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upload database module updated #295

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merged 6 commits into from
Aug 30, 2024
Merged

upload database module updated #295

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a2c90e2
Fixing errors and update to allow to upload to skylims
luissian Aug 28, 2024
dd631e1
fixing errors
luissian Aug 29, 2024
1498fac
fixing litin
luissian Aug 29, 2024
3bd1309
remove variable does not used
luissian Aug 29, 2024
af59823
defined back the log summary file
luissian Aug 29, 2024
24e86b0
updated log summary comments from the PR review
luissian Aug 30, 2024
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22 changes: 11 additions & 11 deletions relecov_tools/__main__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
import relecov_tools.download_manager
import relecov_tools.json_validation
import relecov_tools.map_schema
import relecov_tools.feed_database
import relecov_tools.upload_database
import relecov_tools.read_bioinfo_metadata
import relecov_tools.metadata_homogeneizer
import relecov_tools.gisaid_upload
Expand Down Expand Up @@ -60,7 +60,7 @@ def run_relecov_tools():
)

# stderr.print("[green] `._,._,'\n", highlight=False)
__version__ = "0.0.5"
__version__ = "0.0.6"
stderr.print(
"\n" "[grey39] RELECOV-tools version {}".format(__version__), highlight=False
)
Expand Down Expand Up @@ -373,7 +373,6 @@ def launch(user):
pass


# update_db TODO: Include types of data and database servers in config file
@relecov_tools_cli.command(help_priority=9)
@click.option("-j", "--json", help="data in json format")
@click.option(
Expand All @@ -385,8 +384,8 @@ def launch(user):
help="Select the type of information to upload to database",
)
@click.option(
"-d",
"databaseServer",
"-plat",
"--platform",
type=click.Choice(
[
"iskylims",
Expand All @@ -395,23 +394,24 @@ def launch(user):
),
multiple=False,
default=None,
help="name of the server which information is defined in config file",
help="name of the platform where data is uploaded",
)
@click.option("-u", "--user", help="user name for login")
@click.option("-p", "--password", help="password for the user to login")
@click.option("-s", "--server_url", help="url of the platform server")
@click.option(
"-f",
"--full_update",
is_flag=True,
default=False,
help="Sequentially run every update option",
)
def update_db(user, password, json, type, databaseServer, full_update):
"""feed database with json"""
feed_database = relecov_tools.feed_database.FeedDatabase(
user, password, json, type, databaseServer, full_update
def update_db(user, password, json, type, platform, server_url, full_update):
"""upload the information included in json file to the database"""
update_database_obj = relecov_tools.upload_database.UpdateDatabase(
user, password, json, type, platform, server_url, full_update
)
feed_database.update_db()
update_database_obj.update_db()


# read metadata bioinformatics
Expand Down
86 changes: 44 additions & 42 deletions relecov_tools/conf/configuration.json
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Original file line number Diff line number Diff line change
Expand Up @@ -270,54 +270,56 @@
"GISAID_configuration": {
"submitter": "GISAID_ID"
},
"external_url": {
"iskylims": {
"server": "http://relecov-iskylims.isciiides.es",
"url": "/wetlab/api/",
"store_samples": "createSampleData",
"url_project_fields": "sampleProjectFields",
"url_sample_fields": "sampleFields",
"param_sample_project": "project",
"project_name": "relecov",
"token": ""
},
"relecov": {
"server": "http://relecov-platform.isciiides.es",
"url": "/api/",
"upload_database": {
"platform":{
"iskylims": {
"server_url": "http://relecov-iskylims.isciiides.es",
"api_url": "/wetlab/api/",
"store_samples": "create-sample",
"url_project_fields": "projects-fields",
"url_sample_fields": "sample-fields",
"param_sample_project": "project",
"project_name": "relecov",
"token": ""
},
"relecov": {
"server_url": "http://relecov-platform.isciiides.es",
"api_url": "/api/",
"store_samples": "createSampleData",
"bioinfodata": "createBioinfoData",
"variantdata": "createVariantData",
"sftp_info": "sftpInfo",
"token": ""
}
},
"iskylims_fixed_values": {
"patientCore": "",
"sampleProject": "Relecov",
"onlyRecorded": "Yes",
"sampleLocation": "Not defined"
}
},
"iskylims_fixed_values": {
"patient_core": "",
"sample_project": "Relecov",
"only_recorded": "Yes",
"sample_location": "Not defined"
},
"relecov_sample_metadata": [
"authors",
"collecting_institution",
"collecting_lab_sample_id",
"ena_broker_name",
"ena_sample_accession",
"gisaid_accession_id",
"gisaid_virus_name",
"microbiology_lab_sample_id",
"r1_fastq_filepath",
"r2_fastq_filepath",
"schema_name",
"schema_version",
"sequencing_date",
"sequence_file_R1_md5",
"sequence_file_R2_md5",
"sequence_file_R1_fastq",
"sequence_file_R2_fastq",
"sequencing_sample_id",
"submitting_lab_sample_id"
]
},
"relecov_sample_metadata": [
"authors",
"collecting_institution",
"collecting_lab_sample_id",
"ena_broker_name",
"ena_sample_accession",
"gisaid_accession_id",
"gisaid_virus_name",
"microbiology_lab_sample_id",
"r1_fastq_filepath",
"r2_fastq_filepath",
"schema_name",
"schema_version",
"sequencing_date",
"sequence_file_R1_md5",
"sequence_file_R2_md5",
"sequence_file_R1_fastq",
"sequence_file_R2_fastq",
"sequencing_sample_id",
"submitting_lab_sample_id"
],
"ENA_fields": {
"ENA_configuration": {
"study_alias": "RELECOV",
Expand Down
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