remade __iterate_function. Should fix enumeration issue 63

replaced twine with poetry in pypi build
chalklab · Aug 9, 2021 · 6d2730b · 6d2730b
1 parent 08f09a9
commit 6d2730b
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Showing 6 changed files with 141 additions and 90 deletions.
diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
@@ -34,6 +34,7 @@ jobs:
 
       - name: Build Python package and Upload to TestPyPi
         shell: bash -l {0}
+        if: ${{ matrix.python-version == env.PYTHON_MAIN_VERSION }}
         env:
           TEST_PYPI_TOKEN_PASSWORD: ${{ secrets.TEST_PYPI_TOKEN }}
         run: |
@@ -64,6 +65,6 @@ jobs:
         env:
           PYPI_TOKEN_PASSWORD: ${{ secrets.PYPI_TOKEN }}
         run: |
-          pip install wheel twine
-          python setup.py sdist bdist_wheel
-          twine upload --username "__token__" --password $PYPI_TOKEN_PASSWORD dist/*
+          poetry update
+          poetry build
+          poetry publish --username "__token__" --password $TEST_PYPI_TOKEN_PASSWORD
diff --git a/example.py b/example.py
@@ -328,4 +328,4 @@
 lic = 'https://creativecommons.org/licenses/by-nc-nd/4.0/'
 example.rights(holder, lic)
 
-print(json.dumps(example.output, ensure_ascii=False))
+print(json.dumps(example.output, indent=4, ensure_ascii=False))
diff --git a/example2.py b/example2.py
@@ -294,9 +294,9 @@
 
 example.dataseries([dataser1])
 
-example.datagroup(
-    [{"@id": "datagroup", "@type": "sdo:datagroup",
-      "datapoints": ["datapoint"]}])
+# example.datagroup(
+#     [{"@id": "datagroup", "@type": "sdo:datagroup",
+#       "datapoints": ["datapoint"]}])
 
 # add source
 src = {'citation': 'Chalk Research Group',

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "SciDataLib"
-version = "0.2.3.1"
+version = "0.2.3.2"
 description = "Python library for development of SciData JSON-LD files"
 authors = [
     "Stuart Chalk <schalk@unf.edu>",

diff --git a/scidatalib/scidata.py b/scidatalib/scidata.py
@@ -415,38 +415,29 @@ def evaluation(self, evaln: str) -> str:
 
     def aspects(self, aspects: list) -> list:
         """Add to or replace the aspects of the file"""
-        cnt_index = {}
 
         scidata: dict = self.meta['@graph']['scidata']
         meth: dict = scidata['methodology']
         curr_aspects: list = meth['aspects']
-
-        for item in aspects:
-            cat_index = {}
-            item, category, count, cat_index = self.__iterate_function(
-                item, 1, cnt_index, cat_index)
-            cnt_index[category] = count
+        uidindex = []
+        for listentry in aspects:
+            item, uidindex = self.__iterate_function2(listentry, uidindex)
             curr_aspects.append(item)
 
         meth['aspects'] = curr_aspects
-
         scidata['methodology'] = meth
         self.meta['@graph']['scidata'] = scidata
         return curr_aspects
 
     def facets(self, facets: list) -> list:
         """Add to or replace the facets of the file"""
-        cnt_index = {}
 
         scidata: dict = self.meta['@graph']['scidata']
         system: dict = scidata['system']
         curr_facets: list = system['facets']
-
-        for item in facets:
-            cat_index = {}
-            item, category, count, cat_index = self.__iterate_function(
-                item, 1, cnt_index, cat_index)
-            cnt_index[category] = count
+        uidindex = []
+        for listentry in facets:
+            item, uidindex = self.__iterate_function2(listentry, uidindex)
             curr_facets.append(item)
 
         system['facets'] = curr_facets
@@ -472,21 +463,17 @@ def scope(self, scope: [str, list]) -> str:
 
     def attribute(self, attributes: list) -> list:
         """Add one or more attributes"""
-        cnt_index = {}
 
         scidata: dict = self.meta['@graph']['scidata']
         dataset: dict = scidata['dataset']
         if 'attribute' in dataset.keys():
             curr_attributes: list = dataset['attribute']
         else:
             curr_attributes = []
+        uidindex = []
 
-        for item in attributes:
-            cat_index = {}
-            cnt_index = {'attribute': len(curr_attributes)}
-            item, category, count, cat_index = self.__iterate_function(
-                item, 1, cnt_index, cat_index)
-            cnt_index[category] = count
+        for listentry in attributes:
+            item, uidindex = self.__iterate_function2(listentry, uidindex)
             curr_attributes.append(item)
 
         dataset['attribute'] = curr_attributes
@@ -496,21 +483,17 @@ def attribute(self, attributes: list) -> list:
 
     def datapoint(self, points: list) -> list:
         """Add one or more datapoints"""
-        cnt_index = {}
 
         scidata: dict = self.meta['@graph']['scidata']
         dataset: dict = scidata['dataset']
         if 'datapoint' in dataset.keys():
             curr_points: list = dataset['datapoint']
         else:
             curr_points = []
+        uidindex = []
 
