From 354a89f13a012208a1680f5b8f5405ce67ec7458 Mon Sep 17 00:00:00 2001
From: dansand <sonderfjord@gmail.com>
Date: Thu, 16 May 2024 14:09:24 +1000
Subject: [PATCH] more changes

---
 .github/scripts/config.py         |  2 +-
 .github/scripts/parse_utils.py    |  3 +++
 .github/scripts/ro_crate_utils.py | 18 +++++++++++++++---
 .github/scripts/yaml_utils.py     |  9 +++++----
 4 files changed, 24 insertions(+), 8 deletions(-)

diff --git a/.github/scripts/config.py b/.github/scripts/config.py
index 313a1a5..0fe2d77 100644
--- a/.github/scripts/config.py
+++ b/.github/scripts/config.py
@@ -5,7 +5,7 @@
 #DOIS
 MATE_DOI =     'http://dx.doi.org/10.25914/yrzp-g882'
 MATE_WEBSITE = 'https://mate.science/'
-MATE_GITHUB =  'https://github.com/ModelAtlasofTheEarth'
+MATE_GITHUB =  'https://github.com/ModelAtlasofTheEarth/'
 MATE_THREDDS_BASE = "https://dapds00.nci.org.au/thredds/catalog/nm08/MATE/{}/catalog.html"
 
 #URIs
diff --git a/.github/scripts/parse_utils.py b/.github/scripts/parse_utils.py
index d1d3376..1cb6911 100644
--- a/.github/scripts/parse_utils.py
+++ b/.github/scripts/parse_utils.py
@@ -22,7 +22,10 @@ def validate_slug(proposed_slug):
     except AssertionError as err:
         error_log += f"{err}\n"
 
+    #try a workaround for local tests
     cmd = "python3 .github/scripts/generate_identifier.py"
+    if os.path.exists('../.github/scripts/generate_identifier.py'):
+        os.path.exists('../.github/scripts/generate_identifier.py')
 
     try:
         slug = subprocess.check_output(cmd, shell=True, text=True, stderr=open(os.devnull)).strip()
diff --git a/.github/scripts/ro_crate_utils.py b/.github/scripts/ro_crate_utils.py
index 74d85ba..33ab733 100644
--- a/.github/scripts/ro_crate_utils.py
+++ b/.github/scripts/ro_crate_utils.py
@@ -2,7 +2,7 @@
 import string
 import json
 import random
-from config import MATE_DOI, NCI_RECORD, AUSCOPE_RECORD, MATE_THREDDS_BASE
+from config import *
 import re
 import glob
 from collections.abc import MutableMapping
@@ -615,8 +615,20 @@ def defaults_and_customise_ro_crate(issue_dict, ro_crate, timestamp=False):
     root_index = find_index_by_id(ro_crate, './')
     ro_crate['@graph'][root_index]['isPartOf'].append(MATE_DOI)
     ro_crate['@graph'][root_index]['publisher'] = [AUSCOPE_RECORD, NCI_RECORD]
-    thredds_string = MATE_THREDDS_BASE.format(ro_crate['@graph'][root_index]['alternateName'])
-    ro_crate['@graph'][root_index]['url'] = thredds_string
+    #add the mate.science url for this model
+    #the logic is that the metadata captures all of the access points:
+    # the root identifier is the doi that points to the geonetwork record
+    # the root url points to the model on the mate website and the mate github
+    # the model_outputs/model_outputs url is the thredds URL
+    mate_science_url = MATE_WEBSITE + 'models/{}/'
+    mate_gh_url = MATE_GITHUB + '{}/'
+    slug = ro_crate['@graph'][root_index]['alternateName']
+    ro_crate['@graph'][root_index]['url'] = [mate_science_url.format(slug), mate_gh_url.format(slug)]
+    thredds_string = MATE_THREDDS_BASE.format(slug)
+    roc_index = find_index_by_id(ro_crate, 'model_outputs')
+    ro_crate['@graph'][roc_index]['url'] = thredds_string
+    roc_index = find_index_by_id(ro_crate, 'model_inputs')
+    ro_crate['@graph'][roc_index]['url'] = thredds_string
 
 
     #add date time as the date published ro-crate
diff --git a/.github/scripts/yaml_utils.py b/.github/scripts/yaml_utils.py
index 19921d8..e0eecb4 100644
--- a/.github/scripts/yaml_utils.py
+++ b/.github/scripts/yaml_utils.py
@@ -2,6 +2,7 @@
 import copy
 from ruamel.yaml import YAML
 import io
+from config import MATE_DOI, NCI_RECORD, AUSCOPE_RECORD, MATE_THREDDS_BASE
 
 
 def navigate_and_assign(source, path, value):
@@ -159,7 +160,6 @@ def ensure_path_starts_with_pattern(file_path, pattern='./graphics/'):
 
 def configure_yaml_output_dict(output_dict, issue_dict,
                                image_path='./graphics/',
-                               thredds_base ="dapds00.nci.org.au/thredds/catalog/nm08/MATE/{}/catalog.html",
                                timestamp=False):
 
                                #nci_file_path_base
@@ -180,13 +180,14 @@ def configure_yaml_output_dict(output_dict, issue_dict,
     else:
         path_slug = 'PENDING'
 
-    thredds_string = thredds_base.format(path_slug)
+    thredds_string = MATE_THREDDS_BASE.format(path_slug)
     ## add the NCI_file_path
     if issue_dict["include_model_output"]:
-        output_dict['dataset']['nci_file_path'] = thredds_string + '/model_output_data'
+        #for now, just link both to the thredds base.
+        output_dict['dataset']['nci_file_path'] = thredds_string #+ '/model_output_data'
 
     if issue_dict["include_model_code"]:
-        output_dict['model_files']['nci_file_path'] =  thredds_string + '/model_code_inputs'
+        output_dict['model_files']['nci_file_path'] =  thredds_string #+ '/model_code_inputs'
 
 
     #change format of ORCiD ids if required