Merge pull request #68 from wormjam-consortium/devel

Fix the annotation bug, and reformat scripts with Black
wormjam-consortium · Mar 1, 2021 · 9fa6ecb · 9fa6ecb
2 parents 94bd632 + 2e39d25
commit 9fa6ecb
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Showing 5 changed files with 65 additions and 45 deletions.
diff --git a/.github/tests/failure_reporter.py b/.github/tests/failure_reporter.py
@@ -3,19 +3,25 @@
 import sys
 import datetime
 
-DISCORD_ENDPOINT = sys.argv[1] #Github Actions Channel Webhook
-GITHUB_BUILD_NUMBER = sys.argv[2] # Github build counter
-GITHUB_BUILD_WEB_URL = sys.argv[3] # github unique run ID used for link construction
-GITHUB_REPO_SLUG = sys.argv[4] # user/repo
-GITHUB_REPO_BRANCH = sys.argv[5].split("/")[-1] #branch - process the string and grab the last term
+DISCORD_ENDPOINT = sys.argv[1]  # Github Actions Channel Webhook
+GITHUB_BUILD_NUMBER = sys.argv[2]  # Github build counter
+GITHUB_BUILD_WEB_URL = sys.argv[3]  # github unique run ID used for link construction
+GITHUB_REPO_SLUG = sys.argv[4]  # user/repo
+GITHUB_REPO_BRANCH = sys.argv[5].split("/")[
+    -1
+]  # branch - process the string and grab the last term
 
 payload_json = {
     "embeds": [
         {
             "title": "WormJam CI Report",
-            "color": 10027008, #red
+            "color": 10027008,  # red
             "description": "A build has failed from [%s](%s) on branch %s"
-            % (GITHUB_REPO_SLUG, "https://github.com/" + GITHUB_REPO_SLUG,GITHUB_REPO_BRANCH),
+            % (
+                GITHUB_REPO_SLUG,
+                "https://github.com/" + GITHUB_REPO_SLUG,
+                GITHUB_REPO_BRANCH,
+            ),
             "fields": [
                 {"name": "Build Number", "value": str(GITHUB_BUILD_NUMBER)},
                 {
@@ -25,13 +31,13 @@
                 },
             ],
             "thumbnail": {
-                "url":"https://avatars1.githubusercontent.com/u/44036562?s=280&v=4, " #github actions logo
+                "url": "https://avatars1.githubusercontent.com/u/44036562?s=280&v=4, "  # github actions logo
             },
             "timestamp": str(datetime.datetime.now().isoformat()),
         }
     ]
 }
-#send failure message
+# send failure message
 r = requests.post(
     DISCORD_ENDPOINT,
     data=json.dumps(payload_json),

diff --git a/.github/tests/release_manager.py b/.github/tests/release_manager.py
@@ -4,36 +4,42 @@
 import datetime
 
 
-DISCORD_ENDPOINT = sys.argv[1] #Github Actions Channel Webhook
+DISCORD_ENDPOINT = sys.argv[1]  # Github Actions Channel Webhook
 GITHUB_REPO_SLUG = sys.argv[2]  # user/repo
-GITHUB_REPO_BRANCH = sys.argv[3].split("/")[-1] #branch - process the string and grab the last term
+GITHUB_REPO_BRANCH = sys.argv[3].split("/")[
+    -1
+]  # branch - process the string and grab the last term
 
 timestamp = datetime.datetime.now().strftime("%Y_%m_%d__%H_%M_%S")
 filename = "WormJam" + timestamp + ".tar.gz"
 
-#prepare files for sending
+# prepare files for sending
 packaged_model_file = {filename: open("WormJam.tar.gz", "rb")}
 
