def submit_job():
"""
Endpoint to submit a database to be processed and added to the metadata database
This is using docstring for specifications
---
tags:
- jobs
parameters:
- in: body
name: body
description: copy database job object
required: false
schema:
$ref: '#/definitions/submit'
operationId: jobs
consumes:
- application/json
produces:
- application/json
security:
submit_auth:
- 'write:submit'
- 'read:submit'
schemes: ['http', 'https']
deprecated: false
externalDocs:
description: Project repository
url: http://github.com/rochacbruno/flasgger
definitions:
submit:
title: Database copy job
description: A job to process a database and add it to the metadata database from a source MySQL server to a target MySQL server.
type: object
required:
-metadata_uri
-database_uri
-update_type
-comment
-email
-source
properties:
metadata_uri:
type: string
example: 'mysql://*****:*****@server:port/metadata_db'
database_uri:
type: string
example: 'mysql://*****:*****@server:port/db'
e_release:
type: integer
example: 91
eg_release:
type: integer
example: 38
release_date:
type: string
example: '2017-12-06'
current_release:
type: integer
example: 1
email:
type: string
example: 'undefined'
update_type:
type: string
example: 'new_assembly'
comment:
type: string
example: 'handover of new species'
source:
type: string
example: '*****@*****.**'
responses:
200:
description: submit of a metadata job
schema:
$ref: '#/definitions/submit'
examples:
{metadata_uri : "mysql://*****:*****@mysql-ens-general-dev-1:4484/ensembl_metadata_new_test", database_uri : "mysql://ensro@mysql-ensembl-mirror:4240/octodon_degus_otherfeatures_91_1", update_type : "new_assembly", source : "Handover", comment : "handover new Leopard database", email : "*****@*****.**"}
"""
if json_pattern.match(request.headers['Content-Type']):
request.json["metadata_uri"] = app.config["METADATA_URI"]
app.logger.debug('Submitting metadata job %s', request.json)
try:
job = get_hive().create_job(app.analysis, request.json)
except ValueError as e:
raise HTTPRequestError(str(e), 404)
results = {
"job_id": job.job_id
}
email = request.json.get('email')
email_notification = request.json.get('email_notification')
if email != None and email != '' and email_notification != None:
app.logger.debug('Submitting email request for %s', email)
email_results = email_when_complete.delay(
request.url_root + "jobs/" + str(job.job_id) + "?format=email",
email)
results['email_task'] = email_results.id
return jsonify(results)
else:
app.logger.error('Could not handle input of type %s',
request.headers['Content-Type'])
raise HTTPRequestError('Could not handle input of type %s' %
request.headers['Content-Type'])
def delete_job(process, job_id):
"""
Endpoint to delete a given job result using job_id
---
tags:
- jobs
parameters:
- name: process
in: path
type: string
required: true
default: 1
description: process name
- name: job_id
in: path
type: integer
required: true
default: 1
description: id of the job
operationId: jobs
consumes:
- application/json
produces:
- application/json
security:
delete_auth:
- 'write:delete'
- 'read:delete'
schemes: ['http', 'https']
deprecated: false
externalDocs:
description: Project repository
url: http://github.com/rochacbruno/flasgger
definitions:
job_id:
type: object
properties:
job_id:
type: integer
items:
$ref: '#/definitions/job_id'
id:
type: integer
properties:
id:
type: integer
items:
$ref: '#/definitions/id'
responses:
200:
description: Job_id that has been deleted
schema:
$ref: '#/definitions/job_id'
examples:
id: 1
"""
hive = get_hive(process)
job = hive.get_job_by_id(job_id)
try:
hive.delete_job(job)
except ValueError as e:
raise HTTPRequestError(str(e), 404)
return jsonify({"id": job_id, "process": process})
def job_result(job_id):
"""
Endpoint to retrieve a given job result using job_id
This is using docstring for specifications
---
tags:
- jobs
parameters:
- name: job_id
in: path
type: integer
required: true
default: 1
