calendar.html: update and add choice of period

one of 2011-2014, 2015-2018 or 2019-2022
project-gemmi · Jul 11, 2024 · 81a8ddb · 81a8ddb
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diff --git a/README.md b/README.md
@@ -1,15 +1,16 @@
 
 These statistics serve as an example how to use `gemmi-grep`
- (one of the utilities provided by the [project gemmi][1])
- to quickly extract data from mmCIF files.
+(one of the utilities provided by the [project gemmi][1])
+to quickly extract data from mmCIF files.
 
-The data is extracted from a local copy of the PDB archive in mmCIF format
-(we rsync it once a week).
+The data of interest is extracted from a local copy of the PDB archive
+(mmCIF coordinate files) to a file `grep.out`:
 
-We use `gemmi-grep` in the `extract.sh` script to extract all the needed
-metadata (and some more).
-Reading all the archive (34GB of compressed files) takes 20-30min.
-The output is redirected to a file (`grep.out`) that is later used
+    $ ./extract.sh --auto
+
+This script uses `gemmi-grep` to extract metadata to a file `grep.out`.
+Reading all the archive (69GB of compressed files) takes about 30min.
+The output is redirected to a file (`grep.out`) that is then used
 to prepare JSON files used in our web pages.
 
 ### Filter-able statistics
@@ -30,7 +31,7 @@ https://project-gemmi.github.io/pdb-stats/
 
 ### Synchrotron work patterns
 
-`./coldates.py >calendar.json` writes the data used in calendar.html:
+`./coldates.py` prepares json files for calendar.html, see `extract.sh`.
 
 https://project-gemmi.github.io/pdb-stats/calendar.html
 

diff --git a/calendar.html b/calendar.html
@@ -12,6 +12,8 @@
 body { font: 14px sans-serif; margin: 0; shape-rendering: crispEdges; }
 h1 { text-align: center; font-size: 30px; font-weight: normal; }
 h4 { text-align: center; font-size: 15px; font-weight: normal; }
+h5 { text-align: center; font-size: 14px; font-weight: normal; }
+h5 a { margin: 0 50px 0 50px; }
 h2 { text-align: center; font-size: 18px; margin: 30px 0 0 0; }
 .cal { min-height: 280px; padding-left: 50px; }
 @media only screen and (max-width: 600px) { .cal { padding-left: 0; } }
@@ -42,7 +44,13 @@
 <body>
 <h1>Synchrotron Work Patterns</h1>
 <h4>Data <a href="http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx.dic/Items/_diffrn_detector.pdbx_collection_date.html">collection</a>
-dates from <b>PDB entries released before 2021-01-21</b>.</h4>
+dates from <b>PDB entries released before 2024-07-09</b>.</h4>
+
+<h5>
+<a href="#from2011">2011-2014</a>
+<a href="#from2015">2015-2018</a>
+<a href="#from2019">2019-2022</a>
+</h5>
 
 <div class="cal" id="APS">
 <h2>APS <span style="background-image: url(flags/us.svg)"></span></h2>
@@ -111,7 +119,7 @@ <h2>all home sources</h2>
 <div id="footnote" style="clear:both;">
  This is part of the
  <a href="https://project-gemmi.github.io/">project GEMMI</a>.
- Uses <a href="https://bl.ocks.org/micahstubbs/89c6bd879d64aa511372064c6cf85711">this dc.js example</a>,
+ Uses <a href="https://bl.ocks.org/micahstubbs/89c6bd879d64aa511372064c6cf85711">this d3.js example</a>,
  <a href="https://github.com/lipis/flag-icon-css">SVG flags</a> and
  wwPDB data.
  <p><b><a href="https://github.com/project-gemmi/pdb-stats">
@@ -122,6 +130,13 @@ <h2>all home sources</h2>
 <script type="text/javascript">
 "use strict";
 
+var ystart = 2015;
+
+const fragment = window.location.hash.slice(1);
+if (fragment == "from2011" || fragment == "from2019") {
+  ystart = +fragment.slice(4);
+}
+
 var width = 520,
     height = 60,
     cellSize = 8;
@@ -144,8 +159,21 @@ <h2>all home sources</h2>
       + "H" + (w0 + 1) * cellSize + "Z";
 }
 
