/
nautilus.go
427 lines (367 loc) · 9.01 KB
/
nautilus.go
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
420
421
422
423
424
425
426
427
package main
import (
"database/sql"
"fmt"
"github.com/lib/pq" // For use of NullTime
_ "github.com/mattn/go-oci8"
"github.com/spf13/cobra"
"io/ioutil"
"log"
"sync"
"time"
)
type NautilusSDG struct {
Sdg_id string
Sample_subject_id string
Exref sql.NullString
Collection_site sql.NullString
Universal_id string
}
type NautilusVisit struct {
Visit_id string
Sample_subject_id string
Sdg_id string
Received_on time.Time
Sd_group_name string
Sd_visit_name string
Visit_description sql.NullString
Visit_time_date time.Time
}
type NautilusAliquot struct {
SdgId sql.NullInt64
SampleSubjectName sql.NullString
CollectionSite sql.NullString
PotentialUniversalId sql.NullString
VisitName sql.NullString
AliquotId int
AliquotName sql.NullString
ParentAliquotId sql.NullInt64
VisitId int
ReceivedOn pq.NullTime
SampleTypeCode sql.NullString
SecondarySampleCode sql.NullString
SampleType sql.NullString
SecondarySampleType sql.NullString
FullSampleTypeDesc sql.NullString
CollectionEventName sql.NullString
DrawNote sql.NullString
TissueType sql.NullString
SpecimenCategory sql.NullString
CollectMethod sql.NullString
ReceivedDateTime pq.NullTime
VolumeReceived sql.NullFloat64
VolumeRemaining sql.NullFloat64
VolumeUnits sql.NullString
Concentration sql.NullFloat64
ConcentrationUnits sql.NullString
UnitId sql.NullInt64
DisposedFlag sql.NullString
AvailableFlag sql.NullString // Can probably get rid of one of these as they are mutually exclusive.
Disposed sql.NullString
LocationId sql.NullInt64
CollectDateTime pq.NullTime
}
var dbSync sync.WaitGroup
const layout = "Mon Jan _2 15:04:05 MST 2006"
var nautilusStagingCmd = &cobra.Command{
Use: "nautilus",
Short: "Run Nautilus portion of brp_demoETL",
Run: func(cmd *cobra.Command, args []string) {
if len(args) == 0 {
log.Fatal("Error: You must provide a target.")
}
staging.Add(1)
nautilusStaging(args)
}}
var nautilusStaging = func(args []string) {
defer staging.Done()
nautilus := sources["nautilus"]
target_config := targets[args[0]]
source, err := sql.Open("oci8", fmt.Sprintf("%s/%s@%s:%d/%s",
nautilus.User,
nautilus.Password,
nautilus.Host,
nautilus.Port,
nautilus.Db))
if err != nil {
log.Println(err)
}
sdg_c := make(chan []NautilusSDG)
visit_c := make(chan []NautilusVisit)
aliquot_c := make(chan []NautilusAliquot)
// Retrieve Source Data
go retrieveNautilusSDGs(source, sdg_c)
go retrieveNautilusVisits(source, visit_c)
go retrieveNautilusAliquots(source, aliquot_c)
defer source.Close()
// Create connection to target (we assume postgres)
target, err := sql.Open("postgres", fmt.Sprintf("host=%s user=%s dbname=%s sslmode=disable",
target_config.Host,
target_config.User,
target_config.Db))
// Drop/Create Nautilus Tables on Target
qs, err := ioutil.ReadFile("ddl/nautilus.sql")
_, err = target.Query(string(qs))
if err != nil {
log.Fatal(err)
}
dbSync.Add(3)
// Persist to target
go persistNautilusSDGs(target, sdg_c)
go persistNautilusVisits(target, visit_c)
go persistNautilusAliquots(target, aliquot_c)
dbSync.Wait()
defer target.Close()
log.Println("Nautilus Staging Completed.")
}
var retrieveNautilusSDGs = func(db *sql.DB, c chan []NautilusSDG) {
var sdgs []NautilusSDG
qs, err := ioutil.ReadFile("extract/NautilusSDG.sql")
rows, err := db.Query(string(qs))
if err != nil {
log.Fatal(err)
}
defer rows.Close()
for rows.Next() {
var sdg NautilusSDG
err := rows.Scan(
&sdg.Sdg_id,
&sdg.Sample_subject_id,
&sdg.Exref,
&sdg.Collection_site,
&sdg.Universal_id,
)
if err != nil {
log.Fatal(err)
}
sdgs = append(sdgs, sdg)
}
c <- sdgs
log.Println("Loaded Nautilus SDGs")
}
var retrieveNautilusVisits = func(db *sql.DB, c chan []NautilusVisit) {
var visits []NautilusVisit
// Read NautilusVisit SQL
qs, err := ioutil.ReadFile("extract/NautilusVisit.sql")
if err != nil {
log.Fatal(err)
}
// Retrieve visits from DB.
