有条不紊的信息主要文件 - Python

Question

我一直致力于从一系列表格中创建MongoDB。

我已将表连接成这样的数据框：

subid,firstvisit,name,contact,dob,gender,visitdate1,age,visitcategory,samplenumber,label_on_sample,completed_by
    1,12/31/11,Bob,,12/31/00,Male,,,,,,
    1,,,,,,12/31/15,17,Baseline Visit,,,
    1,,,,,,12/31/16,18,Follow Up Visit,,,
    1,,,,,,12/31/17,18,Follow Up Visit,,,
    1,,,,12/31/00,Male,,17,,XXX123,1,Sally
    2,1/1/12,,,1/1/01,Female,,,,,,
    2,,,,,,1/1/11,10,Baseline Visit,,,
    2,,,,,,1/1/12,11,Follow Up Visit,,,
    2,,,,,,1/1/13,12,Follow Up Visit,,,
    2,,,,,,1/1/14,13,Follow Up Visit,,,
    2,,,,,,1/1/15,14,Follow Up Visit,,,
    2,,,,1/1/01,Female,,15,,YYY456,2,
    2,,,,1/1/01,Female,,15,,ZZZ789,2,Sally'

输出如下：

[
    {
        "subject_id": "1",
        "name": "Bob",
        "dob": "12/31/00",
        "gender": "Male",
        "visits": {
            "12/31/15": {
                "age": "17",
                "visit_category": "Baseline Visit"
            },
            "12/31/16": {
                "age": "18",
                "visit_category": "Follow Up Visit"
            },
            "12/31/17": {
                "age": "18",
                "visit_category": "Follow Up Visit"
            }
        },
        "samples": {
            "XXX123": {
                "completed_by": "Sally",
                "label_on_sample": "1"
            }
        }
    },
    {
        "subject_id": "2",
        "name": null,
        "dob": "1/1/01",
        "gender": "Female",
        "visits": {
            "1/1/11": {
                "age": "10",
                "visit_category": "Baseline Visit"
            },
            "1/1/12": {
                "age": "11",
                "visit_category": "Follow Up Visit"
            },
            "1/1/13": {
                "age": "12",
                "visit_category": "Follow Up Visit"
            },
            "1/1/14": {
                "age": "13",
                "visit_category": "Follow Up Visit"
            },
            "1/1/15": {
                "age": "14",
                "visit_category": "Follow Up Visit"
            }
        },
        "samples": {
            "YYY456": {
                "completed_by": null,
                "label_on_sample": "2"
            },
            "ZZZ789": {
                "completed_by": "Sally",
                "label_on_sample": "2"
            }
        }
    }
]

使用这样的函数：

def solution(df):
    by_subject_id = defaultdict(lambda: {
        'name': None,
        'dob': None,
        'gender': None,
        'visits': {},
        'samples': {}
    })

    for row in df.iterows():
            non_empty = {k: v for k, v in row[1].items() if v != ''}
            subject_id = non_empty['subid']  # must have to group by
            first_visit = non_empty.get('firstvisit')  # optional
            sample = non_empty.get('samplenumber')  # optional
            visit = non_empty.get('visitdate1')  # optional

            if first_visit:
                by_subject_id[subject_id].update({
                    'name': non_empty.get('name'),
                    'dob': non_empty.get('dob'),
                    'gender': non_empty.get('gender')
                })
            elif visit:
                by_subject_id[subject_id]['visits'][visit] = {
                    'age': non_empty.get('age'),
                    'visit_category': non_empty.get('visitcategory')
                }
            elif sample:
                by_subject_id[subject_id]['samples'][sample] = {
                    'completed_by': non_empty.get('completed_by'),
                    'label_on_sample': non_empty.get('label_on_sample')
                }
    return [{'subject_id': k, **v} for k, v in by_subject_id.items()]


result = solution(df)
with open('result.json', 'w') as outfile:
    json.dump(result, outfile) 

如果我只想从基线访问中收集信息并将其存储在主题ID下，例如＆＃34; age_at_baseline＆＃34;例如。

[
        {
            "subject_id": "1",
            "name": "Bob",
            "dob": "12/31/00",
            "gender": "Male",
            "age_at_baseline": "17"
            "visits": {
                "12/31/15": {
                    "age": "17",
                    "visit_category": "Baseline Visit"
                },
                "12/31/16": {
                    "age": "18",
                    "visit_category": "Follow Up Visit"
                },
                "12/31/17": {
                    "age": "18",
                    "visit_category": "Follow Up Visit"
                }
            },

捕获它的最佳方法是什么？我一直在玩条件，但它要么破坏我的代码，要么运行正常，但记录为空。

感谢您的任何建议。