description: id of the job
- name: format
in: query
type: string
required: false
description: optional parameter (email, failures)
- name: email
in: query
type: string
required: false
description: Email address to use in report
operationId: jobs
consumes:
- application/json
produces:
- application/json
security:
results_auth:
- 'write:results'
- 'read:results'
schemes: ['http', 'https']
deprecated: false
externalDocs:
description: Project repository
url: http://github.com/rochacbruno/flasgger
definitions:
job_id:
type: object
properties:
job_id:
type: integer
items:
$ref: '#/definitions/job_id'
result:
type: object
properties:
result:
type: string
items:
$ref: '#/definitions/result'
responses:
200:
description: Result of a metadata job
schema:
$ref: '#/definitions/job_id'
examples:
id: 1
input:
metadata_uri: mysql://user:password@server:port/ensembl_metadata
database_uri: mysql://user:password@server:port/saccharomyces_cerevisiae_core_91_4
timestamp: 1515494114.263158
output:
runtime: 31 seconds
metadata_uri: mysql://user:password@server:port/ensembl_metadata
database_uri: mysql://user:password@server:port/saccharomyces_cerevisiae_core_91_4
status: complete
"""
fmt = request.args.get('format')
app.logger.debug('Format %s', fmt)
if fmt == 'email':
email = request.args.get('email')
return job_email(email, job_id)
elif fmt == 'failures':
return failure(job_id)
elif fmt is None:
app.logger.info('Retrieving job with ID %s', job_id)
try:
job_result = get_hive().get_result_for_job_id(job_id, child=True)
except ValueError as e:
raise HTTPRequestError(str(e), 404)
return jsonify(job_result)
else:
raise HTTPRequestError("Format " + fmt + " not valid")
def handovers():
"""
Endpoint to submit an handover job
This is using docstring for specifications
---
tags:
- handovers
parameters:
- in: body
name: body
description: healthcheck object
required: false
schema:
$ref: '#/definitions/handovers'
operationId: handovers
consumes:
- application/json
produces:
- application/json
security:
handovers_auth:
- 'write:handovers'
- 'read:handovers'
schemes: ['http', 'https']
deprecated: false
externalDocs:
description: Project repository
url: http://github.com/rochacbruno/flasgger
definitions:
handovers:
title: handover job
description: A job to handover a database, the database will be healthchecked, copied and added to metadata database
type: object
required:
-src_uri
-contact
-type
-comment
properties:
src_uri:
type: string
example: 'mysql://user@server:port/saccharomyces_cerevisiae_core_91_4'
comment:
type: string
example: 'handover new Panda OF'
contact:
type: string
example: '*****@*****.**'
responses:
200:
description: submit of an handover job
schema:
$ref: '#/definitions/handovers'
examples:
{src_uri: "mysql://user@server:port/saccharomyces_cerevisiae_core_91_4", contact: "*****@*****.**", comment: "handover new Panda OF"}
"""
if json_pattern.match(request.headers['Content-Type']):
app.logger.debug('Submitting handover request %s', request.json)
spec = request.json
if 'src_uri' not in spec or 'contact' not in spec or 'comment' not in spec:
raise HTTPRequestError(
"Handover specification incomplete - please specify src_uri, contact and comment"
)
ticket = handover_database(spec)
app.logger.info('Ticket: %s', ticket)
return jsonify(ticket)
else:
raise HTTPRequestError('Could not handle input of type %s' %
request.headers['Content-Type'])
def job(process, job_id):
"""
Endpoint to retrieve a given job result for a process and job id
---
tags:
- jobs
parameters:
- name: process
in: path
type: string
required: true
default: 1
description: process name
- name: job_id
in: path
type: integer
required: true
default: 1
description: id of the job
operationId: jobs
produces:
- application/json
security:
results_auth:
- 'write:results'
- 'read:results'
schemes: ['http', 'https']
deprecated: false
externalDocs:
description: Project repository
url: http://github.com/rochacbruno/flasgger
definitions:
