Advanced Tutorial

The code in this tutorial can also be found in the advanced ipython notebook.

TODO write some text for each code listing

Create a document with global information

import datetime as dt
from odml2 import Document, SB, Value

glob = Document()

glob.root = SB(
    "ResearchLab",
    name="Dr. Doe Lab",
    researchers=[
        SB("Person",
            label="Doe, John",
            first_name="John",
            last_name="Doe"
        ),
        SB("Person",
            label="Foo, Bar",
            first_name="Bar",
            last_name="Foo"
        )
    ],
    animals=[
        SB("Animal",
            label="subj 11",
            subject_id=11,
            date_of_birth=dt.date(2015, 11, 24),
            species="Mus musculus"
        ),
        SB("Animal",
            label="subj 12",
            subject_id=12,
            date_of_birth=dt.date(2015, 11, 25),
            species="Mus musculus"
        )
    ]
)

glob.save("global.yml")

with open("global.yml") as f:
    print(f.read())

date: null
document_version: 1
format_version: 2
author: null
namespaces: null
definitions: null
metadata:
  type: ResearchLab
  uuid: 49301a53-13de-44bd-bbf8-0a8756acbd67
  name: Dr. Doe Lab
  animals:
  - type: Animal
    uuid: 510520c9-a2af-479c-81dd-1448500d3222
    label: subj 11
    date_of_birth: 2015-11-24
    species: Mus musculus
    subject_id: 11
  - type: Animal
    uuid: a5b1167c-bce2-4ef7-97be-522060f75557
    label: subj 12
    date_of_birth: 2015-11-25
    species: Mus musculus
    subject_id: 12
  researchers:
  - type: Person
    uuid: 81dbf66f-80b5-444b-a57e-64868765a57d
    label: Doe, John
    first_name: John
    last_name: Doe
  - type: Person
    uuid: ddd2717c-de93-482b-90e0-b281b46ac1e0
    label: Foo, Bar
    first_name: Bar
    last_name: Foo

Select data from documents

# select a person with last name 'Doe' from all sections
experimenter = (s for s in glob.iter_sections()
                if s.type == "Person" and
                   s["last_name"] == "Doe").next()

# select the animal with id 11 from all animals
animal = (a for a in glob.root["animals"]
          if a["subject_id"] == 11).next()

Create a document with session information

session = Document()
session.root = SB("RecordingSession",
    label="session 42",
    session_nr=42,
    recording_date=dt.date.today()
)

session.save("session.yml")

Copy data from other documents

session = Document()
session.load("session.yml")

# copy global data to session document
session.root["experimenter"] = experimenter
session.root["subject"] = animal

session.root["subject"]["health"] = "good"
if "health" not in animal:
    print("It's a copy")

It's a copy

Link data from other documents

session = Document()
session.load("session.yml")

session.namespaces.set("glob", "global.yml")

# copy global data to session document
session.root["experimenter"] = experimenter
session.root["subject"] = animal

try:
    session.root["subject"]["health"] = "good"
except:
    print("It's a link, can't change a section" +
          "from another document")

It's a link, can't change a section from another document