Merge branch 'develop' into flow_updates

USEPA · Nov 6, 2024 · 6b21498 · 6b21498
2 parents 64352d7 + 06ef94f
commit 6b21498
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diff --git a/.zenodo.json b/.zenodo.json
@@ -0,0 +1,28 @@
+{
+    "description": "Generates and provides a standardized elementary flow list for use in life cycle assessment (LCA) data as well as mappings to convert data from other sources.", 
+    "license": "MIT",
+    "title": "fedelemflowlist",
+    "upload_type": "software", 
+    "creators": [
+        {
+            "affiliation": "US Environmental Protection Agency", 
+            "name": "Wesley Ingwersen",
+            "orcid": "https://orcid.org/0000-0002-9614-701X"
+        }, 
+        {
+            "affiliation": "Eastern Research Group, Inc.", 
+            "name": "Ben Young",
+            "orcid": "https://orcid.org/0000-0001-6276-8670"
+        }, 
+        {
+            "affiliation": "Eastern Research Group, Inc.", 
+            "name": "Ashley Edelen"
+        },
+        {
+            "affiliation": "Eastern Research Group, Inc.", 
+            "name": "Sarah Cashman",
+            "orcid": "https://orcid.org/0000-0001-9859-9557"
+        }
+    ],
+    "access_right": "open"
+}
diff --git a/Jupyter/README.md b/Jupyter/README.md
@@ -1,3 +1,3 @@
 # Create a mapping file for use in openLCA through Binder
 
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/USEPA/Federal-LCA-Commons-Elementary-Flow-List/HEAD?labpath=Jupyter%2Frun_mappings.ipynb)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/USEPA/fedelemflowlist/HEAD?labpath=Jupyter%2Frun_mappings.ipynb)
diff --git a/Jupyter/run_mappings.ipynb b/Jupyter/run_mappings.ipynb
@@ -15,25 +15,24 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "## Step 1\n",
     "import pandas as pd\n",
     "import fedelemflowlist\n",
     "from fedelemflowlist.globals import flowmappingpath, flowmapping_fields\n",
     "import os\n",
+    "from pathlib import Path\n",
     "import ipywidgets as widgets\n",
     "from IPython.display import display, FileLink\n",
     "\n",
     "if not os.path.exists('./scratch'):\n",
     "    os.mkdir('./scratch')\n",
     "\n",
     "uploader = widgets.FileUpload(\n",
-    "     accept   = '.csv'\n",
-    "    ,multiple = False\n",
+    "     accept   = '.csv',\n",
+    "     multiple = False\n",
     ")\n",
     "\n",
     "display(uploader)"
@@ -59,14 +58,14 @@
     "if not uploader.value:\n",
     "    raise ValueError('Input Excel file is required to continue. Make sure to select the Upload button above before continuing.')\n",
     "\n",
-    "input_file = next(iter(uploader.value))\n",
-    "input_full = r\"./scratch/\" + input_file\n",
+    "input_file = uploader.value[0]\n",
+    "input_full = r\"./scratch/\" + input_file['name']\n",
     "\n",
     "if os.path.exists(input_full):\n",
     "    os.remove(input_full)\n",
     "    \n",
     "with open(input_full,\"wb\") as fp:\n",
-    "    fp.write(uploader.value[input_file]['content'])\n",
+    "    fp.write(input_file['content'])\n",
     "\n",
     "mapping = pd.read_csv(input_full)\n",
     "mapping_length = len(mapping)\n",
@@ -126,17 +125,27 @@
     "#Subset all flows to get just those used in selected mapping\n",
     "flows_used_in_mapping =  pd.merge(all_flows,mapping_flow_uuids)\n",
     "\n",
-    "fedelemflowlist.write_jsonld(flows_used_in_mapping,output_full,mapping_w_conversion)\n",
-    "print(\"mapping file created as json\")\n",
-    "download = FileLink(output_full,result_html_prefix=\"Click here to download: \")\n",
-    "display(download)\n"
+    "fedelemflowlist.write_jsonld(flows = flows_used_in_mapping,\n",
+    "                             path = Path(output_full),\n",
+    "                             mappings = mapping_w_conversion)\n",
+    "print(\"mapping file created as json\")\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%%html\n",
+    "<a href=\"scratch/flows_w_mappings.zip\" download=\"flows_w_mappings.zip\">Download Mapping File</a>"
    ]
   }
  ],
  "metadata": {
   "celltoolbar": "Tags",
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -150,7 +159,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.5"
+   "version": "3.12.3"
   }
  },
  "nbformat": 4,

diff --git a/README.md b/README.md
@@ -1,5 +1,6 @@
 <!-- badges: start -->
 [![Applied Sciences](http://img.shields.io/badge/Applied%20Sciences-10.3390/app12199687-blue.svg)](https://doi.org/10.3390/app12199687)
+[![DOI](https://zenodo.org/badge/120324037.svg)](https://zenodo.org/doi/10.5281/zenodo.6604309)
 <!-- badges: end -->
 
 # fedelemflowlist
@@ -12,9 +13,9 @@
  and a [Flow Mapping](./format%20specs/FlowMapping.md) are defined and provided by `fedelemflowlist`.
   They are implemented as [pandas](https://pandas.pydata.org/) dataframes.
    Standard formats are also described for the input files used in building the flow list, and implemented as .csv files
-   in the [input](https://github.com/USEPA/Federal-LCA-Commons-Elementary-Flow-List/tree/master/fedelemflowlist/input) directory.  
+   in the [input](https://github.com/USEPA/fedelemflowlist/tree/master/fedelemflowlist/input) directory.  
 
