Sourcery refactored main branch by sourcery-ai[bot] · Pull Request #16 · fairdataihub/KnowMore

sourcery-ai · 2022-05-25T17:53:09Z

Branch main refactored by Sourcery.

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sourcery-ai · 2022-05-25T17:53:11Z

app/routes.py

-            error_message = make_response("Invalid data: need a json with key 'datasetIds' and value an array of integers", 400)
-            return error_message
+            return make_response(
+                "Invalid data: need a json with key 'datasetIds' and value an array of integers",
+                400,
+            )
+

        print("json:", request.json)

        payload = job_api.start_python_osparc_job(dataset_dict)

-        resp = make_response(json.dumps(payload), payload["status_code"])
-        return resp
+        return make_response(json.dumps(payload), payload["status_code"])


Function set_routes.create_job refactored with the following changes:

Inline variable that is immediately returned (inline-immediately-returned-variable)

sourcery-ai · 2022-05-25T17:53:11Z

app/routes.py

-        resp = make_response(json.dumps(payload), payload["status_code"])
-        return resp
+        return make_response(json.dumps(payload), payload["status_code"])


Function set_routes.check_job_status refactored with the following changes:

Inline variable that is immediately returned (inline-immediately-returned-variable)

sourcery-ai · 2022-05-25T17:53:11Z

app/osparc/job_api.py

-    payload = start_osparc_job("python", input_file_paths)
-
-    return payload
+    return start_osparc_job("python", input_file_paths)


Function start_python_osparc_job refactored with the following changes:

Inline variable that is immediately returned (inline-immediately-returned-variable)

sourcery-ai · 2022-05-25T17:53:12Z

app/osparc/job_api.py

-    payload = start_osparc_job("matlab", input_file_paths)
-
-    return payload
+    return start_osparc_job("matlab", input_file_paths)


Function start_matlab_osparc_job refactored with the following changes:

Inline variable that is immediately returned (inline-immediately-returned-variable)

sourcery-ai · 2022-05-25T17:53:12Z

app/osparc/job_api.py

                #print(f"file id: {results_file.id}")
                download_path: str = files_api.download_file(file_id=results_file.id)
-                
+


Function check_job_status refactored with the following changes:

Replace f-string with no interpolated values with string (remove-redundant-fstring)

sourcery-ai · 2022-05-25T17:53:13Z

assets/INPUT_FOLDER/main.py

-    # manifest.json: get dataset title, subtitle, publication date
-    # subjects.xlsx: species, n subjects, age range, sex
-    # samples.xlsx: n samples, specimen type, specimen anatomical location
-    data_table_summary = {}
    manifest_json = get_dataset_main_manifest(datasetId)
-    data_table_summary['Dataset id'] = datasetId
-    data_table_summary['Title'] = manifest_json['name']
-    data_table_summary['Subtitle'] = manifest_json['description']
-    data_table_summary['Publication_date'] = manifest_json['datePublished']
+    data_table_summary = {
+        'Dataset id': datasetId,
+        'Title': manifest_json['name'],
+        'Subtitle': manifest_json['description'],
+        'Publication_date': manifest_json['datePublished'],
+    }


Function get_summary_table_data refactored with the following changes:

Merge dictionary assignment with declaration (merge-dict-assign)

Move assignment closer to its usage within a block (move-assign-in-block)

This removes the following comments ( why? ):

# subjects.xlsx: species, n subjects, age range, sex # samples.xlsx: n samples, specimen type, specimen anatomical location # manifest.json: get dataset title, subtitle, publication date

sourcery-ai · 2022-05-25T17:53:13Z

assets/INPUT_FOLDER/main.py

-        data_text[datasetId] = {}
-        # text from dataset description
-        data_text[datasetId]['description'] = get_dataset_description_text(
-            datasetId)
+        data_text[datasetId] = {'description': get_dataset_description_text(datasetId)}


Function get_all_datasets_text refactored with the following changes:

Merge dictionary assignment with declaration (merge-dict-assign)

This removes the following comments ( why? ):

# text from dataset description

sourcery-ai · 2022-05-25T17:53:13Z

assets/INPUT_FOLDER/main.py

-    abstract = summariser(text_to_summarise, top_n=10)
-
    # abstract = "Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum."
-    return abstract
+    return summariser(text_to_summarise, top_n=10)


Function get_abstract refactored with the following changes:

Inline variable that is immediately returned (inline-immediately-returned-variable)

sourcery-ai · 2022-05-25T17:53:13Z

assets/INPUT_FOLDER/main.py

-            dataset_mat = get_dataset_mat_files(datasetId)
-            if dataset_mat:
+            if dataset_mat := get_dataset_mat_files(datasetId):


Function get_all_datasets_mat_files refactored with the following changes:

Use named expression to simplify assignment and conditional (use-named-expression)

Simplify sequence length comparison (simplify-len-comparison)

sourcery-ai · 2022-05-25T17:53:13Z

assets/INPUT_FOLDER/main.py

-#list_datasetId = ['60', '64', '65', '16', '61', '89', '97']
-#list_datasetId = ['60', '64', '65']
-
-# storage dict to be saved as a json and returned to front-end
-dataset_data = {}
-


Lines 693-710 refactored with the following changes:

Merge dictionary assignment with declaration (merge-dict-assign)

Move assignment closer to its usage within a block (move-assign-in-block)

Convert for loop into dictionary comprehension (dict-comprehension)

This removes the following comments ( why? ):

#list_datasetId = ['60', '64', '65', '16', '61', '89', '97'] # storage dict to be saved as a json and returned to front-end #list_datasetId = ['60', '64', '65']

sourcery-ai · 2022-05-25T17:53:20Z

Sourcery Code Quality Report

❌ Merging this PR will decrease code quality in the affected files by 0.25%.

Quality metrics	Before	After	Change
Complexity	7.66 ⭐	7.75 ⭐	0.09 👎
Method Length	84.80 🙂	82.96 🙂	-1.84 👍
Working memory	8.71 🙂	8.82 🙂	0.11 👎
Quality	62.12% 🙂	61.87% 🙂	-0.25% 👎

Other metrics	Before	After	Change
Lines	1164	1125	-39

Changed files	Quality Before	Quality After	Quality Change
app/routes.py	66.89% 🙂	67.83% 🙂	0.94% 👍
app/osparc/job_api.py	65.35% 🙂	64.82% 🙂	-0.53% 👎
assets/INPUT_FOLDER/main.py	60.19% 🙂	59.83% 🙂	-0.36% 👎

Here are some functions in these files that still need a tune-up:

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
assets/INPUT_FOLDER/main.py	get_summary_table_data	13 🙂	273 ⛔	15 😞	33.96% 😞	Try splitting into smaller methods. Extract out complex expressions
assets/INPUT_FOLDER/main.py	get_all_datasets_mat_files	19 😞	220 ⛔	13 😞	34.63% 😞	Refactor to reduce nesting. Try splitting into smaller methods. Extract out complex expressions
assets/INPUT_FOLDER/main.py	get_text_correlation	22 😞	306 ⛔	7 🙂	40.36% 😞	Refactor to reduce nesting. Try splitting into smaller methods
assets/INPUT_FOLDER/main.py	get_protocolsio_text	15 🙂	153 😞	15 😞	40.67% 😞	Try splitting into smaller methods. Extract out complex expressions
app/osparc/job_api.py	check_job_status	10 🙂	291 ⛔	10 😞	43.81% 😞	Try splitting into smaller methods. Extract out complex expressions

Legend and Explanation

The emojis denote the absolute quality of the code:

⭐ excellent
🙂 good
😞 poor
⛔ very poor

The 👍 and 👎 indicate whether the quality has improved or gotten worse with this pull request.

Please see our documentation here for details on how these metrics are calculated.

We are actively working on this report - lots more documentation and extra metrics to come!

Help us improve this quality report!

lgtm-com · 2022-05-25T18:00:02Z

This pull request fixes 1 alert when merging 26e3365 into 9ba2afb - view on LGTM.com

fixed alerts:

1 for Unnecessary pass

'Refactored by Sourcery'

26e3365

sourcery-ai bot requested a review from bvhpatel May 25, 2022 17:53

sourcery-ai bot commented May 25, 2022

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Sourcery refactored main branch#16

Sourcery refactored main branch#16
sourcery-ai[bot] wants to merge 1 commit intomainfrom
sourcery/main

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		#print(f"file id: {results_file.id}")
		download_path: str = files_api.download_file(file_id=results_file.id)

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