+d3.selectAll('h5 a')
+  .each(function() {
+    var h = this.getAttribute('href');
+    if (h === '#from' + ystart) {
+      d3.select(this).attr('href', null);
+    } else {
+      d3.select(this).on('click', function() {
+        window.location.href = 'calendar.html' + h;
+        window.location.reload();
+      });
+    }
+  });
+
 var svg = d3.selectAll(".cal").selectAll("svg")
-    .data(d3.range(2015, 2019))
+    .data(d3.range(ystart, ystart+4))
   .enter().append("svg")
     .attr("width", width)
     .attr("height", function(d, i) {
@@ -207,12 +235,13 @@ <h2>all home sources</h2>
   "#202030", "#202020", "#1c1c1c", "#1c1c1c", "#1c1c1c",
   "#000000"];
 
-d3.json('calendar.json', function(error, json) {
+d3.json('calendar'+ystart+'.json', function(error, json) {
   if (error) throw error;
   d3.selectAll(".cal").each(function() {
     var data = {}
     var syn_data = json[this.id];
-    for (var year = 2015; year < 2019; year++) {
+    for (var i = 0; i < 4; i++) {
+      var year = ystart + i;
       var arr = syn_data[''+year];
       for (var j = 0; j < arr.length; ++j) {
         var key = format(new Date(year, 0, 1+j));

diff --git a/calendar.json b/calendar.json
diff --git a/calendar2011.json b/calendar2011.json
diff --git a/calendar2015.json b/calendar2015.json
diff --git a/calendar2019.json b/calendar2019.json
diff --git a/coldates.py b/coldates.py
@@ -10,7 +10,9 @@
               'SOLEIL', 'PAL/PLS', 'CLSI', 'DESY']
 ALL_OUTPUT = OUTPUT_SYN + ['home']
 
-OUTPUT_YEARS = [2015, 2016, 2017, 2018]
+FIRST_YEAR = int(sys.argv[1])
+LAST_YEAR = int(sys.argv[2])
+OUTPUT_YEARS = range(FIRST_YEAR, LAST_YEAR+1)
 
 def days_in_year(year):
     if year % 4 == 0:

diff --git a/extract.sh b/extract.sh
@@ -3,10 +3,11 @@
 # This web page is part of an example how to use gemmi-grep.
 # gemmi-grep is an part of the GEMMI library, funded by GPhL and CCP4.
 
-PATH="$PATH":../gemmi/build
+PATH=../gemmi/build:"$PATH"
+PYTHONPATH=../gemmi/build
 
 # check that module gemmi is present
-python3 -c "import gemmi"
+[ "$1" = "--auto" ] && python3 -c "import gemmi"
 
 gemmi grep --delimiter=';' \
        _software.classification \
@@ -34,6 +35,8 @@ gemmi grep --delimiter=';' \
 if [ "$1" = "--auto" ]; then
   ./process.py >data.json
   sed -i s"/\(Last update:\) ....-..-../\1 $(date -Idate)/" xray.html
-  ./coldates.py >calendar.json
+  ./coldates.py 2011 2014 >calendar2011.json
+  ./coldates.py 2015 2018 >calendar2015.json
+  ./coldates.py 2019 2022 >calendar2019.json
   sed -i s"/\(released before\) ....-..-../\1 $(date -Idate)/" calendar.html
 fi
diff --git a/process.py b/process.py
@@ -59,6 +59,7 @@ def parse_date(txt):
     'NSLS':                    'n NSLS (US, NY)',
     'SSRF':                    'h Shanghai SRF (CN)',
     'Photon Factory':          'p Photon Factory (JP)',
+    'PHOTON FACTORY':          'p Photon Factory (JP)',
     'SPring-8':                '8 SPring-8 (JP)',
     'BESSY':                   'b BESSY (DE)',
     'Australian Synchrotron':  'u Australian S. (AU)',
@@ -73,6 +74,7 @@ def parse_date(txt):
     'EMBL/DESY, HAMBURG':      'D DESY (DE)',
     'LNLS':                    'L LNLS (BR)',
     'LNLS SIRUS':              'L LNLS (BR)',
+    'LNLS SIRIUS':             'L LNLS (BR)',
     'PETRA III EMBL c/o DESY': 'D DESY (DE)',
     'PETRA II STORAGE RING':   'D DESY (DE)',
     'ALBA':                    'Z ALBA (ES)',
@@ -104,6 +106,7 @@ def parse_date(txt):
     'LCLS':                    'F SLAC (US, CA)',
     'SLAC':                    'F SLAC (US, CA)',
     'SLAC LCLS':               'F SLAC (US, CA)',
+    'SwissFEL ARAMIS':         'F SwissFEL (CH)',
 
     # ?
     'SYNCHROTRON':             '?',