rows, err := db.Query(string(qs))
if err != nil {
log.Println(err)
}
// Scan to struct
for rows.Next() {
var visit NautilusVisit
err := rows.Scan(
&visit.Visit_id,
&visit.Sample_subject_id,
&visit.Sdg_id,
&visit.Received_on,
&visit.Sd_group_name,
&visit.Sd_visit_name,
&visit.Visit_description,
&visit.Visit_time_date,
)
if err != nil {
log.Fatal(err)
}
visits = append(visits, visit)
}
c <- visits
log.Println("Loaded Nautilus Visits")
}
var retrieveNautilusAliquots = func(db *sql.DB, c chan []NautilusAliquot) {
var aliquots []NautilusAliquot
qs, err := ioutil.ReadFile("extract/NautilusAliquot.sql")
if err != nil {
log.Fatal(err)
}
rows, err := db.Query(string(qs))
if err != nil {
log.Fatal(err)
}
for rows.Next() {
var aliquot NautilusAliquot
err := rows.Scan(
&aliquot.SdgId,
&aliquot.SampleSubjectName,
&aliquot.CollectionSite,
&aliquot.PotentialUniversalId,
&aliquot.VisitName,
&aliquot.AliquotId,
&aliquot.AliquotName,
&aliquot.ParentAliquotId,
&aliquot.VisitId,
&aliquot.ReceivedOn,
&aliquot.SampleTypeCode,
&aliquot.SecondarySampleCode,
&aliquot.SampleType,
&aliquot.SecondarySampleType,
&aliquot.FullSampleTypeDesc,
&aliquot.CollectionEventName,
&aliquot.DrawNote,
&aliquot.TissueType,
&aliquot.SpecimenCategory,
&aliquot.CollectMethod,
&aliquot.ReceivedDateTime,
&aliquot.VolumeReceived,
&aliquot.VolumeRemaining,
&aliquot.VolumeUnits,
&aliquot.Concentration,
&aliquot.ConcentrationUnits,
&aliquot.UnitId,
&aliquot.DisposedFlag,
&aliquot.AvailableFlag,
&aliquot.Disposed,
&aliquot.LocationId,
&aliquot.CollectDateTime,
)
if err != nil {
log.Fatal(err)
}
aliquots = append(aliquots, aliquot)
}
c <- aliquots
log.Println("Loaded Nautilus Aliquots")
}
var persistNautilusSDGs = func(db *sql.DB, c chan []NautilusSDG) {
defer dbSync.Done()
txn, err := db.Begin()
if err != nil {
log.Fatal(err)
}
for _, sdg := range <-c {
stmt, err := txn.Prepare(`insert into nautilus_sdg_staging values($1, $2, $3, $4, $5)`)
if err != nil {
log.Fatal(err)
}
if stmt != nil {
_, err := stmt.Exec(
sdg.Sdg_id,
sdg.Sample_subject_id,
sdg.Exref,
sdg.Collection_site,
sdg.Universal_id)
if err != nil {
log.Fatal(err)
}
err = stmt.Close()
}
}
err = txn.Commit()
if err != nil {
log.Fatal(err)
}
}
var persistNautilusVisits = func(db *sql.DB, c chan []NautilusVisit) {
defer dbSync.Done()
txn, err := db.Begin()
if err != nil {
log.Fatal(err)
}
for _, visit := range <-c {
stmt, err := txn.Prepare(`insert into nautilus_visit_staging values($1, $2, $3, $4, $5, $6, $7, $8)`)
if err != nil {
log.Fatal(err)
}
if stmt != nil {
_, err = stmt.Exec(
visit.Visit_id,
visit.Sample_subject_id,
visit.Sdg_id,
visit.Received_on,
visit.Sd_group_name,
visit.Sd_visit_name,
visit.Visit_description,
visit.Visit_time_date)
if err != nil {
log.Fatal(err)
}
err = stmt.Close()
}
}
err = txn.Commit()
if err != nil {
log.Fatal(err)
}
}
var persistNautilusAliquots = func(db *sql.DB, c chan []NautilusAliquot) {
defer dbSync.Done()
txn, err := db.Begin()
if err != nil {
log.Fatal(err)
}
for _, a := range <-c {
stmt, err := txn.Prepare(`insert into nautilus_aliquot_staging values(
$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
)`)
if err != nil {
log.Fatal(err)
}
if stmt != nil {
_, err = stmt.Exec(
a.SdgId,
a.SampleSubjectName,
a.CollectionSite,
a.PotentialUniversalId,
a.VisitName,
a.AliquotId,
a.AliquotName,
a.ParentAliquotId,
a.VisitId,
a.ReceivedOn,
a.SampleTypeCode,
a.SecondarySampleCode,
a.SampleType,
a.SecondarySampleType,
a.FullSampleTypeDesc,
a.CollectionEventName,
a.DrawNote,
a.TissueType,
a.SpecimenCategory,
a.CollectMethod,
a.ReceivedDateTime,
a.VolumeReceived,
a.VolumeRemaining,
a.VolumeUnits,
a.Concentration,
a.ConcentrationUnits,
a.UnitId,
a.DisposedFlag,
a.AvailableFlag,
a.Disposed,
a.LocationId,
a.CollectDateTime)
if err != nil {
log.Fatal(err)
}
err = stmt.Close()
}
}
err = txn.Commit()
if err != nil {
log.Fatal(err)
}
}
var nautilusTransform = func(args []string) {
target_config := targets[args[0]]
db, err := sql.Open("postgres", fmt.Sprintf("host=%s user=%s dbname=%s sslmode=disable",
target_config.Host,
target_config.User,
target_config.Db))
if err != nil {
log.Fatal(err)
}
defer db.Close()
stmt, _ := ioutil.ReadFile("transform/NautilusTransform.sql")
_, err = db.Query(string(stmt))
if err != nil {
log.Fatal(err)
}
log.Println("Nautilus transforms complete.")
}