-#construct embed to send to discord
-#This embed is used for both messages
+# construct embed to send to discord
+# This embed is used for both messages
 payload_json = {
     "embeds": [
         {
             "title": "WormJam Release",
-            "color": 2132223, #this is github action colour
+            "color": 2132223,  # this is github action colour
             "description": "Release from [%s](%s) for model version %s"
-            % (GITHUB_REPO_SLUG, "https://github.com/" + GITHUB_REPO_SLUG,GITHUB_REPO_BRANCH),
+            % (
+                GITHUB_REPO_SLUG,
+                "https://github.com/" + GITHUB_REPO_SLUG,
+                GITHUB_REPO_BRANCH,
+            ),
             "fields": [
                 {"name": "Version", "value": str(GITHUB_REPO_BRANCH)},
             ],
             "thumbnail": {
-                "url": "https://avatars1.githubusercontent.com/u/44036562?s=280&v=4" #github actions logo
+                "url": "https://avatars1.githubusercontent.com/u/44036562?s=280&v=4"  # github actions logo
             },
             "timestamp": str(datetime.datetime.now().isoformat()),
         }
     ]
 }
-#Send the report
+# Send the report
 r = requests.post(
     DISCORD_ENDPOINT,
     data=json.dumps(payload_json),

diff --git a/.github/tests/send_reports.py b/.github/tests/send_reports.py
@@ -4,29 +4,35 @@
 import datetime
 
 
-DISCORD_ENDPOINT = sys.argv[1] #Github Actions Channel Webhook
-DISCORD_ENDPOINT_2 = sys.argv[2] # Model Uploads Channel Webhook
+DISCORD_ENDPOINT = sys.argv[1]  # Github Actions Channel Webhook
+DISCORD_ENDPOINT_2 = sys.argv[2]  # Model Uploads Channel Webhook
 GITHUB_BUILD_NUMBER = sys.argv[3]  # Github build counter
 GITHUB_BUILD_WEB_URL = sys.argv[4]  # github unique run ID used for link construction
 GITHUB_REPO_SLUG = sys.argv[5]  # user/repo
-GITHUB_REPO_BRANCH = sys.argv[6].split("/")[-1] #branch - process the string and grab the last term
+GITHUB_REPO_BRANCH = sys.argv[6].split("/")[
+    -1
+]  # branch - process the string and grab the last term
 
 timestamp = datetime.datetime.now().strftime("%Y_%m_%d__%H_%M_%S")
 filename = "WormJam" + timestamp + ".tar.gz"
 
-#prepare files for sending
+# prepare files for sending
 report_file = {"Report.html": open("Report.html", "rb")}
 packaged_model_file = {filename: open("WormJam.tar.gz", "rb")}
 
-#construct embed to send to discord
-#This embed is used for both messages
+# construct embed to send to discord
+# This embed is used for both messages
 payload_json = {
     "embeds": [
         {
             "title": "WormJam CI Report",
-            "color": 2132223, #this is github action colour
+            "color": 2132223,  # this is github action colour
             "description": "Model Build from [%s](%s) on branch %s"
-            % (GITHUB_REPO_SLUG, "https://github.com/" + GITHUB_REPO_SLUG,GITHUB_REPO_BRANCH),
+            % (
+                GITHUB_REPO_SLUG,
+                "https://github.com/" + GITHUB_REPO_SLUG,
+                GITHUB_REPO_BRANCH,
+            ),
             "fields": [
                 {"name": "Build Number", "value": str(GITHUB_BUILD_NUMBER)},
                 {
@@ -36,21 +42,21 @@
                 },
             ],
             "thumbnail": {
-                "url": "https://avatars1.githubusercontent.com/u/44036562?s=280&v=4" #github actions logo
+                "url": "https://avatars1.githubusercontent.com/u/44036562?s=280&v=4"  # github actions logo
             },
             "timestamp": str(datetime.datetime.now().isoformat()),
         }
     ]
 }
-#Send the report
+# Send the report
 r = requests.post(
     DISCORD_ENDPOINT,
     data=json.dumps(payload_json),
     headers={"Content-Type": "application/json"},
 )
 r2 = requests.post(DISCORD_ENDPOINT, files=report_file)
 print(r, r2)
-#send the model
+# send the model
 r3 = requests.post(
     DISCORD_ENDPOINT_2,
     data=json.dumps(payload_json),

diff --git a/.github/tests/support/annotation.py b/.github/tests/support/annotation.py
@@ -1,14 +1,15 @@
 from lxml import etree
 
