def updateStatus(self, majorStatus, minorStatus, **kwargs):
""" passes status """
my_dict = {"t_id": self.jobId, "inst_id": self.instanceId, "major_status": majorStatus,
"minor_status": minorStatus}
if 'resources' in kwargs:
if kwargs['resources']:
RM = kwargs['resources']
if not isinstance(RM, ResourceMonitor):
raise Exception("resource must be of type resource monitor")
my_dict['memory'] = RM.getMemory(unit='Mb')
my_dict['cpu'] = RM.getCpuTime()
del kwargs['resources']
my_dict.update(kwargs)
if majorStatus in FINAL_STATII:
# keep only NUMLINES of log file.
theLog = self.error_log.splitlines()
if len(theLog) > NUMLINES_LOG:
self.error_log = "\n".join(theLog[-(NUMLINES_LOG-1):-1])
my_dict['log']=self.error_log
# print '*DEBUG* my_dict: %s'%str(my_dict)
res = Rpost("%s/jobstatus/" % DAMPE_WORKFLOW_URL, data={"args": dumps(my_dict)})
res.raise_for_status()
if not res.json().get("result", "nok") == "ok":
raise Exception(res.json().get("error", "ErrorMissing"))
if majorStatus in ["Done", "Failed", "Terminated"]:
witness = open(oPath.join(self.wd, "%s" % majorStatus.upper()), 'w')
witness.write(self.getJobName())
witness.close()
return
def postmark_spamcheck(self, message, options):
data = {'email': message, 'options': options}
result = POST(self.postmark_spamcheck_url, data)
result.raise_for_status()
content = loads(result.content)
if 'error' in content:
raise Exception(content['message'])
return content
def postmark_spamcheck(self, message, options):
data = {'email': message, 'options': options}
result = POST(self.postmark_spamcheck_url, data)
result.raise_for_status()
content = loads(result.content)
if 'error' in content:
raise Exception(content['message'])
return content
def registerDS(self, filename=None, overwrite=False):
site = cfg.get("site", "name")
if filename is None:
files = [fi['target'] for fi in self.OutputFiles]
else:
files = [filename]
for fi in files:
tg = oPath.expandvars(fi)
res = Rpost("%s/datacat/" % DAMPE_WORKFLOW_URL, data={"filename": tg, "site": site,
"action": "register",
"overwrite": str(overwrite)})
res.raise_for_status()
if not res.json().get("result", "nok") == "ok":
raise Exception(res.json().get("error", "No error provided."))
def test_genbank_extension(self):
headers = self.headers
url = self.run_url
block1 = {
"metadata": {
"authors": [],
"version": "0.0.0",
"tags": {}
},
"options": [],
"components": [],
"rules": {},
"notes": {}
}
res = POST(self.api_url + "block", data=json(block1), headers=headers)
block_id = res.json()["id"]
input1 = {
"genbank": "extensions/compute/genbank_to_block/sequence.gb",
"sequence": "/api/file/block/" + block_id + "/sequence"
}
res = POST(url + "genbank_to_block",
data=json(input1),
headers=headers)
self.assertTrue(res.status_code == 200)
res = res.json()
self.assertTrue("block" in res)
block = parse(res["block"])
block["sequence"]["url"] = input1["sequence"]
res = PUT(self.api_url + "block/" + block_id,
data=json(block),
headers=headers)
self.assertTrue(res.status_code == 200)
res = GET(self.api_url + "block/" + block_id, headers=headers)
self.assertTrue(res.status_code == 200)
self.assertTrue(res.json()["id"] == block_id)
self.assertTrue(res.json()["sequence"]["url"] == input1["sequence"])
res = GET(self.api_url + "file/block%2f" + block_id + "%2fsequence",
headers=headers)
self.assertTrue(res.status_code == 200)
self.assertTrue(len(res.text) > 1000)
def test_cloning(self):
headers = self.headers
url = self.api_url
proj1 = {
"metadata": {
"authors": [],
"version": "0.0.0",
"tags": {}
},
"components": [
],
"settings": {}
}
res = POST(url + "project", data = json(proj1), headers=headers)
pid1 = res.json()['id']
res = POST(url + "clone/" + pid1, headers=headers)
pid2 = res.json()['id']
res = POST(url + "clone/" + pid2, headers=headers)
pid3 = res.json()['id']
res = POST(url + "clone/" + pid3, headers=headers)
pid4 = res.json()['id']
res = GET(url + "project/" + pid4, headers=headers)
