aboutsummaryrefslogtreecommitdiff
path: root/gn3/db/sample_data.py
blob: b67fe1c050706cf81bab1499696be674533fd313 (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
"""Module containing functions that work with sample data"""
from typing import Any, Tuple, Dict, Callable

import re
import MySQLdb

from gn3.csvcmp import extract_strain_name
from gn3.csvcmp import parse_csv_column


_MAP = {
    "PublishData": ("StrainId", "Id", "value"),
    "PublishSE": ("StrainId", "DataId", "error"),
    "NStrain": ("StrainId", "DataId", "count"),
}


def __extract_actions(
    original_data: str, updated_data: str, csv_header: str
) -> Dict:
    """Return a dictionary containing elements that need to be deleted, inserted,
    or updated.

    """
    result: Dict[str, Any] = {
        "delete": {"data": [], "csv_header": []},
        "insert": {"data": [], "csv_header": []},
        "update": {"data": [], "csv_header": []},
    }
    strain_name = ""
    for _o, _u, _h in zip(
        original_data.strip().split(","),
        updated_data.strip().split(","),
        csv_header.strip().split(","),
    ):
        if _h == "Strain Name":
            strain_name = _o
        if _o == _u:  # No change
            continue
        if _o and _u == "x":  # Deletion
            result["delete"]["data"].append(_o)
            result["delete"]["csv_header"].append(_h)
        elif _o == "x" and _u:  # Insert
            result["insert"]["data"].append(_u)
            result["insert"]["csv_header"].append(_h)
        elif _o and _u:  # Update
            result["update"]["data"].append(_u)
            result["update"]["csv_header"].append(_h)
    for key, val in result.items():
        if not val["data"]:
            result[key] = None
        else:
            result[key]["data"] = f"{strain_name}," + ",".join(
                result[key]["data"]
            )
            result[key]["csv_header"] = "Strain Name," + ",".join(
                result[key]["csv_header"]
            )
    return result


def get_trait_csv_sample_data(
    conn: Any, trait_name: int, phenotype_id: int
) -> str:
    """Fetch a trait and return it as a csv string"""
    __query = (
        "SELECT concat(st.Name, ',', ifnull(pd.value, 'x'), ',', "
        "ifnull(ps.error, 'x'), ',', ifnull(ns.count, 'x')) as 'Data' "
        ",ifnull(ca.Name, 'x') as 'CaseAttr', "
        "ifnull(cxref.value, 'x') as 'Value' "
        "FROM PublishFreeze pf "
        "JOIN PublishXRef px ON px.InbredSetId = pf.InbredSetId "
        "JOIN PublishData pd ON pd.Id = px.DataId "
        "JOIN Strain st ON pd.StrainId = st.Id "
        "LEFT JOIN PublishSE ps ON ps.DataId = pd.Id "
        "AND ps.StrainId = pd.StrainId "
        "LEFT JOIN NStrain ns ON ns.DataId = pd.Id "
        "AND ns.StrainId = pd.StrainId "
        "LEFT JOIN CaseAttributeXRefNew cxref ON "
        "(cxref.InbredSetId = px.InbredSetId AND "
        "cxref.StrainId = st.Id) "
        "LEFT JOIN CaseAttribute ca ON ca.Id = cxref.CaseAttributeId "
        "WHERE px.Id = %s AND px.PhenotypeId = %s ORDER BY st.Name"
    )
    case_attr_columns = set()
    csv_data: Dict = {}
    with conn.cursor() as cursor:
        cursor.execute(__query, (trait_name, phenotype_id))
        for data in cursor.fetchall():
            if data[1] == "x":
                csv_data[data[0]] = None
            else:
                sample, case_attr, value = [
                    re.sub(r"(\\n|\\r|\\t|\\)", "", x).strip()
                    for x in [data[0], data[1], data[2]]
                ]
                if not csv_data.get(sample):
                    csv_data[sample] = {}
                csv_data[sample][case_attr] = value
                case_attr_columns.add(case_attr)
        if not case_attr_columns:
            return "Strain Name,Value,SE,Count\n" + "\n".join(csv_data.keys())
        columns = sorted(case_attr_columns)
        csv = "Strain Name,Value,SE,Count," + ",".join(columns) + "\n"
        for key, value in csv_data.items():
            if not value:
                csv += key + (len(case_attr_columns) * ",x") + "\n"
            else:
                vals = [str(value.get(column, "x")) for column in columns]
                csv += key + "," + ",".join(vals) + "\n"
        return csv
    return "No Sample Data Found"