-#debugging
+# debugging
 from xml.etree import ElementTree
 
-#if no database SBtab, then db_dict is an empty dict
+# if no database SBtab, then db_dict is an empty dict
+
 
 def _annotate(db_dict, ref):
     """Function to access reference links, and handle when those links are not in DB table
-	
-	Takes a dict of databases and a database name"""
+
+    Takes a dict of databases and a database name"""
     if ref in db_dict:
         return db_dict[ref]["!IdentifiersOrgPrefix"]
     else:
@@ -25,12 +26,11 @@ def _check_db_type(db_dict, ref):
 
 def gen_annotation_tree(metaid, db_dict, data, NS_MAP):
 
-    annotation_tree = etree.SubElement(
-    etree.SubElement(
-        etree.Element("annotation"), "{%s}" % NS_MAP["rdf"] + "RDF"
-    ),
-    "{%s}" % NS_MAP["rdf"] + "Description",
-    attrib={"{%s}" % NS_MAP["rdf"] + "about": "#" + metaid},
+    annotation_tree = etree.Element("annotation")
+
+    description = etree.SubElement(etree.SubElement(annotation_tree, "{%s}" % NS_MAP["rdf"] + "RDF"),
+        "{%s}" % NS_MAP["rdf"] + "Description",
+        attrib={"{%s}" % NS_MAP["rdf"] + "about": "#" + metaid},
     )
     # get a list of which DBs are annotated for this entry, as well as what type of DB they are
     annotated_dbs = [
@@ -46,12 +46,12 @@ def gen_annotation_tree(metaid, db_dict, data, NS_MAP):
     bqbiol_occurs_in_and_rdf_bag = False
     if "Is" in db_types:
         bqbiol_is_and_rdf_bag = etree.SubElement(
-            etree.SubElement(annotation_tree, "{%s}" % NS_MAP["bqbiol"] + "is"),
+            etree.SubElement(description, "{%s}" % NS_MAP["bqbiol"] + "is"),
             "{%s}" % NS_MAP["rdf"] + "Bag",
         )
     if "In" in db_types:
         bqbiol_occurs_in_and_rdf_bag = etree.SubElement(
-            etree.SubElement(annotation_tree, "{%s}" % NS_MAP["bqbiol"] + "isPartOf"),
+            etree.SubElement(description, "{%s}" % NS_MAP["bqbiol"] + "isPartOf"),
             "{%s}" % NS_MAP["rdf"] + "Bag",
         )
     for db in annotated_dbs:
@@ -82,4 +82,4 @@ def gen_annotation_tree(metaid, db_dict, data, NS_MAP):
                     },
                 )
 
-    return annotation_tree
+    return annotation_tree
diff --git a/.github/tests/tsv_to_sbml.py b/.github/tests/tsv_to_sbml.py
@@ -7,7 +7,7 @@
 import pyparsing as pp
 from lxml import etree
 
-#debugging
+# debugging
 from xml.etree import ElementTree
 
 from support.helper_classes import ModelSystem
@@ -204,7 +204,9 @@ def genID():
             "{%s}" % NS_MAP["fbc"] + "geneProduct",
             attrib=attribs,
         )
-        fbc_gene_prod.append(gen_annotation_tree(attribs["metaid"], db_dict, val, NS_MAP))
+        fbc_gene_prod.append(
+            gen_annotation_tree(attribs["metaid"], db_dict, val, NS_MAP)
+        )
 
 #
 # Pathways
@@ -527,7 +529,7 @@ def quick(frag):
                 + val[i]
             )
 
-    reaction_field.append(gen_annotation_tree(metaid,db_dict,val,NS_MAP))
+    reaction_field.append(gen_annotation_tree(metaid, db_dict, val, NS_MAP))
     try:
         reaction_field.append(process_gene_association(val["!GeneAssociation"]))
     except Exception as e: