added scidatapackage method. Automates calls to aspects, facets, and …

…datapoints methods and links datapoints to associated aspects and facets. See example.py for usage.
chalklab · Nov 2, 2021 · 8348cb1 · 8348cb1
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diff --git a/example.py b/example.py
@@ -297,5 +297,70 @@
 lic = 'https://creativecommons.org/licenses/by-nc-nd/4.0/'
 example.rights(holder, lic)
 
+
+package = [{
+        "aspects": [{
+                "@id": "assay",
+                "@type": "sdo:assay",
+                "description": "Inhibition of human ERG by MK499 binding assay",
+                "assay_organism": "Homo sapiens"
+            }],
+        "facets": [{
+                "@id": "compound",
+                "@type": "sdo:compound",
+                "mw_freebase": "491.52",
+                "full_molformula": "C26H26FN5O4",
+                "standard_inchi_key": "OINHUVBCKUJZAG-UHFFFAOYSA-N"
+            },{
+                "@id": "target",
+                "@type": "sdo:target",
+                "pref_name": "HERG",
+                "tax_id": 9606,
+                "organism": "Homo sapiens"
+            }],
+        "dataset": [{
+                "@id": "datapoint",
+                "@type": "sdo:datapoint",
+                "data": [{
+                        "@id": "datum",
+                        "@type": "sdo:exptdata",
+                        "type": "IC50",
+                        "value": "15.200000000000000000000000000000",
+                        "units": "uM"
+                    }]}]},
+    {
+        "aspects": [{
+                "@id": "assay",
+                "@type": "sdo:assay",
+                "description": "Inhibition of human ERG by MK499 binding assay",
+                "assay_organism": "Homo sapiens"
+            }],
+        "facets": [{
+                "@id": "compound",
+                "@type": "sdo:compound",
+                "mw_freebase": "491.52",
+                "full_molformula": "C26H26FN5O4",
+                "standard_inchi_key": "OINHUVBCKUJZAG-UHFFFAOYSA-N"
+            },{
+                "@id": "target",
+                "@type": "sdo:target",
+                "pref_name": "HERG",
+                "tax_id": 9606,
+                "organism": "Homo sapiens"
+            }],
+        "dataset": [{
+                "@id": "datapoint",
+                "@type": "sdo:datapoint",
+                "data": [{
+                        "@id": "datum",
+                        "@type": "sdo:exptdata",
+                        "type": "IC50",
+                        "value": "12.300000000000000000000000000000",
+                        "units": "uM"
+                    }]}]}]
+
+example.scidatapackage(package)
+
+
 # print(json.dumps(example.output, ensure_ascii=False))
 print(json.dumps(example.output, indent=4, ensure_ascii=False))
diff --git a/scidatalib/scidata.py b/scidatalib/scidata.py
@@ -610,6 +610,19 @@ def datagroup(self, group: list) -> list:
         self.meta['@graph']['scidata'] = scidata
         return new_group
 
+    def scidatapackage(self, package):
+        """Add a package of data where the datapoints are linked with the associated aspects and facets
+        package = [{'aspects':{},'facets':{},'datapoint':{}},{'aspects':{},'facets':{},'datapoint':{}}]"""
+        for packet in package:
+            packet['facets'] = self.facets(packet['facets'])
+            packet['aspects'] = self.aspects(packet['aspects'])
+            atfacet = [a_dict["@id"] for a_dict in packet['facets']]
+            ataspect = [a_dict["@id"] for a_dict in packet['aspects']]
+            for dp in packet['dataset']:
+                dp.update({'facets#': atfacet})
+                dp.update({'aspects#': ataspect})
+            self.datapoint(packet['dataset'])
+
     def sources(self, sources: list, replace=False) -> dict:
         """
         Add to or replace the source reference list