def get_sample_data_ids(
    conn: Any, publishxref_id: int, phenotype_id: int, strain_name: str
) -> Tuple:
    """Get the strain_id, publishdata_id and inbredset_id for a given strain"""
    strain_id, publishdata_id, inbredset_id = None, None, None
    with conn.cursor() as cursor:
        cursor.execute(
            "SELECT st.id, pd.Id, pf.InbredSetId "
            "FROM PublishData pd "
            "JOIN Strain st ON pd.StrainId = st.Id "
            "JOIN PublishXRef px ON px.DataId = pd.Id "
            "JOIN PublishFreeze pf ON pf.InbredSetId "
            "= px.InbredSetId WHERE px.Id = %s "
            "AND px.PhenotypeId = %s AND st.Name = %s",
            (publishxref_id, phenotype_id, strain_name),
        )
        if _result := cursor.fetchone():
            strain_id, publishdata_id, inbredset_id = _result
        if not all([strain_id, publishdata_id, inbredset_id]):
            # Applies for data to be inserted:
            cursor.execute(
                "SELECT DataId, InbredSetId FROM PublishXRef "
                "WHERE Id = %s AND PhenotypeId = %s",
                (publishxref_id, phenotype_id),
            )
            publishdata_id, inbredset_id = cursor.fetchone()
            cursor.execute(
                "SELECT Id FROM Strain WHERE Name = %s", (strain_name,)
            )
            strain_id = cursor.fetchone()[0]
    return (strain_id, publishdata_id, inbredset_id)


# pylint: disable=[R0913, R0914]
def update_sample_data(
    conn: Any,
    trait_name: str,
    original_data: str,
    updated_data: str,
    csv_header: str,
    phenotype_id: int,
) -> int:
    """Given the right parameters, update sample-data from the relevant
    table."""

    def __update_data(conn, table, value):
        if value and value != "x":
            with conn.cursor() as cursor:
                sub_query = " = %s AND ".join(_MAP.get(table)[:2]) + " = %s"
                _val = _MAP.get(table)[-1]
                cursor.execute(
                    (f"UPDATE {table} SET {_val} = %s " f"WHERE {sub_query}"),
                    (value, strain_id, data_id),
                )
                return cursor.rowcount
        return 0

    def __update_case_attribute(
        conn, value, strain_id, case_attr, inbredset_id
    ):
        if value != "x":
            (id_, name) = parse_csv_column(case_attr)
            with conn.cursor() as cursor:
                if id_:
                    cursor.execute(
                        "UPDATE CaseAttributeXRefNew "
                        "SET Value = %s "
                        "WHERE StrainId = %s AND CaseAttributeId = %s "
                        "AND InbredSetId = %s",
                        (value, strain_id, id_, inbredset_id),
                    )
                else:
                    cursor.execute(
                        "UPDATE CaseAttributeXRefNew "
                        "SET Value = %s "
                        "WHERE StrainId = %s AND CaseAttributeId = "
                        "(SELECT CaseAttributeId FROM "
                        "CaseAttribute WHERE Name = %s) "
                        "AND InbredSetId = %s",
                        (value, strain_id, name, inbredset_id),
                    )
                return cursor.rowcount
        return 0

    strain_id, data_id, inbredset_id = get_sample_data_ids(
        conn=conn,
        publishxref_id=int(trait_name),
        phenotype_id=phenotype_id,
        strain_name=extract_strain_name(csv_header, original_data),
    )

    none_case_attrs: Dict[str, Callable] = {
        "Strain Name": lambda x: 0,
        "Value": lambda x: __update_data(conn, "PublishData", x),
        "SE": lambda x: __update_data(conn, "PublishSE", x),
        "Count": lambda x: __update_data(conn, "NStrain", x),
    }
    count = 0
    try:
        __actions = __extract_actions(
            original_data=original_data,
            updated_data=updated_data,
            csv_header=csv_header,
        )

        if __actions.get("update"):
            _csv_header = __actions["update"]["csv_header"]
            _data = __actions["update"]["data"]
            # pylint: disable=[E1101]
            for header, value in zip(_csv_header.split(","), _data.split(",")):
                header = header.strip()
                value = value.strip()
                if header in none_case_attrs:
                    count += none_case_attrs[header](value)
                else:
                    count += __update_case_attribute(
                        conn=conn,
                        value=value,
                        strain_id=strain_id,
                        case_attr=header,
                        inbredset_id=inbredset_id,
                    )
        if __actions.get("delete"):
            _rowcount = delete_sample_data(
                conn=conn,
                trait_name=trait_name,
                data=__actions["delete"]["data"],
                csv_header=__actions["delete"]["csv_header"],
                phenotype_id=phenotype_id,
            )
            if _rowcount:
                count += 1
        if __actions.get("insert"):
            _rowcount = insert_sample_data(
                conn=conn,
                trait_name=trait_name,
                data=__actions["insert"]["data"],
                csv_header=__actions["insert"]["csv_header"],
                phenotype_id=phenotype_id,
            )
            if _rowcount:
                count += 1
    except Exception as _e:
        raise MySQLdb.Error(_e) from _e
    return count


def delete_sample_data(
    conn: Any, trait_name: str, data: str, csv_header: str, phenotype_id: int
) -> int:
    """Given the right parameters, delete sample-data from the relevant
    tables."""

