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Pyelt is a python etl framework for creating and filling data vault datawarehouses

License: GNU General Public License v3.0

Python 100.00%

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python3pkg spgraham dkapitan technicalrican priya-gittest yanpan2017 traanhn nexxyb

pyelt's Issues

Onterecht extra row aangemaakt bij een rerun van exact dezelfde data in een unittest

In de unittest: test06r_hybridlinks wordt er door het opnieuw runnen van exact dezelfde brongegevens een extra rij geproduceerd in de dv laag (dv.zorgverlener_adres_link). (Deze rij verwijst naar een niet bestaand bezoekadres, dat eigenlijk al niet eens de 1e x opgenomen zou mogen worden in de dv laag)

datamart dll unittest maken

Performance hashing evalueren

Op dit moment is de logica als volgt:

hashes worden op bronsysteem berekend
alleen gewijzigde records worden opgehaald
deze worden in SOR laag inserted/updated

Kijken of werken met indexes op de SOR laag tot verbetering kan leiden voor lookups. Op dit moment nog geen index op _hash in de SOR laag

Testen en oplossing implementeren voor toevoegen nieuwe kolom in SAT

Gewenste functionaliteit: bij toevoegen van nieuwe kolom in SAT worden aanmaken van nieuwe records zoveel als mogelijk beperkt (vanuit performance oogpunt).

Hiertoe dient het volgende te gebeuren:

Testen wat er gebeurd als nieuwe kolom wordt aangemaakt. Worden in SAT nieuwe records aangemaakt of niet?
Nagaan of oplossing i) zonder nieuwe records; en ii) met sentinel value in nieuwe kolom voor alle bestaande records (b.v. null) werkt
Gekozen oplossing implementeren in pyelt

COPY ombouwen naar \copy

Bij het draaien van de DV op turing-prod blijven er errors komen vanwege het COPY commando van de files op /tmp/pyelt/data_transfer met de volgende melding (Bijvoorbeeld, hij doet het bij alle copies):

SQL: COPY sor_timeff.afspraak_deelnemer_temp (ifev_id,agb_code,ifev_rel_nr,ifam_mdw_id,ifam_ev_id,ifam_hoedanigheid,ifam_eigenaar_type) FROM  '/tmp/pyelt/datatransfer/NLHP/view_afspraak_deelnemer.csv' DELIMITER ';' CSV HEADER;

ERROR: must be superuser to COPY to or from a file
HINT:  Anyone can COPY to stdout or from stdin. psql's \copy command also works for anyone.

Zou jij het COPY statement om kunnen bouwen naar \copy, zodat de DV ook onder applicatie-user kan draaien en niet alleen onder super-users?

geen zorgprofiel_view terwijl er wel een hub is

test issue voor huboard

versie nummers afronden op 2 decimalen (sys en log)

Zowel in sys schema als in (DDL) logging staan nu versie nummers met veel decimalen. Deze afronden op twee decimalen

runid in sys.currentversion

Er staat nu alleen een date veld. Dit moet create date zijn.
Ik wil ook zien welke run (met alter_date) de versie is gewijzigd

documentatie aanpassen aan laatste code

Documentatie loopt ver achter. Er staan codevoorbeelden in die nu niet meer werken

Primary key constraint op dv.zorgaanbieder_sat_adres maakt het onmogelijk meerdere adressen per zorgaanbieder vast te leggen.

From @costiaanmesu on November 1, 2016 10:1

Copied from original issue: NLHEALTHCARE/FHIRVAULT#18

pyelt unit tests rob controleren en zorgen dat ze weer draaien

Mogelijkheid om transformaties op de SOR laag te doen? Of tijdens het inladen van de data uit een csv file? Of is dit onwenselijk?

jsonb velden implementeren

Log bug

Hoi @hvanreenen ,

Als ik op shannon pull and run aftrap en de "log" reallife monitor constateer ik het volgende:
onderstaand deel duurt ontzetten lang en vervuilt het hele "log" gedeelte. Ik zie stuk niet als ik het lokaal draait. Kun jij hier iets mee?