-        for item in points:
-            cat_index = {}
-            cnt_index = {'datapoint': len(curr_points)}
-            item, category, count, cat_index = self.__iterate_function(
-                item, 1, cnt_index, cat_index)
-            cnt_index[category] = count
+        for listentry in points:
+            item, uidindex = self.__iterate_function2(listentry, uidindex)
             curr_points.append(item)
 
         dataset['datapoint'] = curr_points
@@ -520,21 +503,17 @@ def datapoint(self, points: list) -> list:
 
     def dataseries(self, series: list) -> list:
         """Add one or more datapoints"""
-        cnt_index = {}
 
         scidata: dict = self.meta['@graph']['scidata']
         dataset: dict = scidata['dataset']
         if 'dataseries' in dataset.keys():
             curr_series: list = dataset['dataseries']
         else:
             curr_series = []
+        uidindex = []
 
-        for item in series:
-            cat_index = {}
-            cnt_index = {'dataseries': len(curr_series)}
-            item, category, count, cat_index = self.__iterate_function(
-                item, 1, cnt_index, cat_index)
-            cnt_index[category] = count
+        for listentry in series:
+            item, uidindex = self.__iterate_function2(listentry, uidindex)
             curr_series.append(item)
 
         dataset['dataseries'] = curr_series
@@ -722,6 +701,58 @@ def __make_context(self) -> dict:
         self.meta["@context"] = c + [n, b]
         return self.meta["@context"]
 
+    def __iterate_function2(self, it, uidindex, uid=False):
+
+        if isinstance(it, str):
+            self.__addid(it)
+            return it, uidindex
+        prev_uid = uid
+
+        # Set the category
+        if '@id' in it:
+            category = it['@id']
+        elif 'descriptors' in it or 'identifiers' in it:
+            category = 'compound'
+        else:
+            category = 'undefined'
+
+        if prev_uid:
+            uid = prev_uid + category + '/' + str(1) + '/'
+        else:
+            uid = category + '/' + str(1) + '/'
+
+        def enumuid(uid):
+            if uid in uidindex:
+                uidsplit = uid.rsplit('/', 2)
+                uid = uidsplit[0] + '/' + str(int(uidsplit[1]) + 1) + '/'
+            return uid
+
+        while uid in uidindex:
+            uid = enumuid(uid)
+        uidindex.append(uid)
+
+        temp: dict = {'@id': uid, '@type': 'sdo:' + category}
+
+        for key, value in it.items():
+            if key != '@id':
+
+                if isinstance(value, list):
+                    listuid = uid
+                    for i, listentry in enumerate(value):
+                        value[i], uidindex = self.__iterate_function2(
+                            listentry, uidindex, listuid)
+                    temp[key] = value
+
+                elif isinstance(value, dict):
+                    temp[key], uidindex = self.__iterate_function2(
+                        value, uidindex, uid)
+
+                else:
+                    temp[key] = value
+                    self.__addid(value)
+
+        return temp, uidindex
+
     def __iterate_function(self, it, level, cnt_index, cat_index):
         """
         Recursive function to iteratively update @id, @type, and categories
@@ -830,12 +861,22 @@ def output(self) -> dict:
             for key in list(self.meta['@graph']['scidata'][sect]):
                 if not self.meta['@graph']['scidata'][sect][key]:
                     del self.meta['@graph']['scidata'][sect][key]
-        if not self.meta['@graph']['scidata'].get('methodology', {}).get('aspects', False):
+        if not self.meta['@graph']['scidata'].get(
+                'methodology',
+                {}).get(
+                'aspects',
+                False):
             del self.meta['@graph']['scidata']['methodology']
-        if not self.meta['@graph']['scidata'].get('system', {}).get('facets', False):
+        if not self.meta['@graph']['scidata'].get(
+                'system',
+                {}).get(
+                'facets',
+                False):
             del self.meta['@graph']['scidata']['system']
-        if not self.meta['@graph']['scidata'].get('dataset', {}).get('datapoint', False):
-            if not self.meta['@graph']['scidata'].get('dataset', {}).get('dataseries', False):
+        if not self.meta['@graph']['scidata'].get(
+                'dataset', {}).get('datapoint', False):
+            if not self.meta['@graph']['scidata'].get(
+                    'dataset', {}).get('dataseries', False):
                 del self.meta['@graph']['scidata']['dataset']
         self.__addtoc()
 

diff --git a/tests/test_scidata.py b/tests/test_scidata.py
@@ -158,8 +158,10 @@ def test_aspects(sd):
 
