add gadi path to nci file

ModelAtlasofTheEarth · May 22, 2024 · 089ca20 · 089ca20
1 parent 4b4c778
commit 089ca20
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Showing 3 changed files with 12 additions and 7 deletions.
diff --git a/.github/scripts/config.py b/.github/scripts/config.py
@@ -3,9 +3,11 @@
 # Example of global parameters
 
 #DOIS
-MATE_DOI =     'http://dx.doi.org/10.25914/yrzp-g882'
-MATE_WEBSITE = 'https://mate.science/'
-MATE_GITHUB =  'https://github.com/ModelAtlasofTheEarth/'
+MATE_DOI          = 'http://dx.doi.org/10.25914/yrzp-g882'
+MATE_WEBSITE      = 'https://mate.science/'
+MATE_GITHUB       = 'https://github.com/ModelAtlasofTheEarth/'
+MATE_GADI         = '/g/data/nm08/MATE/'
+
 #MATE_THREDDS_BASE = "https://dapds00.nci.org.au/thredds/catalog/nm08/MATE/{}/catalog.html"
 #updated version: https://opus.nci.org.au/display/NDP/THREDDS+Upgrade
 MATE_THREDDS_BASE = "https://thredds.nci.org.au/thredds/catalog/nm08/MATE/{}/catalog.html"

diff --git a/.github/scripts/crosswalks.py b/.github/scripts/crosswalks.py
@@ -7,6 +7,7 @@
 import copy
 from pyld import jsonld
 import pandas as pd
+from config import MATE_GADI
 
 Ryaml = ruamel.yaml.YAML(typ=['rt', 'string'])
 Ryaml.preserve_quotes = True
@@ -360,10 +361,10 @@ def metadata_to_nci(ro_crate):
     #extract funders and authors into a NCI/ISO format
     funders = extract_funder_details(ro_crate_nested)
     authors = extract_creator_details(ro_crate_nested)
-
     root = 'root'  # Key for root element
-    #license_id = ro_crate_nested.get_nested(f"{root}.license.@id") #get the license id
-    license_id = ro_crate_nested.get_nested(f"{root}.license") #get the license id
+
+    #build up any composite values
+    nci_file_path =  MATE_GADI + ro_crate_nested.get_nested(f"{root}.alternateName")
 
     fields_data = {
         "Title*": list_to_string(ro_crate_nested.get_nested(f"{root}.name")),
@@ -381,7 +382,7 @@ def metadata_to_nci(ro_crate):
         "Owner* (if applicable)": "",
         "Credit": "",
         "Supplemental or supporting material": "",
-        "Local NCI file path": "",
+        "Local NCI file path": nci_file_path,
         "DOI (NCI Internal Field)": list_to_string(ro_crate_nested.get_nested(f"{root}.identifier")),
         "Keyword/s": list_to_string(ro_crate_nested.get_nested(f"{root}.keywords"))
     }

diff --git a/.github/scripts/write_repo_contents.py b/.github/scripts/write_repo_contents.py
@@ -49,6 +49,7 @@
 
 
 #######
+#Not sure why, but placing this block above the flatten block made a difference.
 csv_buffer = StringIO()
 #get a iso record as pandas df...
 nci_iso_record = metadata_to_nci(rocratedict)
@@ -58,6 +59,7 @@
 csv_content = csv_buffer.getvalue()
 model_repo.create_file("metadata_trail/nci_iso.csv","add nci_iso record csv", csv_content)
 
+#This is modifying rocratedict in place, which was not the intention 
 try:
 
     expanded = jsonld.expand(rocratedict)