- The version of the package (see [Releases](https://github.com/USEPA/Federal-LCA-Commons-Elementary-Flow-List/releases/))
+ The version of the package (see [Releases](https://github.com/USEPA/fedelemflowlist/releases/))
  corresponds to the version of the flow list that it provides. The complete or 'master' list contains all valid flows,
   where the 'preferred' flows are the recommended flows for use in LCA data.
 
@@ -25,7 +26,7 @@ The background and methodology behind creation of the flow list, as well as a su
  ['The Federal LCA Commons Elementary Flow List: Background, Approach, Description and Recommendations for Use'](https://cfpub.epa.gov/si/si_public_record_report.cfm?Lab=NRMRL&dirEntryId=347251).
 Definitions for terms used in the flow list can be found in on EPA's Terminology Services in the [Federal LCA Commons Elementary Flow List for Life Cycle Assessment vocabulary](https://sor.epa.gov/sor_internet/registry/termreg/searchandretrieve/glossariesandkeywordlists/search.do?details=&vocabName=FEDEFL). 
 
-See the [Wiki](https://github.com/USEPA/Federal-LCA-Commons-Elementary-Flow-List/wiki/) for installation, more info on repository
+See the [Wiki](https://github.com/USEPA/fedelemflowlist/wiki/) for installation, more info on repository
 contents, use examples, and for instructions on how to contribute to the flow list through additions or edits to flows or flow mappings.
 
 ## Disclaimer

diff --git a/fedelemflowlist/__init__.py b/fedelemflowlist/__init__.py
@@ -16,7 +16,7 @@
 from fedelemflowlist.subset_list import subsets
 import fedelemflowlist.subset_list as subset_list
 
-def get_flows(preferred_only=None, subset=None, download_if_missing=True):
+def get_flows(preferred_only=False, subset=None, download_if_missing=True):
     """Gets a flow list in a standard format
 
     Returns the full master flow list unless preferred flows is lists
@@ -66,7 +66,7 @@ def get_flowmapping(source=None):
     return flowmappings
 
 
-def write_jsonld(flows, path: Path, mappings=None):
+def write_jsonld(flows, path: Path, mappings=None, **kwargs):
     """ Writes a standard openLCA JSON-LD zip archive with elementary flows and optionally
      flowmappings
 
@@ -76,7 +76,7 @@ def write_jsonld(flows, path: Path, mappings=None):
     :return: writes out .zip file
     """
     writer = jsonld.Writer(flow_list=flows, flow_mapping=mappings)
-    writer.write_to(path)
+    writer.write_to(path, zw=kwargs.get('zw'))
 
 def get_alt_conversion():
     """returns a dataframe of all flowables with altunits and alt conversion factors

diff --git a/fedelemflowlist/contexts.py b/fedelemflowlist/contexts.py
@@ -33,7 +33,7 @@
 context_list_na_removed = list()
 for index, row in contexts.iterrows():
     pattern = [compartment_classes[x] for x in range(0, max_compartment_classes)
-               if str(row[x]) != 'nan']
+               if str(row.iloc[x]) != 'nan']
     pattern = ','.join(pattern)
     context_patterns.append(pattern)
     row_list = row.values

