Upgrade to version 1.2

isdb.py

@@ -1,6 +1,6 @@
 """MetGem plugin to download ISDB"""
 
-__version__ = '1.1'
+__version__ = '1.2'
 __description__ = "MetGem plugin to download ISDB"
 __author__ = "Nicolas Elie"
 __email__ = "[email protected]"
@@ -20,16 +20,25 @@ class ISDB(DbSource):
     def get_items(self, tree):
         json_s = tree.find('.//script[@type="application/ld+json"]').text
         json_load = json.loads(json_s)
-        description = json_load['description']
-        identifier = json_load['identifier']
-        version = json_load['version']
-        date = json_load['datePublished']
+        description = json_load.get('description',
+                                    '\u003cp\u003eAn In Silico spectral DataBase (\u003cstrong\u003eISDB\u003c/strong\u003e) of natural products calculated\u0026nbsp;from structures aggregated in the frame of the LOTUS Initiative.\u003c/p\u003e\n\n\u003cp\u003eThis spectral file is in positive ionisation mode only. Fragmented using cfm-predict 3.0\u0026nbsp;\u003ca href=\"https://cfmid.wishartlab.com/\"\u003ehttps://cfmid.wishartlab.com/\u003c/a\u003e\u003c/p\u003e\n\n\u003cp\u003eIntensities at the low, medium and high energy level have been meaned.\u003c/p\u003e\n\n\u003cp\u003e\u0026nbsp;\u003c/p\u003e\n\n\u003cp\u003eIn silico spectral database preparation and use for dereplication initially\u0026nbsp;described in\u0026nbsp;\u003cem\u003eIntegration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication\u003c/em\u003e \u003ca href=\"https://doi.org/10.1021/ACS.ANALCHEM.5B04804\"\u003ehttps://doi.org/10.1021/ACS.ANALCHEM.5B04804\u003c/a\u003e\u003c/p\u003e\n\n\u003cp\u003eSee \u003ca href=\"http://oolonek.github.io/ISDB/\"\u003ehttp://oolonek.github.io/ISDB/\u003c/a\u003e for associated spectral matching scripts\u003c/p\u003e\n\n\u003cp\u003eLOTUS Initiative initially described in\u0026nbsp;\u003ca href=\"https://doi.org/10.7554/eLife.70780\"\u003ehttps://doi.org/10.7554/eLife.70780\u003c/a\u003e\u003c/p\u003e\n\n\u003cp\u003e\u0026nbsp;\u003c/p\u003e\n\n\u003cp\u003e\u0026nbsp;\u003c/p\u003e')
+        identifier = json_load.get('identifier', '')
+        version = json_load.get('version', '')
+        version = f"Version {version}" if version else ''
+        date = json_load.get('datePublished', '')
+        if identifier:
+            description = f"<a href='{identifier}'>{identifier}</a>\n{description}"
+        if date:
+            description = f"({date}) {description}"
+        if version:
+            description = f"{version} {description}"
 
         hrefs = []
 
-        for distrib in json_load['distribution']:
-            if distrib['@type'] == 'DataDownload':
+        for distrib in json_load.get('distribution', []):
+            if distrib.get('@type', '') == 'DataDownload':
                 href = distrib['contentUrl']
-            hrefs.append(href)
-        yield "In-Silico Database", hrefs,\
-              f"Version {version} ({date}) <a href='{identifier}'>{identifier}</a>\n{description}"
+                if href:
+                    hrefs.append(href)
+        if hrefs:
+            yield "In-Silico Database", hrefs, description