job_id:
type: object
properties:
job_id:
type: integer
items:
$ref: '#/definitions/job_id'
result:
type: object
properties:
result:
type: string
items:
$ref: '#/definitions/result'
responses:
200:
description: Result of an event job
schema:
$ref: '#/definitions/job_id'
"""
output_format = request.args.get('format')
if output_format == 'email':
email = request.args.get('email')
if email == None:
raise HTTPRequestError("Email not specified")
return results_email(request.args.get('email'), process, job_id)
elif output_format == None:
return results(process, job_id)
else:
raise HTTPRequestError("Format {} not known".format(output_format))
def handover_result(handover_token):
"""
Endpoint to get an handover job detail
This is using docstring for specifications
---
tags:
- handovers
parameters:
- name: handover_token
in: path
type: string
required: true
default: 15ce20fd-68cd-11e8-8117-005056ab00f0
description: handover token for the database handed over
operationId: handovers
consumes:
- application/json
produces:
- application/json
security:
handovers_auth:
- 'write:handovers'
- 'read:handovers'
schemes: ['http', 'https']
deprecated: false
externalDocs:
description: Project repository
url: http://github.com/rochacbruno/flasgger
definitions:
handovers:
title: Get a handover job details
description: This will retrieve a handover job details
type: object
required:
-handover_token
properties:
handover_token:
type: string
example: '15ce20fd-68cd-11e8-8117-005056ab00f0'
responses:
200:
description: Retrieve an handover job ticket
schema:
$ref: '#/definitions/handovers'
examples:
[{"comment": "handover new Tiger database", "contact": "*****@*****.**", "handover_token": "605f1191-7a13-11e8-aa7e-005056ab00f0", "id": "X1qcQWQBiZ0vMed2vaAt", "message": "Metadata load complete, Handover successful", "progress_total": 3, "report_time": "2018-06-27T15:19:08.459", "src_uri": "mysql://ensro@mysql-ens-general-prod-1:4525/panthera_tigris_altaica_core_93_1", "tgt_uri": "mysql://ensro@mysql-ens-general-dev-1:4484/panthera_tigris_altaica_core_93_1"} ]
"""
es = Elasticsearch([{'host': es_host, 'port': es_port}])
handover_detail = []
res_error = es.search(index=es_index,
body={
"query": {
"bool": {
"must": [{
"term": {
"params.handover_token.keyword":
str(handover_token)
}
}, {
"term": {
"report_type.keyword": "ERROR"
}
}],
"must_not": [],
"should": []
}
},
"from": 0,
"size": 1,
"sort": [{
"report_time": {
"order": "desc"
}
}],
"aggs": {}
})
app.logger.info('Retrieving handover data with token %s', handover_token)
if len(res_error['hits']['hits']) != 0:
for doc in res_error['hits']['hits']:
result = {"id": doc['_id']}
result['message'] = doc['_source']['message']
result['comment'] = doc['_source']['params']['comment']
result['handover_token'] = doc['_source']['params'][
'handover_token']
result['contact'] = doc['_source']['params']['contact']
result['src_uri'] = doc['_source']['params']['src_uri']
result['tgt_uri'] = doc['_source']['params']['tgt_uri']
result['report_time'] = doc['_source']['report_time']
handover_detail.append(result)
else:
res = es.search(index=es_index,
body={
"query": {
"bool": {
"must": [{
"term": {
"params.handover_token.keyword":
str(handover_token)
}
}, {
"term": {
"report_type.keyword": "INFO"
}
}],
"must_not": [],
"should": []
}
},
"from": 0,
"size": 1,
"sort": [{
"report_time": {
"order": "desc"
}
}],
"aggs": {}
})
for doc in res['hits']['hits']:
result = {"id": doc['_id']}
result['message'] = doc['_source']['message']
result['comment'] = doc['_source']['params']['comment']
result['handover_token'] = doc['_source']['params'][
'handover_token']
result['contact'] = doc['_source']['params']['contact']
result['src_uri'] = doc['_source']['params']['src_uri']
result['tgt_uri'] = doc['_source']['params']['tgt_uri']
result['progress_complete'] = doc['_source']['params'][
'progress_complete']
result['progress_total'] = doc['_source']['params'][
'progress_total']