     -copy into temp row 3000 - 4000                         executed on 0 rows in 44.681 seconds (13 minutes and 30.543 seconds since start)

LET op dit is 1 helelelelellel lange zin
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00:00:002016-02-29 00:00:00','2222003015E436MENZZOR2016-01-01 00:00:002016-02-29 00:00:00','2222041015E436MENZZOR2016-01-01 00:00:002016-02-29 00:00:00','2222003017E436CENTVER2016-01-01 00:00:002016-02-29 00:00:00','2222041015E437MENZZOR2016-03-01 00:00:002016-12-31 00:00:00','2222041015E437PASSANT2015-01-01 00:00:002015-12-31 00:00:00','2222003015E437CENTVER2016-03-01 00:00:002016-12-31 00:00:00','2222041017E437CENTVER2016-01-01 00:00:002016-02-29 00:00:00','2222003015E437MENZZOR2016-01-01 00:00:002016-02-29 00:00:00','2222003017E438CENTVER2016-03-01 00:00:002016-12-31 00:00:00','2222002915E438CENTVER2016-03-01 00:00:002016-12-31 00:00:00','2222002915E438MENZZOR2016-01-01 00:00:002016-02-29 00:00:00','2222002915E439CENTVER2016-03-01 00:00:002016-12-31 00:00:00','2222002915E440MENZZOR2016-03-01 00:00:002016-12-31 00:00:00','2222002915E440CENTVER2016-01-01 00:00:002016-02-29 00:00:00','2222002915E440CENTVER2016-03-01 00:00:002016-12-31 00:00:00','2222003015E440MENZZOR2016-01-01 00:00:002016-02-29 00:00:00','2222002915E441PASSANT2015-01-01 00:00:002015-12-31 00:00:00','2222041015E441PASSANT2016-01-01 00:00:002016-12-31 00:00:00','2222002915E441MENZZOR2016-01-01 00:00:002016-02-29 00:00:00','2222002915E443PASSANT2015-01-01 00:00:002015-12-31 00:00:00','2222041015E443PASSANT2015-01-01 00:00:002015-12-31 00:00:00','2222041015E443CENTVER2016-01-01 00:00:002016-02-29 00:00:00','2222002915E443CENTVER2016-03-01 00:00:002016-12-31 00:00:00','2222041015E443MENZZOR2016-01-01 00:00:002016-02-29 00:00:00','2222041015E444CENTVER2016-03-01 00:00:002016-12-31 00:00:00','2222002915E444PASSANT2016-01-01 00:00:002016-12-31 00:00:00','2222041015E444PASSANT2016-01-01 00:00:002016-12-31 00:00:00','2222003015E444MENZZOR2016-01-01 00:00:002016-02-29 00:00:00','2222003015E444CENTVER2016-01-01 00:00:002016-02-29 00:00:00','2222041015E445CENTVER2016-03-01 00:00:002016-12-31 00:00:00','2222002915E445MENZZOR2016-03-01 00:00:002016-12-31 00:00:00','2222003015E304CENTVER2016-03-01 00:00:002016-12-31 00:00:00','2222002915E304MENZZOR2016-01-01 00:00:002016-02-29 00:00:00','2222003015E304PASSANT2016-01-01 00:00:002016-12-31 00:00:00','2222041015C334PASSANT2015-01-01 00:00:002015-12-31 00:00:00','2222002915C334MENZZOR2016-03-01 00:00:002016-12-31 00:00:00','2222041015C334PASSANT2016-01-01 00:00:002016-12-31 00:00:00','2222003015C334CENTVER2016-01-01 00:00:002016-02-29 00:00:00','2222041015C342MENZZOR2016-03-01 00:00:002016-12-31 00:00:00','2222002915C342CENTVER2016-01-01 00:00:002016-02-29 00:00:00','2222003015C342CENTVER2016-01-01 00:00:002016-02-29 00:00:00','2222002915C343PASSANT2016-01-01 00:00:002016-12-31 00:00:00','2222041015C343CENTVER2016-01-01 00:00:002016-02-29 00:00:00','2222002915C343CENTVER2016-03-01 00:00:002016-12-31 00:00:00','2222002917C343CENTVER2016-03-01 00:00:002016-12-31 00:00:00','2222003015C343MENZZOR2016-01-01 00:00:002016-02-29 00:00:00','2222041017C344CENTVER2016-03-01 00:00:002016-12-31 00:00:00','2222003015C344MENZZOR2016-03-01 00:00:002016-12-31 00:00:00','2222003015C344MENZZOR2016-01-01 00:00:002016-02-29 00:00:00','2222003015C344CENTVER2016-01-01 00:00:002016-02-29 00:00:00','2222003017C344CENTVER2016-01-01 00:00:002016-02-29 00:00:00','2222041015C347PASSANT2015-01-01 00:00:002015-12-31 00:00:00','2222041015C347PASSANT2016-01-01 00:00:002016-12-31 00:00:00','2222002915A342PASSANT2015-01-01 00:00:002015-12-31 00:00:00','2222041015A342MENZZOR2016-03-01 00:00:002016-12-31 00:00:00','2222003015A342MENZZOR2016-01-01 00:00:002016-02-29 00:00:00','2222002915A342MENZZOR2016-01-01 00:00:002016-02-29 00:00:00')
     -copy into temp row 4000 - 5000                         executed on 0 rows in 44.909 seconds (14 minutes and 15.453 seconds since start)

Alter statements in dimension table

in /pyelt/process/ddl.py functie create_or_alter_dim

Toevoegen alter statement voor als er velden bij zijn gekomen.