    def __delete_data(conn, table):
        sub_query = " = %s AND ".join(_MAP.get(table)[:2]) + " = %s"
        with conn.cursor() as cursor:
            cursor.execute(
                (f"DELETE FROM {table} " f"WHERE {sub_query}"),
                (strain_id, data_id),
            )
            return cursor.rowcount

    def __delete_case_attribute(conn, strain_id, case_attr, inbredset_id):
        with conn.cursor() as cursor:
            (id_, name) = parse_csv_column(case_attr)
            if id_:
                cursor.execute(
                    "DELETE FROM CaseAttributeXRefNew "
                    "WHERE StrainId = %s AND CaseAttributeId = %s "
                    "AND InbredSetId = %s",
                    (strain_id, id_, inbredset_id),
                )
            else:
                cursor.execute(
                    "DELETE FROM CaseAttributeXRefNew "
                    "WHERE StrainId = %s AND CaseAttributeId = "
                    "(SELECT CaseAttributeId FROM "
                    "CaseAttribute WHERE Name = %s) "
                    "AND InbredSetId = %s",
                    (strain_id, name, inbredset_id),
                )
            return cursor.rowcount

    strain_id, data_id, inbredset_id = get_sample_data_ids(
        conn=conn,
        publishxref_id=int(trait_name),
        phenotype_id=phenotype_id,
        strain_name=extract_strain_name(csv_header, data),
    )

    none_case_attrs: Dict[str, Any] = {
        "Strain Name": lambda: 0,
        "Value": lambda: __delete_data(conn, "PublishData"),
        "SE": lambda: __delete_data(conn, "PublishSE"),
        "Count": lambda: __delete_data(conn, "NStrain"),
    }
    count = 0

    try:
        for header in csv_header.split(","):
            header = header.strip()
            if header in none_case_attrs:
                count += none_case_attrs[header]()
            else:
                count += __delete_case_attribute(
                    conn=conn,
                    strain_id=strain_id,
                    case_attr=header,
                    inbredset_id=inbredset_id,
                )
    except Exception as _e:
        raise MySQLdb.Error(_e) from _e
    return count


# pylint: disable=[R0913, R0914]
def insert_sample_data(
    conn: Any, trait_name: str, data: str, csv_header: str, phenotype_id: int
) -> int:
    """Given the right parameters, insert sample-data to the relevant table."""

    def __insert_data(conn, table, value):
        if value and value != "x":
            with conn.cursor() as cursor:
                columns = ", ".join(_MAP.get(table))
                cursor.execute(
                    (
                        f"INSERT INTO {table} "
                        f"({columns}) "
                        f"VALUES (%s, %s, %s)"
                    ),
                    (strain_id, data_id, value),
                )
                return cursor.rowcount
        return 0

    def __insert_case_attribute(conn, case_attr, value):
        if value != "x":
            with conn.cursor() as cursor:
                (id_, name) = parse_csv_column(case_attr)
                if not id_:
                    cursor.execute(
                        "SELECT Id FROM CaseAttribute WHERE Name = %s",
                        (name,),
                    )
                    if case_attr_id := cursor.fetchone():
                        id_ = case_attr_id[0]

                cursor.execute(
                    "SELECT StrainId FROM "
                    "CaseAttributeXRefNew WHERE StrainId = %s "
                    "AND CaseAttributeId = %s "
                    "AND InbredSetId = %s",
                    (strain_id, id_, inbredset_id),
                )
                if (not cursor.fetchone()) and id_:
                    cursor.execute(
                        "INSERT INTO CaseAttributeXRefNew "
                        "(StrainId, CaseAttributeId, Value, InbredSetId) "
                        "VALUES (%s, %s, %s, %s)",
                        (strain_id, id_, value, inbredset_id),
                    )
                    row_count = cursor.rowcount
                    return row_count
        return 0

    strain_id, data_id, inbredset_id = get_sample_data_ids(
        conn=conn,
        publishxref_id=int(trait_name),
        phenotype_id=phenotype_id,
        strain_name=extract_strain_name(csv_header, data),
    )

    none_case_attrs: Dict[str, Any] = {
        "Strain Name": lambda _: 0,
        "Value": lambda x: __insert_data(conn, "PublishData", x),
        "SE": lambda x: __insert_data(conn, "PublishSE", x),
        "Count": lambda x: __insert_data(conn, "NStrain", x),
    }

    try:
        count = 0

        # Check if the data already exists:
        with conn.cursor() as cursor:
            cursor.execute(
                "SELECT Id FROM PublishData where Id = %s "
                "AND StrainId = %s",
                (data_id, strain_id),
            )
        if cursor.fetchone():  # Data already exists
            return count

        for header, value in zip(csv_header.split(","), data.split(",")):
            header = header.strip()
            value = value.strip()
            if header in none_case_attrs:
                count += none_case_attrs[header](value)
            else:
                count += __insert_case_attribute(
                    conn=conn, case_attr=header, value=value
                )
        return count
    except Exception as _e:
        raise MySQLdb.Error(_e) from _e