diff --git a/fedelemflowlist/flowmapping/EIA_MER.csv b/fedelemflowlist/flowmapping/EIA_MER.csv
@@ -9,3 +9,7 @@ EIA_MER,Primary energy - biomass,,resource,MJ,=,0.0612,Biomass,7feeb363-fbeb-37a
 EIA_MER,Primary energy - hydro,,resource/in water,MJ,=,1,"Energy, hydro",5af7a834-bf92-32eb-a0b2-2f2dcdc9f3d9,resource/water,MJ,Young,Edelen,2/2/2021
 EIA_MER,Primary energy - solar,,resource/in air,MJ,=,1,"Energy, solar",4d1571a6-ffff-3a36-82df-224ed975a094,resource/air,MJ,Young,Edelen,2/2/2021
 EIA_MER,Primary energy - wind,,resource/in air,MJ,=,1,"Energy, wind",35962866-662b-3817-a2a7-39375c7e6a3c,resource/air,MJ,Young,Edelen,2/2/2021
+EIA_MER,Coal,,resource,Quadrillion Btu,=,1.06E+12,Coal,39a07dad-33e8-3644-b6a5-2054c3d53fa9,resource/ground,MJ,Young,,5/15/2024
+EIA_MER,"Natural Gas, Dry",,resource,Quadrillion Btu,=,1.06E+12,Natural gas,ae604834-c49a-3ebb-b15b-06e6e89e427e,resource/air,MJ,Young,,5/15/2024
+EIA_MER,Natural Gas Plant Liquids,,resource,Quadrillion Btu,=,1.06E+12,Natural gas,ae604834-c49a-3ebb-b15b-06e6e89e427e,resource/air,MJ,Young,,5/15/2024
+EIA_MER,Crude Oil,,resource,Quadrillion Btu,=,1.06E+12,Crude oil,4aca0c2c-6e1a-3d90-956c-7141ca8932ce,resource/water,MJ,Young,,5/15/2024
diff --git a/fedelemflowlist/flowmapping/GHGI.csv b/fedelemflowlist/flowmapping/GHGI.csv
@@ -57,6 +57,8 @@ GHGI,HFC-236fa,,air,MMTCO2e,=,101937,HFC-236fa,32057bc6-6839-3dbc-b33d-5b72e542e
 GHGI,HFC-32,,air,MMTCO2e,=,1481481,HFC-32,747fa9a4-559b-37a4-ac9b-5ca630274739,emission/air,kg,Bell,,10/20/2022
 GHGI,NF3,,air,MTCO2e,=,0.05814,Nitrogen trifluoride,80d4ef62-ca97-37d6-87ac-83233956c063,emission/air,kg,Bell,,9/28/2022
 GHGI,SF6,,air,MTCO2e,=,0.04386,Sulfur hexafluoride,8334c424-1603-3274-bec1-15a7bd5c8e86,emission/air,kg,Bell,,9/28/2022
+GHGI,N2O,,air,MTCO2e,=,3.356,Nitrous oxide,cfee0524-7ad6-300b-b050-6249135a2492,emission/air,kg,Young,,6/19/2024
+GHGI,HFE,,air,MTCO2e,=,1000,"HFCs and PFCs, unspecified",n.a.,emission/air,kg CO2e,Young,,6/19/2024
 GHGI,PFC-116 <Perfluoroethane>,,air,MMT CO2e,=,81967,Hexafluoroethane,b24a2de2-da9b-30b8-ae33-3d4ffa692029,emission/air,kg,Young,,10/18/2022
 GHGI,PFC-14 <Perfluoromethane>,,air,MMT CO2e,=,135318,Carbon tetrafluoride,fbfa508b-f3c9-3977-a47d-1138e96914a3,emission/air,kg,Young,,10/18/2022
 GHGI,C2F6,,air,MT,=,1000,Hexafluoroethane,b24a2de2-da9b-30b8-ae33-3d4ffa692029,emission/air,kg,Bell,,11/16/2022
@@ -81,3 +83,10 @@ GHGI,Unspecified mix of PFCs,,air,MMT CO2e,=,1000000000,"HFCs and PFCs, unspecif
 GHGI,Unspecified mix of HFCs and PFCs,,air,MMT CO2e,=,1000000000,"HFCs and PFCs, unspecified",n.a.,emission/air,kg CO2e,Young,,4/25/2023
 GHGI,HFC-41,,air,MMT CO2e,=,1000000000,"HFCs and PFCs, unspecified",n.a.,emission/air,kg CO2e,Young,,4/25/2023
 GHGI,C4F6,,air,MMT CO2e,=,1000000000,"HFCs and PFCs, unspecified",n.a.,emission/air,kg CO2e,Young,,4/25/2023
+GHGI,CO2,,air,MT CO2e (AR5-20),,1000,Carbon dioxide,b6f010fb-a764-3063-af2d-bcb8309a97b7,emission/air,kg,Young,,6/19/2024
+GHGI,CH4,,air,MT CO2e (AR5-20),,11.9047619,Methane,aab83476-ec6c-3742-af85-15d320b7ce80,emission/air,kg,Young,,6/19/2024
+GHGI,N2O,,air,MT CO2e (AR5-20),,3.78788,Nitrous oxide,cfee0524-7ad6-300b-b050-6249135a2492,emission/air,kg,Young,,6/19/2024
+GHGI,HFCs,,air,MT CO2e (AR5-20),,1000,"HFCs and PFCs, unspecified",n.a.,emission/air,kg CO2e,Young,,6/19/2024
+GHGI,SF6,,air,MT CO2e (AR5-20),,0.057143,Sulfur hexafluoride,8334c424-1603-3274-bec1-15a7bd5c8e86,emission/air,kg,Young,,6/19/2024
+GHGI,NF3,,air,MT CO2e (AR5-20),,0.078125,Nitrogen trifluoride,80d4ef62-ca97-37d6-87ac-83233956c063,emission/air,kg,Young,,6/19/2024
+GHGI,PFCs,,air,MT CO2e (AR5-20),,1000,"HFCs and PFCs, unspecified",n.a.,emission/air,kg CO2e,Young,,6/19/2024