Zie __create_or_alter_sat()

Error bij aftrappen ETL #2

Hoi Hj,

dit is de reden waarom het script niet draait en wij dus geen mails krijgen.
Ik heb met dwh2_clinics user op shannon het bash script pull_and_run.sh gedraaid.

Vragen:

We kunnen maandag wel even kijken aangezien het volgens mij niet iets is waar ik meteen mee van doen heb gehad.
Voorstel om de mails ook te laten schieten als het failed. Ik heb nu het idee dat we alleen een mail krijgen als het script totaal heeft gerund (iig tot het einde).

Zie hieronder voor de foutmelding

START FROM SOURCE TO SOR executed in 0.000 seconds (6.632 seconds since start)
START view_afd -> afdeling_hstage executed in 0.000 seconds (6.632 seconds since start)
Traceback (most recent call last):
File "/opt/dwh2/PYELT/pyelt/process/etl.py", line 187, in source_to_sor_by_hash
file_name = mappings.source.to_csv(md5_only=True, filter=mappings.filter, ignore_fields=mappings.ignore_fields, debug=debug)
File "/opt/dwh2/PYELT/pyelt/sources/databases.py", line 110, in to_csv
with open(file_name, 'w', newline='', encoding='utf8') as fp:
PermissionError: [Errno 13] Permission denied: '/tmp/pyelt/datatransfer/NLHP/view_afd_hash.csv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/opt/dwh2/main.py", line 9, in
main_clinics_pipeline_run()
File "/opt/dwh2/CLINICAL_DATAVAULT_CLINICS/pipelines/clinics_main_process.py", line 58, in main_clinics_pipeline_run
pipeline.run()
File "/opt/dwh2/PYELT/pyelt/pipeline.py", line 167, in run
pipe.run(parts)
File "/opt/dwh2/PYELT/pyelt/pipeline.py", line 584, in run
etl.source_to_sor(mapping)
File "/opt/dwh2/PYELT/pyelt/process/etl.py", line 91, in source_to_sor
self.source_to_sor_by_hash(mappings)
File "/opt/dwh2/PYELT/pyelt/process/etl.py", line 303, in source_to_sor_by_hash
self.logger.log_error(mappings.name, err_msg=ex.args[0])
File "/opt/dwh2/PYELT/pyelt/helpers/pyelt_logging.py", line 135, in log_error
while err_msg.endswith('\n'):
AttributeError: 'int' object has no attribute 'endswith'

arrays kunnen opslaan in database

From @hvanreenen on October 12, 2016 6:26

Soms hebben persoon twee prive telefoonnummers, nu moet combinatie persoonnummer + tel soort uniek zijn, maar de werkelijkheid (timeff) vraagt om iets anders

Copied from original issue: NLHEALTHCARE/FHIRVAULT#9

Mogelijkheid variabele delimiters (bijv. \t) bij het inlezen van csv files.

source_to_sor_mappings, regel 105
etl.py, regel 119
files.py regel 51

performance tests jsonb

Uitzoeken hoe de performance is van jsonb velden in vergelijking met gewone velden.

Maak bijvoorbeeld gewone tabel met id, waarde1, waarde2, waarde3
Maak andere json tabel met alleen id, jsonveld, of alleen json veld
Stop in beide de zelfde 1 milj rijen met random text, in jsonveld stop je ook de 3 waardes
kijk naar verschillen in inserts, zoeken, opvragen ed.

alternatief: stop de miljoen rijen in 1 rij als een json-array. Hoe is dan de performance?
Hoe is het met 10.000 rijen?
Hoe is het als je joint met een andere tabel?

Achtergrond van deze vraag: gaan we valuesets (refs) als jsonb opslaan of niet.

ddl fact tables uitbreiden met indexes en foreign key constraints

in /pyelt/process/dll.py functie create_or_alter_fact()

Pyelt framework integreren met Spotify/Luigi

We willen het pyelt framework gaan gebruiken met een jobscheduler om daarmee:

afhankelijkheden tussen proces stappen in kaart te brengen
een manier te hebben om gecontroleerd de ETL te kunnen (her)starten)
een grafische userinterface te hebben gedurende run-time van ETL

Hiertoe zal het pyelt framework worden geintegreerd met Luigi

Deze issue omvat alle werkzaamheden t.a.v. de integratie van deze twee frameworks.

Skeduling per pipe

Per pipe kunnen opgeven of die dagelijks, wekelijks, x-maandelijks moet draaien met daarbij een bestands pattern

PostgreSQL performance optimalisatie

Op basis van eerste kijk in DV, valt mij op dat sommige views (b.v. patient_view) langzaam zijn (8 tot 10 seconden).