result['report_time'] = doc['_source']['report_time']
handover_detail.append(result)
if len(handover_detail) == 0:
raise HTTPRequestError('Handover token %s not found' % handover_token,
404)
else:
return jsonify(handover_detail)
def delete_handover(handover_token):
"""
Endpoint to delete all the reports linked to a handover_token
This is using docstring for specifications
---
tags:
- handovers
parameters:
- name: handover_token
in: path
type: string
required: true
default: 15ce20fd-68cd-11e8-8117-005056ab00f0
description: handover token for the database handed over
operationId: handovers
consumes:
- application/json
produces:
- application/json
security:
delete_auth:
- 'write:delete'
- 'read:delete'
schemes: ['http', 'https']
deprecated: false
externalDocs:
description: Project repository
url: http://github.com/rochacbruno/flasgger
definitions:
handover_token:
type: object
properties:
handover_token:
type: integer
items:
$ref: '#/definitions/handover_token'
id:
type: integer
properties:
id:
type: integer
items:
$ref: '#/definitions/id'
responses:
200:
description: handover_token of the reports that need deleting
schema:
$ref: '#/definitions/handover_token'
examples:
id: 15ce20fd-68cd-11e8-8117-005056ab00f0
"""
try:
app.logger.info('Retrieving handover data with token %s',
handover_token)
es = Elasticsearch([{'host': es_host, 'port': es_port}])
es.delete_by_query(index=es_index,
doc_type='report',
body={
"query": {
"bool": {
"must": [{
"term": {
"params.handover_token.keyword":
str(handover_token)
}
}]
}
}
})
return jsonify(str(handover_token))
except NotFoundError as e:
raise HTTPRequestError(
'Error while looking for handover token: {} - {}:{}'.format(
handover_token, e.error, e.info['error']['reason']), 404)
def job_result(job_id):
"""
Endpoint to retrieve a given job result using job_id
This is using docstring for specifications
---
tags:
- jobs
parameters:
- name: job_id
in: path
type: integer
required: true
default: 1
description: id of the job
- name: format
in: query
type: string
required: false
description: optional parameter (email, failures)
- name: email
in: query
type: string
required: false
description: Email address to use in report
operationId: jobs
consumes:
- application/json
produces:
- application/json
security:
results_auth:
- 'write:results'
- 'read:results'
schemes: ['http', 'https']
deprecated: false
externalDocs:
description: Project repository
url: http://github.com/rochacbruno/flasgger
definitions:
job_id:
type: object
properties:
job_id:
type: integer
items:
$ref: '#/definitions/job_id'
result:
type: object
properties:
result:
type: string
items:
$ref: '#/definitions/result'
responses:
200:
description: Result of an healthcheck job
schema:
$ref: '#/definitions/job_id'
examples:
id: 1
input:
compara_uri: mysql://user@server:port/ensembl_compara_master
data_files_path: /nfs/panda/ensembl/production/ensemblftp/data_files/
db_uri: mysql://user@server:port/ailuropoda_melanoleuca_core_91_1
hc_names: ['org.ensembl.healthcheck.testcase.eg_core.GeneSource']
live_uri: mysql://user@server:port/
production_uri: mysql://user@server:port/ensembl_production_91
staging_uri: mysql://user@server:port/
timestamp: 1515494166.015124
output:
db_name: ailuropoda_melanoleuca_core_91_1
db_uri: mysql://user@server:port/ailuropoda_melanoleuca_core_91_1
results:
org.ensembl.healthcheck.testcase.eg_core.GeneSource:
messages: ['PROBLEM: Found 23262 genes with source Ensembl which should be replaced with an appropriate GOA compatible name for the original source']
status: failed
status: failed
status: complete
"""
fmt = request.args.get('format')
logger.debug("Format " + str(fmt))
if fmt == 'email':
email = request.args.get('email')
return job_email(email, job_id)
elif fmt == 'failures':
return job_failures(job_id)
elif fmt is None:
logger.info("Retrieving job with ID " + str(job_id))
try:
job_result = get_hive().get_result_for_job_id(job_id)
except ValueError as e:
raise HTTPRequestError(str(e), 404)
