Merge pull request #112 from USEPA/release_v1.1.3

Release v1.1.3

lciafmt/__init__.py

@@ -129,11 +129,13 @@ def clear_cache():
     cache.clear()
 
 
-def to_jsonld(df: pd.DataFrame, zip_file: str, write_flows=False):
+def to_jsonld(df: pd.DataFrame, zip_file: str, write_flows=False, **kwargs):
     """Generate a JSONLD file of the methods passed as DataFrame."""
     util.log.info(f"write JSON-LD package to {zip_file}")
     with jsonld.Writer(zip_file) as w:
-        w.write(df, write_flows)
+        w.write(df, write_flows,
+                preferred_only=kwargs.get('preferred_only', False),
+                )
 
 
 def map_flows(df: pd.DataFrame, system=None, mapping=None,

lciafmt/data/lcia.bib

@@ -16,3 +16,32 @@ @article{huijbregts_recipe_2017
 	year = {2017},
 	DOI = {10.1007/s11367-016-1246-y}
 }
+
+@incollection{forster_changes_2007,
+	address = {Cambridge, UK and New York, NY},
+	title = {Changes in {Atmospheric} {Constituents} and in {Radiative} {Forcing}},
+	booktitle = {Climate {Change} 2007: {The} {Physical} {Science} {Basis}. {Contribution} of {Working} {Group} {I} to the {Fourth} {Assessment} {Report} of the {Intergovernmental} {Panel} on {Climate} {Change}},
+	publisher = {Cambridge University Press},
+	author = {Forster, Piers and Ramaswamy, Venkatachalam},
+	year = {2007},
+}
+
+@incollection{myhre_anthropogenic_2013,
+	address = {Cambridge, UK and New York, NY},
+	title = {Anthropogenic and {Natural} {Radiative} {Forcing}},
+	url = {https://archive.ipcc.ch/pdf/assessment-report/ar5/wg1/WG1AR5_Chapter08_FINAL.pdf},
+	booktitle = {Climate {Change} 2013: {The} {Physical} {Science} {Basis}. {Contribution} of {Working} {Group} {I} to the {Fifth} {Assessment} {Report} of the {Intergovernmental} {Panel} on {Climate} {Change}},
+	publisher = {Cambridge University Press},
+	author = {Myhre, Gunnar and Shindell, Drew},
+	year = {2013},
+}
+
+@incollection{smith_earths_2021,
+	address = {Cambridge, UK and New York, NY},
+	title = {The {Earth}'s {Energy} {Budget}, {Climate} {Feedbacks}, and {Climate} {Sensitivity} {Supplementary} {Material}},
+	url = {https://www.ipcc.ch/report/ar6/wg1/downloads/report/IPCC_AR6_WGI_Chapter07_SM.pdf},
+	booktitle = {Climate {Change} 2021: {The} {Physical} {Science} {Basis}. {Contribution} of {Working} {Group} {I} to the {Sixth} {Assessment} {Report} of the {Intergovernmental} {Panel} on {Climate} {Change}},
+	publisher = {Cambridge University Press},
+	author = {Smith, Chris and Nicholls, Zebedee R. J. and Armour, Kyle and Collins, William and Forster, Piers and Meinshausen, Malte and Palmer, Matthew D. and Watanabe, Masahiro},
+	year = {2021},
+}

lciafmt/data/methods.json

@@ -61,6 +61,10 @@
     "path": "ipcc",
     "case_insensitivity": "False",
     "url": "https://github.com/USEPA/LCIAformatter/blob/master/lciafmt/data/IPCC_GWP_values.csv",
+    "bib_id": {"AR6": "smith_earths_2021",
+               "AR5": "myhre_anthropogenic_2013",
+               "AR4": "forster_changes_2007"
+                },
     "citation": "Forster and Ramaswamy 2007 (AR4), Myhre and Shindell 2013 (AR5), Forster and Storelvmo 2021 (AR6)",
     "source_type": "csv"
   }

lciafmt/jsonld.py

@@ -17,6 +17,7 @@
 
 from esupy.util import make_uuid
 from esupy.bibtex import generate_sources
+import fedelemflowlist
 from .util import is_non_empty_str, generate_method_description,\
     log, pkg_version_number, datapath, check_as_class
 
@@ -30,6 +31,7 @@ def __init__(self, zip_file: str):
         self.__indicators = {}
         self.__flows = {}
         self.__sources = {}
+        self.__sources_to_write = {}
         self.__bibids = {}
         self.__bibpath = datapath / 'lcia.bib'
 
@@ -39,19 +41,32 @@ def __enter__(self):
     def __exit__(self, exc_type, exc_val, exc_tb):
         self.__writer.close()
 
-    def write(self, df: pd.DataFrame, write_flows=False):
+    def write(self, df: pd.DataFrame, write_flows=False, preferred_only=False):
         if 'source_method' not in df:
             df['source_method'] = df['Method']
         if 'source_indicator' not in df:
             df['source_indicator'] = ''
         if 'category' not in df:
             df['category'] = df['Method']
 
-        for method in df['source_method'].unique():
+        methods = pd.unique(
+                df[['Method', 'source_method']].values.ravel('K'))
+        indicators = pd.unique(
+                df[['Indicator', 'source_indicator']].values.ravel('K'))
+
+        # identify all relevant bib_ids and sources
+        for method in methods:
             m = check_as_class(method)
+            if isinstance(m, str):
+                # not a recognized method, so no bib_id
+                continue
             bib = m.get_metadata().get('bib_id')
             if bib:
-                self.__bibids[bib] = m.value
+                if isinstance(bib, str):
+                    self.__bibids[bib] = m.value
+                elif isinstance(bib, dict):
+                    for k,v in bib.items():
+                        self.__bibids[v] = f'{m.value} {k}'
         for i in generate_sources(self.__bibpath, self.__bibids):
             self.__sources[i.id] = i
 