Ik vermoed dat we met PostgreSQL performance tuning veel verbetering kunnen doen:

waar zetten we indexes op?
welke soort index gebruiken we?
hoe doen we trade-off tussen read-snelheid vs insert-snelheid
kunnen views van entiteiten nog geoptimaliseerd worden, b.v. wanneer er veel hybrid sats --> index op type kolom

Denk/doe/kijk graag mee.

pyelt tests zorgen dat ze weer werken

Zitten momenteel in een sub mapje. Hierdoor staan imports waarschijnlijk niet meer goed

encryptie op de database

UItzoeken hoe we de inhoud van bepaalde velden kunnen versleutelen en ontsleutelen met bijvoorbeeld een wachtwoord
Kijken of dit eenvoudig te doen is. en zo ja, hoe.
Werkt dit ook op json(b) velden?

Vullen stermodel

Overwegen om alles dagelijks te droppen en weer opnieuw op te bouwen.

Alter statement is niet meer nodig

unittests aanpassen aan laatste code wijzigingen

Na grote refactor acties werken de unit tests niet meer. Deze moeten worden aangepast

Error bij het aftrappen bash script

Hoi Hj,

Zie hieronder

'error: insufficient permission for adding an object to repository database .git/objects'

is dit jou bekend?

dwh2_clinics@shannon-dev:/opt/dwh2> crontab -l
00 01 * * * bash /opt/dwh2/pull_and_run.sh >/dev/null 2>$1
dwh2_clinics@shannon-dev:/opt/dwh2> sh pull_and_run.sh
remote: Counting objects: 76, done.
remote: Compressing objects: 100% (58/58), done.
remote: Total 76 (delta 36), reused 5 (delta 5), pack-reused 13
error: insufficient permission for adding an object to repository database .git/objects
fatal: failed to write object
fatal: unpack-objects failed
remote: Counting objects: 20, done.
remote: Compressing objects: 100% (5/5), done.
remote: Total 20 (delta 0), reused 0 (delta 0), pack-reused 15
error: insufficient permission for adding an object to repository database .git/objects
fatal: failed to write object
fatal: unpack-objects failed
remote: Counting objects: 129, done.
remote: Compressing objects: 100% (89/89), done.
Receiving objects: 100% (129/129), 40.00 KiB | 0 bytes/s, done.
remote: Total 129 (delta 74), reused 17 (delta 17), pack-reused 23
Resolving deltas: 100% (84/84), completed with 12 local objects.
From https://github.com/NLHEALTHCARE/PYELT

branch HEAD -> FETCH_HEAD
Updating fe8f83e..f00eb46
Fast-forward
pyelt/datalayers/dm.py | 61 +++
pyelt/datalayers/dwh.py | 7 +
pyelt/helpers/validations.py | 2 +-
pyelt/mappings/dv_to_datamart_mappings.py | 50 +-
pyelt/mappings/sor_to_dv_mappings.py | 629 ++---------------------
pyelt/pipeline.py | 43 +-
pyelt/process/base.py | 27 +-
pyelt/process/ddl.py | 84 ++-
pyelt/process/etl.py | 3 +-
tests/data/zorgverleners3_rob.csv | 2 +-
tests/unit_tests_rob/global_test_suite.py | 3 +-
tests/unit_tests_rob/json_to_postgres.py | 49 ++
tests/unit_tests_rob/mappings_rob_hybridlinks.py | 28 +-
tests/unit_tests_rob/test05r_process.py | 29 +-
tests/unit_tests_rob/test06r_hybridlinks.py | 16 +-
tests/unit_tests_rob/test07r_jsonb.py | 210 ++++++++
tests/unit_tests_rob/test_domain.py | 48 ++
tests/unit_tests_rob/test_mappings.py | 48 ++
tests/unit_tests_rob/tester.py | 67 +++
19 files changed, 743 insertions(+), 663 deletions(-)
create mode 100644 pyelt/datalayers/dm.py
create mode 100644 tests/unit_tests_rob/json_to_postgres.py
create mode 100644 tests/unit_tests_rob/test07r_jsonb.py
create mode 100644 tests/unit_tests_rob/test_domain.py
create mode 100644 tests/unit_tests_rob/test_mappings.py
create mode 100644 tests/unit_tests_rob/tester.py

encryptie implementeren

Aanpassen to_pygram_fct(cls, schema_name):

@classmethod
def to_pygram_dim(cls, schema_name):
    cls.init_cols()
    # fct = Fact(
    #     name=schema_name + '.' + cls.get_name(),
    #     keyrefs='id',
    #     measures=cls.get_column_names())
    # return fct

dus zonder init()

Upsert (PostgreSQL 9.5) evalueren voor pyelt framework

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