fix broken rebase

OWASP · May 31, 2024 · ee3fe29 · ee3fe29
1 parent b26001a
commit ee3fe29
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Showing 12 changed files with 40 additions and 37 deletions.
diff --git a/Procfile b/Procfile
@@ -1,2 +1,2 @@
-web: gunicorn cre:app --log-file=-g
+web: gunicorn cre:app
 worker: FLASK_APP=`pwd`/cre.py python cre.py --start_worker
diff --git a/application/cmd/cre_main.py b/application/cmd/cre_main.py
@@ -180,9 +180,7 @@ def parse_file(
                 else (
                     defs.Code
                     if doctype == defs.Credoctypes.Code.value
-                    else defs.Tool
-                    if doctype == defs.Credoctypes.Tool.value
-                    else None
+                    else defs.Tool if doctype == defs.Credoctypes.Tool.value else None
                 )
             )
             document = from_dict(
@@ -247,7 +245,9 @@ def register_standard(
     )
     for node in standard_entries:
         if not node:
-            logger.info(f"encountered empty node while importing {standard_entries[0].name}")
+            logger.info(
+                f"encountered empty node while importing {standard_entries[0].name}"
+            )
             continue
         register_node(node, collection)
         if node.embeddings:
@@ -323,7 +323,6 @@ def parse_standards_from_spreadsheeet(
         logger.info(f"Importing {len(docs.get(defs.Credoctypes.CRE.value))} CREs")
         with alive_bar(len(docs.get(defs.Credoctypes.CRE.value))) as bar:
             for cre in docs.pop(defs.Credoctypes.CRE.value):
-
                 register_cre(cre, collection)
                 bar()
 

diff --git a/application/database/db.py b/application/database/db.py
@@ -18,7 +18,6 @@
     FeatureNotSupported,
     NodeClassAlreadyDefined,
 )
-from neomodel import core
 import neo4j
 from sqlalchemy.orm import aliased
 import os
@@ -580,9 +579,9 @@ def gap_analysis(self, name_1, name_2):
             # """
             # OPTIONAL MATCH (BaseStandard:NeoStandard {name: $name1})
             # OPTIONAL MATCH (CompareStandard:NeoStandard {name: $name2})
-            # OPTIONAL MATCH p = allShortestPaths((BaseStandard)-[*..20]-(CompareStandard)) 
+            # OPTIONAL MATCH p = allShortestPaths((BaseStandard)-[*..20]-(CompareStandard))
             # WITH p
-            # WHERE length(p) > 1 AND ALL(n in NODES(p) WHERE (n:NeoCRE or n = BaseStandard or n = CompareStandard) AND NOT n.name in $denylist) 
+            # WHERE length(p) > 1 AND ALL(n in NODES(p) WHERE (n:NeoCRE or n = BaseStandard or n = CompareStandard) AND NOT n.name in $denylist)
             # RETURN p
             # """,
             {"name1": name_1, "name2": name_2, "denylist": denylist},
@@ -600,9 +599,9 @@ def gap_analysis(self, name_1, name_2):
             # """
             # OPTIONAL MATCH (BaseStandard:NeoStandard {name: $name1})
             # OPTIONAL MATCH (CompareStandard:NeoStandard {name: $name2})
-            # OPTIONAL MATCH p = allShortestPaths((BaseStandard)-[:(LINKED_TO|AUTOMATICALLY_LINKED_TO|CONTAINS)*..20]-(CompareStandard)) 
+            # OPTIONAL MATCH p = allShortestPaths((BaseStandard)-[:(LINKED_TO|AUTOMATICALLY_LINKED_TO|CONTAINS)*..20]-(CompareStandard))
             # WITH p
-            # WHERE length(p) > 1 AND ALL(n in NODES(p) WHERE (n:NeoCRE or n = BaseStandard or n = CompareStandard) AND NOT n.name in $denylist) 
+            # WHERE length(p) > 1 AND ALL(n in NODES(p) WHERE (n:NeoCRE or n = BaseStandard or n = CompareStandard) AND NOT n.name in $denylist)
             # RETURN p
             # """,
             {"name1": name_1, "name2": name_2, "denylist": denylist},
@@ -1481,7 +1480,9 @@ def add_node(
             self.session.commit()
             return entry
         else:
-            logger.info(f"did not know of {dbnode.name}:{dbnode.section}:{dbnode.section_id} ,adding")
+            logger.info(
+                f"did not know of {dbnode.name}:{dbnode.section}:{dbnode.section_id} ,adding"
+            )
             self.session.add(dbnode)
             self.session.commit()
             if self.graph:

diff --git a/application/frontend/src/components/DocumentNode/DocumentNode.tsx b/application/frontend/src/components/DocumentNode/DocumentNode.tsx
@@ -20,7 +20,7 @@ export interface DocumentNode {
   hasLinktypeRelatedParent?: Boolean;
 }
 
-const linkTypesToNest = [TYPE_IS_PART_OF, TYPE_RELATED,TYPE_AUTOLINKED_TO];
+const linkTypesToNest = [TYPE_IS_PART_OF, TYPE_RELATED, TYPE_AUTOLINKED_TO];
 const linkTypesExcludedInNesting = [TYPE_CONTAINS];
 const linkTypesExcludedWhenNestingRelatedTo = [TYPE_RELATED, TYPE_IS_PART_OF, TYPE_CONTAINS];
 

diff --git a/application/prompt_client/prompt_client.py b/application/prompt_client/prompt_client.py
@@ -52,10 +52,10 @@ def get_content(self, url):
                 page.close()
                 return text
             except requests.exceptions.RequestException as e:
-                print(f"Error fetching content for URL: {url} - {str(e)}")
+                logger.error(f"Error fetching content for URL: {url} - {str(e)}")
                 return ""
             except playwright._impl._api_types.TimeoutError as te:
-                print(
+                logger.error(
                     f"Page: {url}, took too long to load, playwright timedout, trying again - {str(te)}, attempt num {attempts}"
                 )
 

diff --git a/application/prompt_client/vertex_prompt_client.py b/application/prompt_client/vertex_prompt_client.py
@@ -56,9 +56,9 @@ def __init__(self) -> None:
         if os.environ.get("SERVICE_ACCOUNT_CREDENTIALS"):
             with open(service_account_secrets_file, "w") as f:
                 f.write(os.environ.get("SERVICE_ACCOUNT_CREDENTIALS"))
-                os.environ[
-                    "GOOGLE_APPLICATION_CREDENTIALS"
-                ] = service_account_secrets_file
+                os.environ["GOOGLE_APPLICATION_CREDENTIALS"] = (
+                    service_account_secrets_file
+                )
         elif not os.environ.get("GCP_NATIVE"):
             logger.fatal(
                 "neither GCP_NATIVE nor SERVICE_ACCOUNT_CREDENTIALS have been set"

diff --git a/application/utils/gap_analysis.py b/application/utils/gap_analysis.py
@@ -145,7 +145,9 @@ def preload(target_url: str):
                         if f"{sb}->{sa}" in waiting:
                             waiting.remove(f"{sb}->{sa}")
                 if forward and backward:
-                    print(f"removing standard {sb} from the waiting list as it has returned ")
+                    print(
+                        f"removing standard {sb} from the waiting list as it has returned "
+                    )
                     standards.remove(sb)
         print(f"calculating {len(waiting)} gap analyses")
         time.sleep(30)

diff --git a/application/utils/spreadsheet.py b/application/utils/spreadsheet.py
@@ -145,12 +145,12 @@ def __add_cre_to_spreadsheet(
             for i in range(0, maxgroups):
                 if not working_array[defs.ExportFormat.linked_cre_id_key(str(i))]:
                     grp_added = True
-                    working_array[
-                        defs.ExportFormat.linked_cre_id_key(str(i))
-                    ] = link.document.id
-                    working_array[
-                        defs.ExportFormat.linked_cre_name_key(str(i))
-                    ] = link.document.name
+                    working_array[defs.ExportFormat.linked_cre_id_key(str(i))] = (
+                        link.document.id
+                    )
+                    working_array[defs.ExportFormat.linked_cre_name_key(str(i))] = (
+                        link.document.name
+                    )
                     working_array[
                         defs.ExportFormat.linked_cre_link_type_key(str(i))
                     ] = link.ltype.value