@@ -69,10 +84,19 @@ def write(self, df: pd.DataFrame, write_flows=False):
         dicts = [
             self.__indicators,
             self.__methods,
-            self.__sources
+            self.__sources_to_write
         ]
         if write_flows:
-            dicts.append(self.__flows)
+            log.info("writing flows from the fedelemflowlist ...")
+            flowlist = fedelemflowlist.get_flows(preferred_only)
+            flow_dict = self.__flows
+            flows = flowlist.query('`Flow UUID` in @flow_dict.keys()')
+            if preferred_only:
+                log.info("writing only preferred flows ...")
+            elif len(flows) != len(flow_dict):
+                log.warning("not all flows written...")
+            fedelemflowlist.write_jsonld(flows, path=None,
+                                         zw = self.__writer)
         for d in dicts:
             for v in d.values():
                 self.__writer.write(v)
@@ -100,9 +124,14 @@ def __indicator(self, row) -> o.ImpactCategory:
                                                       row['source_indicator'])
         ind.impact_factors = []
         ind.version = pkg_version_number
-        source = self._return_source(row['Method'])
+        source = (self._return_source(row['source_method']) or
+                  self._return_source(row['Method'] + ' ' +
+                                      row['Indicator']) or
+                  self._return_source(row['source_method'] + ' ' +
+                                      row['source_indicator']))
         if source:
             ind.source = source.to_ref()
+            self.__sources_to_write[source.id] = source
         self.__indicators[uid] = ind
 
         method = self.__method(row)
@@ -121,6 +150,10 @@ def __method(self, row) -> o.ImpactMethod:
         m.id = uid
         m.name = row['Method']
         m.version = pkg_version_number
+        source = self._return_source(row['Method'])
+        if source:
+            m.source = source.to_ref()
+            self.__sources_to_write[source.id] = source
         m.impact_categories = []
         m.description = generate_method_description(row['Method'])
         self.__methods[uid] = m
@@ -160,6 +193,6 @@ def __flow(self, row):
 
     def _return_source(self, name):
         for uid, s in self.__sources.items():
-            if s.name == name:
+            if s.name == name or name.startswith(s.name):
                 return s
         return None

lciafmt/util.py

@@ -21,7 +21,7 @@
 
 
 # set version number of package, needs to be updated with setup.py
-pkg_version_number = '1.1.2'
+pkg_version_number = '1.1.3'
 MODULEPATH = Path(__file__).resolve().parent
 datapath = MODULEPATH / 'data'
 
@@ -272,7 +272,8 @@ def download_method(method_id):
     download_from_remote(meta, paths)
 
 
-def save_json(method_id, mapped_data, method=None, name='', write_flows=False):
+def save_json(method_id, mapped_data, method=None, name='',
+              write_flows=False, **kwargs):
     """Save a method as json file in the outputpath.
 
     :param method_id: class Method
@@ -288,12 +289,13 @@ def save_json(method_id, mapped_data, method=None, name='', write_flows=False):
         filename = name
     if method is not None:
         filename = method.replace('/', '_')
-        mapped_data = mapped_data[mapped_data['Method'] == method]
+        mapped_data = mapped_data.query('Method == @method').reset_index(drop=True)
     path = OUTPUTPATH / meta.category
     mkdir_if_missing(OUTPUTPATH)
     json_pack = path / f'{filename}_json_v{meta.tool_version}.zip'
     json_pack.unlink(missing_ok=True)
-    lciafmt.to_jsonld(mapped_data, json_pack, write_flows=write_flows)
+    lciafmt.to_jsonld(mapped_data, json_pack, write_flows=write_flows,
+                      **kwargs)
 
 
 def compare_to_remote(local_df, method_id):

requirements.txt

@@ -1,4 +1,4 @@
-git+https://github.com/USEPA/Federal-LCA-Commons-Elementary-Flow-List.git#egg=fedelemflowlist
+git+https://github.com/USEPA/fedelemflowlist.git#egg=fedelemflowlist
 git+https://github.com/USEPA/esupy.git#egg=esupy
 olca-schema>=0.0.11
 pandas>=0.23

setup.py

@@ -2,13 +2,13 @@
 
 setup(
     name="lciafmt",
-    version="1.1.2",
+    version="1.1.3",
     packages=["lciafmt"],
     package_dir={'lciafmt': 'lciafmt'},
     package_data={'lciafmt': ["data/*.*"]},
     include_package_data=True,
     python_requires=">=3.9",
-    install_requires=["fedelemflowlist @ git+https://github.com/USEPA/Federal-LCA-Commons-Elementary-Flow-List.git#egg=fedelemflowlist",
+    install_requires=["fedelemflowlist @ git+https://github.com/USEPA/fedelemflowlist.git#egg=fedelemflowlist",
                       "esupy @ git+https://github.com/USEPA/esupy.git#egg=esupy",
                       "olca-schema>=0.0.11",
                       "pandas>=0.22",

tests/test_generate_methods.py

@@ -41,7 +41,8 @@ def test_method_write_json():
     lciafmt.util.save_json(method_id = method_id,
                            name = 'test_TRACI',
                            mapped_data = method,
-                           write_flows=True)
+                           write_flows=True,
+                           preferred_only=True)
     # Test FEDEFL Inventory
     method_id = lciafmt.Method.FEDEFL_INV
     method = lciafmt.get_mapped_method(method_id = method_id,