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Merge pull request #4 from EMBL-EBI-TSI/testing
Merge testing into master for 0.2 release
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1,2 @@ | ||
| *.swp | ||
| *.pyc |
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|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| steps: | ||
| - name: 'gcr.io/cloud-builders/docker' | ||
| args: ['build', '-t', 'eu.gcr.io/tes-wes/taskmaster:testing', '-f', 'dockerfiles/taskmaster/Dockerfile', '.'] | ||
| - name: 'gcr.io/cloud-builders/docker' | ||
| args: ['build', '-t', 'eu.gcr.io/tes-wes/filer:testing', '-f', 'dockerfiles/filer/Dockerfile', '.'] | ||
| images: ['eu.gcr.io/tes-wes/taskmaster:testing', 'eu.gcr.io/tes-wes/filer:testing'] |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,107 @@ | ||
| { | ||
| "outputs": [ | ||
| { | ||
| "url": "ftp://ftp-private.ebi.ac.uk/upload/mouselist.txt", | ||
| "path": "/tmp/vol1/mouselist.txt", | ||
| "type": "FILE" | ||
| }, | ||
| { | ||
| "url": "ftp://ftp-private.ebi.ac.uk/upload/mouse_out", | ||
| "path": "/tmp/vol2/mouse", | ||
| "type": "DIRECTORY" | ||
| } | ||
| ], | ||
| "inputs": [ | ||
| { | ||
| "url": "ftp://ftp-private.ebi.ac.uk/upload/input.txt", | ||
| "path": "/tmp/vol1/in.txt", | ||
| "type": "FILE" | ||
| }, | ||
| { | ||
| "url": "ftp://ftp-private.ebi.ac.uk/upload/mouse", | ||
| "path": "/tmp/vol2/mouse", | ||
| "type": "DIRECTORY" | ||
| } | ||
| ], | ||
| "volumes": [ | ||
| "/tmp/vol1", | ||
| "/tmp/vol2" | ||
| ], | ||
| "executors": [ | ||
| { | ||
| "apiVersion": "batch/v1", | ||
| "kind": "Job", | ||
| "metadata": { | ||
| "annotations": { | ||
| "tes-task-name": "Hello Input" | ||
| }, | ||
| "labels": { | ||
| "job-type": "executor", | ||
| "taskmaster-name": "task-7d5c53f4", | ||
| "executor-no": "0" | ||
| }, | ||
| "name": "task-7d5c53f4-ex-00" | ||
| }, | ||
| "spec": { | ||
| "template": { | ||
| "metadata": { | ||
| "name": "task-7d5c53f4-ex-00" | ||
| }, | ||
| "spec": { | ||
| "containers": [ | ||
| { | ||
| "command": [ | ||
| "cat", | ||
| "/tmp/vol1/in.txt" | ||
| ], | ||
| "image": "alpine", | ||
| "name": "task-7d5c53f4-ex-00", | ||
| "resources": {} | ||
| } | ||
| ], | ||
| "restartPolicy": "Never" | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| { | ||
| "apiVersion": "batch/v1", | ||
| "kind": "Job", | ||
| "metadata": { | ||
| "annotations": { | ||
| "tes-task-name": "Hello Input" | ||
| }, | ||
| "labels": { | ||
| "job-type": "executor", | ||
| "taskmaster-name": "task-7d5c53f4", | ||
| "executor-no": "1" | ||
| }, | ||
| "name": "task-7d5c53f4-ex-01" | ||
| }, | ||
| "spec": { | ||
| "template": { | ||
| "metadata": { | ||
| "name": "task-7d5c53f4-ex-01" | ||
| }, | ||
| "spec": { | ||
| "containers": [ | ||
| { | ||
| "command": [ | ||
| "sh", "-c", | ||
| "find /tmp/vol2 > /tmp/vol1/mouselist.txt" | ||
| ], | ||
| "image": "alpine", | ||
| "name": "task-7d5c53f4-ex-01", | ||
| "resources": {} | ||
| } | ||
| ], | ||
| "restartPolicy": "Never" | ||
| } | ||
| } | ||
| } | ||
| } | ||
| ], | ||
| "resources": { | ||
| "disk_gb": 0.1 | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| import json | ||
|
|
||
| class Filer: | ||
| def __init__(self, name, data, filer_version='v0.5', debug=False): | ||