diff --git a/application/utils/spreadsheet_parsers.py b/application/utils/spreadsheet_parsers.py
@@ -33,7 +33,7 @@ def is_empty(value: Optional[str]) -> bool:
 
 def recurse_print_links(cre: defs.Document) -> None:
     for link in cre.links:
-        pprint(link.document)
+        print(link.document)
         recurse_print_links(link.document)
 
 
@@ -455,9 +455,7 @@ def parse_hierarchical_export_format(
     logger.info("Spreadsheet is hierarchical export format")
     documents: Dict[str, List[defs.Document]] = {defs.Credoctypes.CRE.value: []}
     cre_dict = {}
-    uninitialized_cre_mappings: List[
-        UninitializedMapping
-    ] = (
+    uninitialized_cre_mappings: List[UninitializedMapping] = (
         []
     )  # the csv has a column "Link to Other CRE", this column linksa complete CRE entry to another CRE by name.
     # The other CRE might not have been initialized yet at the time of linking so it cannot be part of our main document collection yet
@@ -509,9 +507,9 @@ def parse_hierarchical_export_format(
         if cre:
             cre_dict = update_cre_in_links(cre_dict, cre)
 
-        mapping[
-            "Link to other CRE"
-        ] = f'{mapping["Link to other CRE"]},{",".join(cre.tags)}'
+        mapping["Link to other CRE"] = (
+            f'{mapping["Link to other CRE"]},{",".join(cre.tags)}'
+        )
 
         if not is_empty(str(mapping.get("Link to other CRE")).strip()):
             other_cres = list(
@@ -526,7 +524,9 @@ def parse_hierarchical_export_format(
             for other_cre in other_cres:
                 logger.info(f"{cre.id}: Found 'other cre' {other_cre}")
                 if not cre_dict.get(other_cre):
-                    logger.info(f"{cre.id}: We don't know yet of 'other cre' {other_cre}, adding to uninitialized mappings")
+                    logger.info(
+                        f"{cre.id}: We don't know yet of 'other cre' {other_cre}, adding to uninitialized mappings"
+                    )
                     uninitialized_cre_mappings.append(
                         UninitializedMapping(
                             complete_cre=cre,
@@ -535,7 +535,9 @@ def parse_hierarchical_export_format(
                         )
                     )
                 else:
-                    logger.info(f"{cre.id}: We knew yet 'other cre' {other_cre}, adding regular link")
+                    logger.info(
+                        f"{cre.id}: We knew yet 'other cre' {other_cre}, adding regular link"
+                    )
                     new_cre = cre_dict[other_cre.strip()]
                     # we only need a shallow copy here
                     cre = cre.add_link(

diff --git a/application/web/web_main.py b/application/web/web_main.py
@@ -35,7 +35,6 @@
 from application.utils.spreadsheet import write_csv
 import oauthlib
 import google.auth.transport.requests
-from application.utils.hash import make_array_hash, make_cache_key
 
 from application import tracer
 

diff --git a/cre.py b/cre.py
@@ -16,9 +16,8 @@
 app = create_app(mode=os.getenv("FLASK_CONFIG") or "default")
 migrate = Migrate(app, sqla, render_as_batch=True)
 
-# flask <x> commands
-
 
+# flask <x> commands
 @app.cli.command()  # type: ignore
 @click.option(
     "--cover/--no-cover", default=False, help="Run tests under code coverage."

diff --git a/migrations/versions/7f27babf58e1_drop_description_from_uq_node_constraint.py b/migrations/versions/7f27babf58e1_drop_description_from_uq_node_constraint.py
@@ -5,6 +5,7 @@
 Create Date: 2024-03-24 13:56:58.321752
 
 """
+
 from alembic import op
 import sqlalchemy as sa