return jsonify(job_result)
else:
raise HTTPRequestError("Format " + fmt + " not valid")
def submit_job():
"""
Endpoint to submit an healthcheck job
This is using docstring for specifications
---
tags:
- jobs
parameters:
- in: body
name: body
description: healthcheck object
required: false
schema:
$ref: '#/definitions/submit'
operationId: jobs
consumes:
- application/json
produces:
- application/json
security:
submit_auth:
- 'write:submit'
- 'read:submit'
schemes: ['http', 'https']
deprecated: false
externalDocs:
description: Project repository
url: http://github.com/rochacbruno/flasgger
definitions:
submit:
title: Healthcheck job
description: A job to run multiple healthchecks or healthchecks groups on a given database URI.
type: object
required:
-db_uri
-compara_uri
-live_uri
-production_uri
-staging_uri
-hc_names
-data_files_path
properties:
db_uri:
type: string
example: 'mysql://user@server:port/saccharomyces_cerevisiae_core_91_4'
compara_uri:
type: string
example: 'mysql://*****:*****@server:port/compara_master'
live_uri:
type: string
example: 'mysql://*****:*****@server:port/'
staging_uri:
type: string
example: 'mysql://*****:*****@server:port/'
production_uri:
type: string
example: 'mysql://*****:*****@server:port/ensembl_production_xx'
hc_names:
type: array
items:
type: string
example: 'org.ensembl.healthcheck.testcase.generic.StableID'
hc_groups:
type: array
items:
type: string
example: ''
data_files_path:
type: string
example: '/nfs/panda/ensembl/production/ensemblftp/data_files/'
email:
type: string
example: 'undefined'
responses:
200:
description: submit of an healthcheck job
schema:
$ref: '#/definitions/submit'
examples:
{db_uri: "mysql://user@server:port/saccharomyces_cerevisiae_core_91_4", staging_uri: "mysql://user@server:port/", live_uri: "mysql://user@server:port/", production_uri: "mysql://user@server:port/ensembl_production_91", compara_uri: "mysql://user@server:port/ensembl_compara_master", hc_names: ["org.ensembl.healthcheck.testcase.generic.StableID"]}
"""
if json_pattern.match(request.headers['Content-Type']):
logger.debug("Submitting HC " + str(request.json))
try:
job = get_hive().create_job(app.analysis, request.json)
except ValueError as e:
raise HTTPRequestError(str(e), 404)
results = {"job_id": job.job_id};
email = request.json.get('email')
if email is not None and email != '':
logger.debug("Submitting email request for " + email)
email_results = email_when_complete.delay(request.url_root + "jobs/" + str(job.job_id) + "?format=email",
email)
results['email_task'] = email_results.id
return jsonify(results), 201
else:
logger.error("Could not handle input of type " + request.headers['Content-Type'])
raise HTTPRequestError("Could not handle input of type " + request.headers['Content-Type'])
def delete(job_id):
"""
Endpoint to delete a given job result using job_id
This is using docstring for specifications
---
tags:
- jobs
parameters:
- name: job_id
in: path
type: integer
required: true
description: id of the job
- name: kill
in: query
type: integer
required: false
default: 0
description: set to 1 to kill the process
operationId: jobs
consumes:
- application/json
produces:
- application/json
security:
delete_auth:
- 'write:delete'
- 'read:delete'
schemes: ['http', 'https']
deprecated: false
externalDocs:
description: Project repository
url: http://github.com/rochacbruno/flasgger
definitions:
job_id:
type: object
properties:
job_id:
type: integer
items:
$ref: '#/definitions/job_id'
id:
type: integer
properties:
id:
type: integer
items:
$ref: '#/definitions/id'
responses:
200:
description: Job_id that has been deleted
schema:
$ref: '#/definitions/job_id'
examples:
id: 1
"""
try:
if 'kill' in request.args.keys() and request.args['kill'] == 1:
kill_job(job_id)
job = get_hive().get_job_by_id(job_id)
hive.delete_job(job)
except ValueError as e:
raise HTTPRequestError(str(e), 404)
return jsonify({"id": job_id})
def list_databases_endpoint():
"""