| self.name = name | ||
| self.spec = { | ||
| "kind": "Job", | ||
| "apiVersion": "batch/v1", | ||
| "metadata": { "name": name }, | ||
| "spec": { | ||
| "template": { | ||
| "metadata": { "name": "tesk-filer" }, | ||
| "spec": { | ||
| "containers": [ { | ||
| "name": "filer", | ||
| "image": "eu.gcr.io/tes-wes/filer:"+filer_version, | ||
| "args": [], | ||
| "env": [], | ||
| "volumeMounts": [], | ||
| "imagePullPolicy": "IfNotPresent" | ||
| } | ||
| ], | ||
| "volumes": [], | ||
| "restartPolicy": "Never" | ||
| } | ||
| } | ||
| } | ||
| } | ||
|
|
||
| if debug: | ||
| self.spec['spec']['template']['spec']['containers'][0]['imagePullPolicy'] = 'Always' | ||
|
|
||
| container = self.spec['spec']['template']['spec']['containers'][0] | ||
| container['env'].append({ "name": "JSON_INPUT", "value": json.dumps(data) }) | ||
| #container['env'].append({ "name": "JSON_INPUT", "value": 'test' }) | ||
|
|
||
| def set_ftp(self, user, pw): | ||
| env = self.spec['spec']['template']['spec']['containers'][0]['env'] | ||
| env.append({ "name": "TESK_FTP_USERNAME", "value": user }) | ||
| env.append({ "name": "TESK_FTP_PASSWORD", "value": pw }) | ||
|
|
||
| def set_volume_mounts(self, pvc): | ||
| tempspec = self.spec['spec']['template']['spec'] | ||
| tempspec['containers'][0]['volumeMounts'] = pvc.volume_mounts | ||
| tempspec['volumes'] = [ { "name": "task-volume", "persistentVolumeClaim": { "claimName": pvc.name} } ] | ||
|
|
||
| def get_spec(self, mode): | ||
| self.spec['spec']['template']['spec']['containers'][0]['args'] = [mode, "$(JSON_INPUT)"] | ||
| self.spec['spec']['template']['metadata']['name'] = self.name | ||
| return self.spec |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| from kubernetes import client, config | ||
| import logging | ||
| import time | ||
|
|
||
| class Job: | ||
| def __init__(self, body, name='task-job', namespace='default'): | ||
| self.name = name | ||
| self.namespace = namespace | ||
| self.status = 'Initialized' | ||
| self.bv1 = client.BatchV1Api() | ||
| self.body = body | ||
| self.body['metadata']['name'] = self.name | ||
|
|
||
| def run_to_completion(self, poll_interval, check_cancelled): | ||
| logging.debug(self.body) | ||
| self.bv1.create_namespaced_job(self.namespace, self.body) | ||
| status = self.get_status() | ||
| while status == 'Running': | ||
| if check_cancelled(): | ||
| self.delete() | ||
| return 'Cancelled' | ||
|
|
||
| time.sleep(poll_interval) | ||
|
|
||
| status = self.get_status() | ||
|
|
||
| return status | ||
|
|
||
| def get_status(self): | ||
| job = self.bv1.read_namespaced_job(self.name, self.namespace) | ||
| try: | ||
| if job.status.conditions[0].type == 'Complete' and job.status.conditions[0].status: | ||
| self.status = 'Complete' | ||
| elif job.status.conditions[0].type == 'Failed' and job.status.conditions[0].status: | ||
| self.status = 'Failed' | ||
| else: | ||
| self.status = 'Error' | ||
| except TypeError: # The condition is not initialized, so it is not complete yet, wait for it | ||
| self.status = 'Running' | ||
|
|
||
| return self.status | ||
|
|
||
| def delete(self): | ||
| self.bv1.delete_namespaced_job(self.name, self.namespace, client.V1DeleteOptions()) |
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