 
 def test_facets(sd):
-    sd.namespaces({'obo': 'http://purl.obolibrary.org/obo/',
-        "sdo": "https://stuchalk.github.io/scidata/ontology/scidata.owl#"})
+    sd.namespaces({
+        'obo': 'http://purl.obolibrary.org/obo/',
+        "sdo": "https://stuchalk.github.io/scidata/ontology/scidata.owl#"
+    })
     compd = {
         "@id": "substance",
         "title": "3 ppm cyanide standard solution",
@@ -241,46 +243,53 @@ def test_facets(sd):
            "aggregation": "sub:aq",
            "mixtype": "sub:homogeneousSolution",
            "phase": "sub:liquid",
-           "constituents": [{"@id": "substance/1/constituent/1/",
-                             "@type": "sdo:constituent",
-                             "source": "compound/1/",
-                             "role": "chm:analyte",
-                             "properties": [{"@id": "substance/1/constituent/1/property/1/",
-                                             "@type": "sdo:property",
-                                             "quantity": "mass of substance per volume",
-                                             "property": "Concentration (w/v)",
-                                             "value": {"@id": "substance/1/constituent/1/property/1/value/1/",
-                                                       "@type": "sdo:value",
-                                                       "number": 2.99,
-                                                       "unitref": "qudt:PPM"}},
-                                            {"@id": "substance/1/constituent/1/property/2/",
-                                             "@type": "sdo:property",
-                                             "quantity": "volume",
-                                             "property": "Volume of solution",
-                                             "value": {"@id": "substance/1/constituent/1/property/2/value/1/",
-                                                       "@type": "sdo:value",
-                                                       "number": 100.0,
-                                                       "unitref": "qudt:MilliL"}}]},
-                            {"@id": "substance/1/constituent/2/",
-                             "@type": "sdo:constituent",
-                             "source": "compound/2/",
-                             "role": "chm:reagent",
-                             "properties": [{"@id": "substance/1/constituent/2/property/1/",
-                                             "@type": "sdo:property",
-                                             "quantity": "mass of substance per volume",
-                                             "property": "Concentration (w/v)",
-                                             "value": {"@id": "substance/1/constituent/2/property/1/value/1/",
-                                                       "@type": "sdo:value",
-                                                       "number": 2.99,
-                                                       "unitref": "qudt:PPM"}},
-                                            {"@id": "substance/1/constituent/2/property/2/",
-                                             "@type": "sdo:property",
-                                             "quantity": "volume",
-                                             "property": "Volume of solution",
-                                             "value": {"@id": "substance/1/constituent/2/property/2/value/1/",
-                                                       "@type": "sdo:value",
-                                                       "number": 100.0,
-                                                       "unitref": "qudt:MilliL"}}]}],
+           "constituents":
+           [{"@id": "substance/1/constituent/1/",
+             "@type": "sdo:constituent",
+             "source": "compound/1/",
+             "role": "chm:analyte",
+             "properties": [
+                 {"@id": "substance/1/constituent/1/property/1/",
+                  "@type": "sdo:property",
+                  "quantity": "mass of substance per volume",
+                  "property": "Concentration (w/v)",
+                  "value": {
+                      "@id": "substance/1/constituent/1/property/1/value/1/",
+                      "@type": "sdo:value",
+                      "number": 2.99,
+                      "unitref": "qudt:PPM"}},
+                 {"@id": "substance/1/constituent/1/property/2/",
+                  "@type": "sdo:property",
+                  "quantity": "volume",
+                  "property": "Volume of solution",
+                  "value": {
+                      "@id": "substance/1/constituent/1/property/2/value/1/",
+                      "@type": "sdo:value",
+                      "number": 100.0,
+                      "unitref": "qudt:MilliL"}}]},
+            {"@id": "substance/1/constituent/2/",
+             "@type": "sdo:constituent",
+             "source": "compound/2/",
+             "role": "chm:reagent",
+             "properties": [
+                 {"@id": "substance/1/constituent/2/property/1/",
+                  "@type": "sdo:property",
+                  "quantity": "mass of substance per volume",
+                  "property": "Concentration (w/v)",
+                  "value": {
+                      "@id": "substance/1/constituent/2/property/1/value/1/",
+                      "@type": "sdo:value",
+                      "number": 2.99,
+                      "unitref": "qudt:PPM"}},
+                 {"@id": "substance/1/constituent/2/property/2/",
+                  "@type": "sdo:property",
+                  "quantity": "volume",
+                  "property": "Volume of solution",
+                  "value": {
+                      "@id": "substance/1/constituent/2/property/2/value/1/",
+                      "@type": "sdo:value",
+                      "number": 100.0,
+                      "unitref": "qudt:MilliL"}}]}],
            "properties": [{"@id": "substance/1/property/1/",
                            "@type": "sdo:property",
                            "quantity": "volume",