Endpoint to retrieve a list of databases from a server given as URI
This is using docstring for specifications
---
tags:
- databases
parameters:
- in : query
name: db_uri
type: string
required: true
default: mysql://user@server:port/
description: MySQL server db_uri
- in : query
name: query
type: string
required: true
default: homo_sapiens
description: query use to find databases
operationId: databases
consumes:
- application/json
produces:
- application/json
security:
list_databases_auth:
- 'write:list_databases'
- 'read:list_databases'
schemes: ['http', 'https']
deprecated: false
externalDocs:
description: Project repository
url: http://github.com/rochacbruno/flasgger
definitions:
db_uri:
type: db_uri
properties:
db_uri:
type: string
items:
$ref: '#/definitions/db_uri'
query:
type: query
properties:
query:
type: string
items:
$ref: '#/definitions/query'
list_databases:
type: object
properties:
list_databases:
type: string
items:
$ref: '#/definitions/list_databases'
responses:
200:
description: list_databases of a MySQL server
schema:
$ref: '#/definitions/list_databases'
examples:
["homo_sapiens_cdna_91_38", "homo_sapiens_core_91_38","homo_sapiens_funcgen_91_38","homo_sapiens_otherfeatures_91_38","homo_sapiens_rnaseq_91_38","homo_sapiens_variation_91_38"]
"""
db_uri = request.args.get('db_uri')
query = request.args.get('query')
logger.debug("Finding dbs matching " + query + " on " + db_uri)
try:
db_list = list_databases(db_uri, query)
except ValueError as e:
raise HTTPRequestError(str(e))
return jsonify(db_list)
def jobs(job_id):
"""
Endpoint to retrieve a given job result using job_id
This is using docstring for specifications
---
tags:
- jobs
parameters:
- name: job_id
in: path
type: integer
required: true
description: id of the job
- name: format
in: query
type: string
required: false
description: optional output format (failures, email)
operationId: jobs
consumes:
- application/json
produces:
- application/json
security:
results_auth:
- 'write:results'
- 'read:results'
schemes: ['http', 'https']
deprecated: false
externalDocs:
description: Project repository
url: http://github.com/rochacbruno/flasgger
definitions:
job_id:
type: object
properties:
job_id:
type: integer
items:
$ref: '#/definitions/job_id'
result:
type: object
properties:
result:
type: string
items:
$ref: '#/definitions/result'
responses:
200:
description: Result of an healthcheck job
schema:
$ref: '#/definitions/job_id'
examples:
id: 1
input:
drop: 1
source_db_uri: mysql://user@server:port/saccharomyces_cerevisiae_core_91_4
target_db_uri: mysql://user:password@server:port/saccharomyces_cerevisiae_core_91_4
timestamp: 1515494114.263158
output:
runtime: 31 seconds
source_db_uri: mysql://user@server:port/saccharomyces_cerevisiae_core_91_4
target_db_uri: mysql://user:password@server:port/saccharomyces_cerevisiae_core_91_4
status: complete
"""
fmt = request.args.get('format')
if fmt == 'email':
return job_email(request.args.get('email'), job_id)
elif fmt == 'failures':
return failure(job_id)
elif fmt is None:
logger.info("Retrieving job with ID " + str(job_id))
try:
job_results = get_hive().get_result_for_job_id(job_id)
except ValueError as e:
raise HTTPRequestError(str(e), 404)
return jsonify(job_results)
else:
raise HTTPRequestError("Format " + str(fmt) + " not known")
def submit():
"""
Endpoint to submit a database copy job
This is using docstring for specifications
---
tags:
- jobs
parameters:
- in: body
name: body
description: copy database job object
requiered: false
schema:
$ref: '#/definitions/submit'
operationId: jobs
consumes:
- application/json
produces:
- application/json
security:
submit_auth:
- 'write:submit'
- 'read:submit'
schemes: ['http', 'https']
deprecated: false
externalDocs:
description: Project repository
url: http://github.com/rochacbruno/flasgger
definitions:
submit:
title: Database copy job
description: A job to copy a database from a source MySQL server to a target MySQL server.
