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searx/engines/pdbe.py

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+# SPDX-License-Identifier: AGPL-3.0-or-later
+"""
+ PDBe (Protein Data Bank in Europe)
+"""
+
+from json import loads
+from flask_babel import gettext
+
+# about
+about = {
+    "website": 'https://www.ebi.ac.uk/pdbe',
+    "wikidata_id": 'Q55823905',
+    "official_api_documentation": 'https://www.ebi.ac.uk/pdbe/api/doc/search.html',
+    "use_official_api": True,
+    "require_api_key": False,
+    "results": 'JSON',
+}
+
+categories = ['science']
+
+hide_obsolete = False
+
+# status codes of unpublished entries
+pdb_unpublished_codes = ['HPUB', 'HOLD', 'PROC', 'WAIT', 'AUTH', 'AUCO', 'REPL', 'POLC', 'REFI', 'TRSF', 'WDRN']
+# url for api query
+pdbe_solr_url = 'https://www.ebi.ac.uk/pdbe/search/pdb/select?'
+# base url for results
+pdbe_entry_url = 'https://www.ebi.ac.uk/pdbe/entry/pdb/{pdb_id}'
+# link to preview image of structure
+pdbe_preview_url = 'https://www.ebi.ac.uk/pdbe/static/entry/{pdb_id}_deposited_chain_front_image-200x200.png'
+
+
+def request(query, params):
+
+    params['url'] = pdbe_solr_url
+    params['method'] = 'POST'
+    params['data'] = {'q': query, 'wt': "json"}  # request response in parsable format
+    return params
+
+
+def construct_body(result):
+    # set title
+    title = result['title']
+
+    # construct content body
+    content = """{title} - {authors} {journal} ({volume}) {page} ({year})"""
+
+    # replace placeholders with actual content
+    try:
+        if result['journal']:
+            content = content.format(
+                title=result['citation_title'],
+                authors=result['entry_author_list'][0],
+                journal=result['journal'],
+                volume=result['journal_volume'],
+                page=result['journal_page'],
+                year=result['citation_year'],
+            )
+        else:
+            content = content.format(
+                title=result['citation_title'],
+                authors=result['entry_author_list'][0],
+                journal='',
+                volume='',
+                page='',
+                year=result['release_year'],
+            )
+        thumbnail = pdbe_preview_url.format(pdb_id=result['pdb_id'])
+    except KeyError:
+        content = None
+        thumbnail = None
+
+    # construct url for preview image
+    try:
+        thumbnail = pdbe_preview_url.format(pdb_id=result['pdb_id'])
+    except KeyError:
+        thumbnail = None
+
+    return [title, content, thumbnail]
+
+
+def response(resp):
+
+    results = []
+    json = loads(resp.text)['response']['docs']
+
+    # parse results
+    for result in json:
+        # catch obsolete entries and mark them accordingly
+        if result['status'] in pdb_unpublished_codes:
+            continue
+        if hide_obsolete:
+            continue
+        if result['status'] == 'OBS':
+            # expand title to add some sort of warning message
+            title = gettext('{title} (OBSOLETE)').format(title=result['title'])
+            try:
+                superseded_url = pdbe_entry_url.format(pdb_id=result['superseded_by'])
+            except:  # pylint: disable=bare-except
+                continue
+
+            # since we can't construct a proper body from the response, we'll make up our own
+            msg_superseded = gettext("This entry has been superseded by")
+            content = '{msg_superseded}: {url} ({pdb_id})'.format(
+                msg_superseded=msg_superseded, url=superseded_url, pdb_id=result['superseded_by']
+            )
+
+            # obsoleted entries don't have preview images
+            thumbnail = None
+        else:
+            title, content, thumbnail = construct_body(result)
+
+        results.append(
+            {
+                'url': pdbe_entry_url.format(pdb_id=result['pdb_id']),
+                'title': title,
+                'content': content,
+                'thumbnail': thumbnail,
+            }
+        )
+
+    return results