Hi!
What do we want :
Using the API (bioblend 0.4.3, Galaxy-dist ( 22 jan 2014 ) ): upload files
from user's FTP directory to Galaxy and launch workflow
How we do it :
1. Determine the user's *libraryID* and *historyID*
2. Upload files : *gi.libraries.upload_file_from_server (libraryID,
server_dir)* and get the *datasetID* in user's library (*libraryID*).
3. Check the status of the upoaded file : *gi.datasets.show_dataset
(datasetID)*.
4. If state of dataset is *'ok'* (*gi.datasets.show_dataset (datasetID)
['state']*), we import it to the history (*historyID*):
*gi.histories.upload_dataset_from_library
(historyID, datasetID, 'library')*
5. Now we can run workflow
Problem:
For the new user the command *gi.datasets.show_dataset (datasetID)* works
properly and displays information about the required dataset, but after a
while (after some upload iterations) the command
*gi.datasets.show_dataset(datasetID)* displays information about wrong
dataset ( with identical *datasetID*, but not the current member of user's
library (*libraryID*).
But in bioblend docs:
" *show_dataset(dataset_id, deleted=False)*
Display information about and/or content of a dataset. This can be a
history or a library dataset."
Example:
libraryID = gi.libraries.get_libraries()[ 0 ][ 'id' ]
u'*417e33144b294c21*'
lib = gi.libraries.show_library(libraryID, True)
[ {
u'url': u'/api/libraries/417e33144b294c21/contents/c8990a1b374598b0',
u'type': u'file',
u'id': u*'c8990a1b374598b0*',
u'name': u'/opo_opo.csfasta'
}
]
datasetID = *c8990a1b374598b0*
http://<server>/api/datasets/c8990a1b374598b0?key=<api_key>
gi.datasets.show_dataset('c8990a1b374598b0')
{
u'accessible': True, u'visible': True,
u'copied_from_ldda_id': u'911dde3ddb677bcd',
u'file_size': 0, u'file_ext': u'data',
*u'id': u'c8990a1b374598b0', *
u'misc_info': u'failure running job', u'hda_ldda': u'hda',
u'download_url':
u'/api/histories/5969b1f7201f12ae/contents/c8990a1b374598b0/display',
u'state': u'error', u'display_types': [], u'display_apps': [],
u'misc_blurb': u'tool error',
u'peek': u'<table cellspacing="0" cellpadding="3"></table>', u'data_type':
u'data', u'tags': [],
u'deleted': True, u'history_id': u'5969b1f7201f12ae', u'genome_build':
u'?', u'hid': 220,
u'visualizations': [], u'metadata_dbkey': u'?',
*u'name': u'dataset_1.dat', *<-?????
u'uuid': None,
u'model_class': u'HistoryDatasetAssociation', u'purged': False,
u'api_type': u'file'
}
BUT
---
http://
<server>/api/libraries/417e33144b294c21/contents/c8990a1b374598b0?key=<api_key>
gi.libraries.show_dataset(librarypID, '*c8990a1b374598b0*')
{
"data_type": "csfasta",
"date_uploaded": "2014-04-08T12:07:14.357356",
"file_name":
"/home/pandorin/galaxy-dist/database/files/000/dataset_228.dat",
"file_size": 82283303,
"folder_id": "417e33144b294c21",
"genome_build": "?",
"id": "c8990a1b374598b0",
"ldda_id": "*c8990a1b374598b0*",
"message": "",
"metadata_data_lines": null,
"metadata_dbkey": "?",
"metadata_sequences": null,
"misc_blurb": "78.5 MB",
"misc_info": "\nuploaded csfasta file",
"model_class": "LibraryDataset",
"name": "*opo_opo.csfasta*",
"template_data": {},
"uploaded_by": "new...@mail.ru",
"uuid": null
}
In *libraries.show_dataset() *no '*state*' attribute.
Best regards,
Anatoly
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