type: object
required:
-source_db_uri
-target_db_uri
properties:
source_db_uri:
type: string
example: 'mysql://user@server:port/saccharomyces_cerevisiae_core_91_4'
target_db_uri:
type: string
example: 'mysql://*****:*****@server:port/'
only_tables:
type: string
example: 'undefined'
skip_tables:
type: string
example: 'undefined'
update:
type: integer
example: 0
drop:
type: integer
example: 0
convert_innodb:
type: integer
example: 0
email:
type: string
example: 'undefined'
responses:
200:
description: submit of a copy job
schema:
$ref: '#/definitions/submit'
examples:
{source_db_uri: "mysql://user@server:port/saccharomyces_cerevisiae_core_91_4", target_db_uri: "mysql://*****:*****@server:port/saccharomyces_cerevisiae_core_91_4", only_tables: undefined, skip_tables: undefined, update: undefined, drop: 1, convert_innodb: 0, skip_optimize: 0, email: undefined }
"""
if json_pattern.match(request.headers['Content-Type']):
logger.debug("Submitting Database copy " + str(request.json))
try:
job = get_hive().create_job(app.analysis, request.json)
except ValueError as e:
raise HTTPRequestError(str(e))
results = {
"job_id": job.job_id
}
email = request.json.get('email')
if email != None and email != '':
logger.debug("Submitting email request for " + email)
email_results = email_when_complete.delay(
request.url_root + "jobs/" + str(job.job_id) + "?format=email",
email)
results['email_task'] = email_results.id
return jsonify(results)
else:
logger.error("Could not handle input of type " +
request.headers['Content-Type'])
raise HTTPRequestError("Could not handle input of type " +
request.headers['Content-Type'])
def list_servers_endpoint(user):
"""
Endpoint to list the mysql servers accesible by a given user
This is using docstring for specifications
---
tags:
- servers
parameters:
- name: user
in: path
type: string
required: true
default: ensro
description: MySQL server user name
- in: query
name: query
type: string
required: true
default: server_name
description: MySQL server host name used to filter down the list
operationId: servers
consumes:
- application/json
produces:
- application/json
security:
list_servers_auth:
- 'write:list_servers'
- 'read:list_servers'
schemes: ['http', 'https']
deprecated: false
externalDocs:
description: Project repository
url: http://github.com/rochacbruno/flasgger
definitions:
user:
type: object
properties:
user:
type: string
items:
$ref: '#/definitions/user'
query:
type: object
properties:
query:
type: string
items:
$ref: '#/definitions/query'
list_servers:
type: object
properties:
list_servers:
type: string
items:
$ref: '#/definitions/list_servers'
responses:
200:
description: list_servers of a MySQL server
schema:
$ref: '#/definitions/host'
examples:
["mysql://user@server:port/"]
"""
query = request.args.get('query')
if query is None:
raise HTTPRequestError("Query not specified")
if user in get_servers():
logger.debug("Finding servers matching " + query + " for " + user)
user_urls = get_servers()[user] or []
urls = filter(lambda x: query in x, user_urls)
return jsonify(list(urls))
else:
raise HTTPRequestError("User " + user + " not found", 404)
def get_status_endpoint(host):
"""
Endpoint to retrieve the status of a give MySQL host
This is using docstring for specifications
---
tags:
- hosts
parameters:
