align=center text-align: center style="position:relative; min-height:470px; max-height:2048px;">
                   </iframe>
                 {% endif %}
               </div>
             </div>
             <div id="menu1" class="tab-pane fade">
               <div class="box text-center container-fluid no-padding" align='center'>
-                <iframe src=../images/{{ID_w[0]}}quality_at_glance_DQ.html frameborder=0 scrolling=yes width=90% height=500vh align=center text-align: center style=position:relative>
+                <iframe src=../images/{{ ID }}quality_at_glance_DQ.html frameborder=0 scrolling=yes width=90% height=500vh align=center text-align: center style=position:relative>
                 </iframe>
               </div>
             </div>
             <div id="menu2" class="tab-pane fade">
               <div class="box text-center container-fluid no-padding" align='center'>
-                <iframe src=../images/{{ID_w[0]}}quality_at_glance_FQ.html frameborder=0 scrolling=yes width=90% align=center text-align: center style="position:relative; min-height:470px; max-height:2048px;">
+                <iframe src=../images/{{ ID }}quality_at_glance_FQ.html frameborder=0 scrolling=yes width=90% align=center text-align: center style="position:relative; min-height:470px; max-height:2048px;">
                 </iframe>
               </div>
             </div>

diff --git a/templates/validation_report_layout.html b/templates/validation_report_layout.html
@@ -6,7 +6,7 @@
     <div class="dropdown">
       <a class="navbar-brand" href="main.html">
         <h5>
-          Validation Report for {{ID_T}}
+          Validation Report for {{ ID }}
         </h5>
       </a>
       <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation">