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sispub
openbis
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d53b75f2
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d53b75f2
authored
1 year ago
by
Adam Laskowski
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SSDM-13568: Updated pybis docs
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c36cdd13
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SSDM-13578 : 2PT : Database and V3 Implementation - include the new AFS "free"...
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api-openbis-python3-pybis/src/python/README.md
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d53b75f2
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@@ -638,6 +638,27 @@ dataframe = experiments.df # get Pandas DataFrame of result list
exp = o.get_experiment('/MY_SPACE/MY_PROJECT/MY_EXPERIMENT')
```
***Note: Attributes download***
The
`get_experiments()`
method, by default, returns fewer details to make the download process faster.
However, if you want to include specific attributes in the results, you can do so by using the
`attrs`
parameter.
The
`get_experiments()`
method results include only
`identifier`
,
`permId`
,
`type`
,
`registrator`
,
`registrationDate`
,
`modifier`
,
`modificationDate`
```
get attributes
experiments = o.get_experiments(
project = 'YEASTS',
space = 'MY_SPACE',
type = 'DEFAULT_EXPERIMENT',
attrs = ["parents", "children"]
)
identifier permId type registrator registrationDate modifier modificationDate parents children
-- --------------------- -------------------- ----------------- ------------- ------------------- ---------- ------------------- ------------------------- ----------
0 /MY_SPACE/YEASTS/EXP1 20230407070122991-46 DEFAULT_EXPERIMENT admin 2023-04-07 09:01:23 admin 2023-04-07 09:02:22 ['/MY_SPACE/YEASTS/EXP2'] []
```
### Experiment attributes
```
...
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@@ -917,6 +938,26 @@ samples.df # returns a Pandas DataFrame object
samples = o.get_samples(props="*") # retrieve all properties of all samples
```
***Note: Attributes download***
The
`get_samples()`
method, by default, returns fewer details to make the download process faster.
However, if you want to include specific attributes in the results, you can do so by using the
`attrs`
parameter.
The
`get_samples()`
method results include only
`identifier`
,
`permId`
,
`type`
,
`registrator`
,
`registrationDate`
,
`modifier`
,
`modificationDate`
```
get attributes
experiments = o.get_samples(
space = 'MY_SPACE',
type = 'YEAST',
attrs = ["parents", "children"]
)
identifier permId type registrator registrationDate modifier modificationDate parents children
-- --------------------- -------------------- ----------------- ------------- ------------------- ---------- ------------------- ------------------------- ----------
0 /MY_SPACE/YEASTS/SAMPLE1 20230407070121337-47 YEAST admin 2023-04-07 09:06:23 admin 2023-04-07 09:06:22 ['/MY_SPACE/YEASTS/EXP2'] []
```
### freezing samples
```
...
...
@@ -957,6 +998,26 @@ for dataset in datasets:
dataset = datasets[0]
```
***Note: Attributes download***
The
`get_datasets()`
method, by default, returns fewer details to make the download process faster.
However, if you want to include specific attributes in the results, you can do so by using the
`attrs`
parameter.
The
`get_datasets()`
method results include only
`permId`
,
`type`
,
`experiment`
,
`sample`
,
`registrationDate`
,
`modificationDate`
,
`location`
,
`status`
,
`presentInArchive`
,
`size`
```
get attributes
experiments = o.get_datasets(
space = 'MY_SPACE',
attrs = ["parents", "children"]
)
permId type experiment sample registrationDate modificationDate location status presentInArchive size parents children
-- -------------------- -------- ------------------------ --------------------- ------------------- ------------------- --------------------------------------- --------- ------------------ ------ ------------------------ ------------------------
0 20230526101657295-48 RAW_DATA /MY_SPACE/DEFAULT/DEFAULT /MY_SPACE/DEFAULT/EXP1 2023-05-26 12:16:58 2023-05-26 12:17:37 1F60C7DC-63D8-4C07/20230526101657295-48 AVAILABLE False 469 [] ['20230526101737019-49']
1 20230526101737019-49 RAW_DATA /MY_SPACE/DEFAULT/DEFAULT /MY_SPACE/DEFAULT/EXP1 2023-05-26 12:17:37 2023-05-26 12:17:37 1F60C7DC-63D8-4C07/20230526101737019-49 AVAILABLE False 127 ['20230526101657295-48'] []
```
**More dataset functions:**
```
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