BarneyLabstep
commented
1 month ago Hi Henri,
The entry itself is stored as a JSON document so it requires a bit of extra knowledge about the format to edit it. Here are some examples of how to add some different types of elements. For other elements or formatting options you can use the web app to produce the desired result and the inspect the network request sent to see the shape of the JSON document object (look for the state field that is sent).
import labstep
import os
user = labstep.authenticate(apikey='YOUR_API_KEY')
initialEntry = {
"type": "doc",
"content": []
}
experiment = user.newExperiment('API Experiment',entry=initialEntry)
# Adding text to the entry
entry = experiment.getEntry()
newContent = {
"type": "paragraph",
"attrs": {"align": None},
"content": [
{
"type": "text", ## NOTE: this type of node MUST be embdedded in a paragraph node
"text": "This is a new paragraph"
}
]
}
entry['content'].append(newContent)
experiment.edit(entry=entry)
## Adding a file / image to the entry (images rendered automatically)
entry = experiment.getEntry()
file = experiment.addFile(os.path.abspath(__file__)) ## Replace with path to file
newContent = {
"type": "paragraph",
"attrs": {"align": None},
"content": [
{
"type": "file", ## NOTE: this type of node MUST be embdedded in a paragraph node
"attrs": {
"id": file["id"],
"fullWidth": False
}
}
]
}
entry['content'].append(newContent)
experiment.edit(entry=entry)
## Adding a data field to the entry
dataField = experiment.addDataField('My Data Field',fieldType='file')
file = user.newFile(os.path.abspath(__file__)) ## Replace with path to file
dataField.setValue(file)
newContent = {"type": "metadata", "attrs": {"id": dataField["id"]}}
entry['content'].append(newContent)
experiment.edit(entry=entry)
## Adding an inventory field to the entry
inventoryField = experiment.addInventoryField('Sample')
newContent = {
"type": "paragraph",
"attrs": {"align": None},
"content": [
{
"type": "protocol_value", ## NOTE: this type of node MUST be embdedded in a paragraph node
"attrs": {"id": inventoryField["id"]}
}
]
}
entry['content'].append(newContent)
experiment.edit(entry=entry)
## Adding an inline spreadsheet to the entry
data = {
"rowCount": 12,
"columnCount": 12,
"colHeaderData": {},
"data": {
"dataTable": {
0: {
0: {
"value": 'Column 1'
},
1: {
"value": 'Column 2'
}
},
1: {
0: {
"value": "A2"
},
1: {
"value": "B2"
}
}
}
}
}
table = experiment.addTable('Spreadsheet 1',data=data)
newContent = {"type": "protocol_table", "attrs": {"id": table["id"]}}
entry['content'].append(newContent)
experiment.edit(entry=entry)
## Adding a protocol to the entry
protocol = user.newProtocol('My Protocol')
experiment_protocol = experiment.addProtocol(protocol)
newContent = {
"type": "paragraph",
"attrs": {"align": None},
"content": [
{
"type": "experiment", ## NOTE: this type of node MUST be embdedded in a paragraph node
"attrs": {"id": experiment_protocol["id"]}
}
]
}
entry['content'].append(newContent)
experiment.edit(entry=entry)
## Adding a basic table to the entry
newContent = {
"type": "table",
"content": [
{
"type": "table_row",
"content": [
{
"type": "table_cell",
"attrs": {
"colspan": 1,
"rowspan": 1,
"colwidth": None,
"background": None
},
"content": [
{
"type": "paragraph",
"attrs": {
"align": None
},
"content": [
{
"type": "text",
"text": "Column 1"
}
]
}
]
},
{
"type": "table_cell",
"attrs": {
"colspan": 1,
"rowspan": 1,
"colwidth": None,
"background": None
},
"content": [
{
"type": "paragraph",
"attrs": {
"align": None
},
"content": [
{
"type": "text",
"text": "Column 2"
}
]
}
]
}
]
},
{
"type": "table_row",
"content": [
{
"type": "table_cell",
"attrs": {
"colspan": 1,
"rowspan": 1,
"colwidth": None,
"background": None
},
"content": [
{
"type": "paragraph",
"attrs": {
"align": None
}
}
]
},
{
"type": "table_cell",
"attrs": {
"colspan": 1,
"rowspan": 1,
"colwidth": None,
"background": None
},
"content": [
{
"type": "paragraph",
"attrs": {
"align": None
}
}
]
}
]
}
]
}
entry['content'].append(newContent)
experiment.edit(entry=entry)
'''
For other elements or formatting options...
Please use the web app to produce the desired result and
inspect the network request sent to see the shape of the JSON document object
'''
HenrivdGeest
Im new to using the api. Logon and creating a new experiment worked from the start. However, adding text to my experiment seems harder. I tried:
I ran the script multiple times while changing the dataTable, and it seems that getTables() does retrieve all my tries, but Online I can see some text+image which I also added via the web browser.
I also tried addFile(), but that did not work either. Only comments are ending up in the notes section, so that does work. Any ideas ?