- name: host
in: path
type: string
required: true
default: server_name
description: MySQL server host name
- name: dir_name
in: query
type: string
description: database directory name on MySQL server
operationId: hosts
consumes:
- application/json
produces:
- application/json
security:
status_auth:
- 'write:status'
- 'read:status'
schemes: ['http', 'https']
deprecated: false
externalDocs:
description: Project repository
url: http://github.com/rochacbruno/flasgger
definitions:
host:
type: object
properties:
host:
type: string
items:
$ref: '#/definitions/host'
status:
type: object
properties:
status:
type: string
items:
$ref: '#/definitions/status'
dir_name:
type: dir_name
properties:
dir_name:
type: string
items:
$ref: '#/definitions/dir_name'
responses:
200:
description: Status of a MySQL server
schema:
$ref: '#/definitions/host'
examples:
dir: /instances
disk_available_g: 1504
disk_total_g: 6048
disk_used_g: 4258
disk_used_pct: 70.4
host: server_name
load_15m: 0.05
load_1m: 0.0
load_5m: 0.01
memory_available_m: 270
memory_total_m: 48394
memory_used_m: 23624
memory_used_pct: 48.8
n_cpus: 16
"""
dir_name = request.args.get('dir_name')
if (dir_name is None):
dir_name = '/instances'
logger.debug("Finding status of " + host + " (dir " + dir_name + ")")
try:
status = get_status(host=host, dir_name=dir_name)
except OSError as e:
raise HTTPRequestError(str(e))
return jsonify(status)
def database_sizes_endpoint():
"""
Endpoint to retrieve a list of databases and their size from a MySQL server given as URI
This is using docstring for specifications
---
tags:
- databases
parameters:
- in : query
name: db_uri
type: string
required: true
default: mysql://user@server:port/
description: MySQL server db_uri
- in : query
name: query
type: string
required: true
default: homo_sapiens
description: query use to find databases
- in : query
name: dir_name
type: string
required: false
default: /instances
description: Directory name where the database files are located on the MySQL server
operationId: database_sizes
consumes:
- application/json
produces:
- application/json
security:
database_sizes_auth:
- 'write:database_sizes'
- 'read:database_sizes'
schemes: ['http', 'https']
deprecated: false
externalDocs:
description: Project repository
url: http://github.com/rochacbruno/flasgger
definitions:
db_uri:
type: db_uri
properties:
db_uri:
type: string
items:
$ref: '#/definitions/db_uri'
query:
type: query
properties:
query:
type: string
items:
$ref: '#/definitions/query'
dir_name:
type: dir_name
properties:
dir_name:
type: string
items:
$ref: '#/definitions/dir_name'
database_sizes:
type: object
properties:
database_sizes:
type: string
items:
$ref: '#/definitions/database_sizes'
responses:
200:
description: database_sizes of all the databases from a MySQL server
schema:
$ref: '#/definitions/database_sizes'
examples:
{ "mus_caroli_core_91_11": 4890, "ncbi_taxonomy": 362 }
"""
db_uri = request.args.get('db_uri')
query = request.args.get('query')
dir_name = request.args.get('dir_name')
if (dir_name is None):
dir_name = '/instances'
logger.debug("Finding sizes of dbs matching " + str(query) + " on " +
db_uri)
try:
db_sizes = get_database_sizes(db_uri, query, dir_name)
except ValueError as e:
raise HTTPRequestError(str(e))
return jsonify(db_sizes)