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Robokop v5.0 #92

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merged 6 commits into from
Nov 29, 2023
Merged

Robokop v5.0 #92

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fee790d
adding v5.0
YaphetKG Nov 1, 2023
e15a373
cde-links branch
YaphetKG Nov 6, 2023
6aac2fd
pin linkml
YaphetKG Nov 6, 2023
487b2c1
Update config.yaml
YaphetKG Nov 7, 2023
bb61ab9
pop total items before result
YaphetKG Nov 8, 2023
48650b8
print extracted elements
YaphetKG Nov 8, 2023
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6 changes: 5 additions & 1 deletion dags/dug_helpers/dug_utils.py
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All this looks fine, but I'm going to have to bring this over into the DugPipeline class at some point. What does the addition of line 391 do here? I just want to make sure I'm clear.

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total_items is one of the keys that is returned in the response. it looks something like

{ "total_items": 100 
  "dbgap" : {"elements" : [...]}
  "cde" : {"elements" : [...]}
  }

When doing the reduce on line 393 this causes problems since we are trying to gather element IDs and the total items key is an outlier

Original file line number Diff line number Diff line change
Expand Up @@ -388,6 +388,7 @@ def _search_elements(self, curie, search_term):
raise Exception(f"Validation error - Did not find {curie} for"
f"Search term: {search_term}")
else:
del response['total_items']
for element_type in response:
all_elements_ids = [e['id'] for e in
reduce(lambda x, y: x + y['elements'], response[element_type], [])]
Expand Down Expand Up @@ -434,12 +435,15 @@ def crawl_concepts(self, concepts, data_set_name):
casting_config = query['casting_config']
tranql_source = query['tranql_source']
dug_element_type = query['output_dug_type']
extracted_dug_elements += crawler.expand_to_dug_element(
new_elements = crawler.expand_to_dug_element(
concept=concept,
casting_config=casting_config,
dug_element_type=dug_element_type,
tranql_source=tranql_source
)
log.debug("extracted:")
log.debug(str(list([el.get_searchable_dict() for el in new_elements])))
extracted_dug_elements += new_elements
concept.clean()
percent_complete = int((counter / total) * 100)
if percent_complete % 10 == 0:
Expand Down
12 changes: 12 additions & 0 deletions dags/metadata.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -97,6 +97,18 @@ kgx:
files:
- cde/annotated_edges_v4.0.jsonl
- cde/annotated_nodes_v4.0.jsonl
- version: v5.0
name: baseline-graph
format: jsonl
files:
- baseline-5.0/edges_v5.0.jsonl
- baseline-5.0/nodes_v5.0.jsonl
- version: v5.0
name: cde-graph
format: jsonl
files:
- cde/annotated_edges_v5.0.jsonl
- cde/annotated_nodes_v5.0.jsonl
dug_inputs:
versions:
- name: bdc
Expand Down
4 changes: 2 additions & 2 deletions dags/roger/config/config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ annotation_base_data_uri: https://stars.renci.org/var/dug/

kgx:
biolink_model_version: v3.1.2
dataset_version: v4.0
dataset_version: v5.0
merge_db_id: 1
merge_db_temp_dir: workspace
data_sets:
Expand Down Expand Up @@ -85,7 +85,7 @@ indexing:
desc: "summary"
collection_name: "cde_category"
collection_id: "cde_category"
collection_action: "files"
action: "files"

elasticsearch:
host: elasticsearch
Expand Down
3 changes: 2 additions & 1 deletion requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,8 @@ flatten-dict
redisgraph-bulk-loader==0.12.3
pytest
PyYAML
git+https://github.com/helxplatform/dug@2.12.0
git+https://github.com/helxplatform/dug@cde-links-2
orjson
kg-utils==0.0.6
bmt==1.1.0
linkml-runtime==1.6.0