hist = GET(url + "ancestors/" + pid4, headers=headers)
self.assertTrue(hist.status_code==200)
hist = hist.json()
self.assertTrue(len(hist)==3)
self.assertTrue(hist[0]==pid3)
self.assertTrue(hist[1]==pid2)
self.assertTrue(hist[2]==pid1)
child = GET(url + "descendants/" + pid1, headers=headers)
self.assertTrue(child.status_code==200)
child = child.json()
self.assertTrue(len(child)==5)
self.assertTrue(len(child['leaves'])==1)
def test_cloning(self):
headers = self.headers
url = self.api_url
proj1 = {
"metadata": {
"authors": [],
"version": "0.0.0",
"tags": {}
},
"components": [],
"settings": {}
}
res = POST(url + "project", data=json(proj1), headers=headers)
pid1 = res.json()['id']
res = POST(url + "clone/" + pid1, headers=headers)
pid2 = res.json()['id']
res = POST(url + "clone/" + pid2, headers=headers)
pid3 = res.json()['id']
res = POST(url + "clone/" + pid3, headers=headers)
pid4 = res.json()['id']
res = GET(url + "project/" + pid4, headers=headers)
hist = GET(url + "ancestors/" + pid4, headers=headers)
self.assertTrue(hist.status_code == 200)
hist = hist.json()
self.assertTrue(len(hist) == 3)
self.assertTrue(hist[0] == pid3)
self.assertTrue(hist[1] == pid2)
self.assertTrue(hist[2] == pid1)
child = GET(url + "descendants/" + pid1, headers=headers)
self.assertTrue(child.status_code == 200)
child = child.json()
self.assertTrue(len(child) == 5)
self.assertTrue(len(child['leaves']) == 1)
def test_genbank_extension(self):
headers = self.headers
url = self.run_url
block1 = {
"metadata": {
"authors": [],
"version": "0.0.0",
"tags": {} },
"options":[],
"components":[],
"rules": {},
"notes": {}
}
res = POST(self.api_url + "block", data = json(block1), headers=headers)
block_id = res.json()["id"]
input1 = {
"genbank":"extensions/compute/genbank_to_block/sequence.gb",
"sequence":"/api/file/block/"+block_id+"/sequence"
}
res = POST(url + "genbank_to_block", data = json(input1), headers=headers)
self.assertTrue(res.status_code==200)
res = res.json()
self.assertTrue("block" in res)
block = parse(res["block"])
block["sequence"]["url"] = input1["sequence"]
res = PUT(self.api_url + "block/" + block_id, data = json(block), headers=headers)
self.assertTrue(res.status_code==200)
res = GET(self.api_url + "block/" + block_id, headers=headers)
self.assertTrue(res.status_code==200)
self.assertTrue(res.json()["id"] == block_id)
self.assertTrue(res.json()["sequence"]["url"] == input1["sequence"])
res = GET(self.api_url + "file/block%2f"+block_id+"%2fsequence", headers=headers)
self.assertTrue(res.status_code==200)
self.assertTrue(len(res.text) > 1000)
def test_running_extensions(self):
headers = self.headers
url = self.run_url
res = POST(self.api_url + "file/DNA", data="ACGTACGACTACGACTGACGACTACGAGCT", headers=headers)
input1 = {"DNA":res.text}
res = POST(url + "translate_dna_example", data = json(input1), headers=headers)
self.assertTrue(res.status_code==200)
self.assertTrue(list(res.json().keys())[0]=='Protein')
self.assertTrue(res.json()["Protein"]=="TYDYD*RLRA")
input1["Protein"] = "/api/file/myDir/Prot"
res = POST(url + "translate_dna_example", data = json(input1), headers=headers)
self.assertTrue(res.status_code==200)
self.assertTrue(res.json()["Protein"]=='/api/file/myDir/Prot')
def test_running_extensions(self):
headers = self.headers
url = self.run_url
res = POST(self.api_url + "file/DNA",
data="ACGTACGACTACGACTGACGACTACGAGCT",
headers=headers)
input1 = {"DNA": res.text}
res = POST(url + "translate_dna_example",
data=json(input1),
headers=headers)
self.assertTrue(res.status_code == 200)
self.assertTrue(list(res.json().keys())[0] == 'Protein')
self.assertTrue(res.json()["Protein"] == "TYDYD*RLRA")
input1["Protein"] = "/api/file/myDir/Prot"
res = POST(url + "translate_dna_example",
data=json(input1),
headers=headers)
self.assertTrue(res.status_code == 200)
self.assertTrue(res.json()["Protein"] == '/api/file/myDir/Prot')
def test_block_creation(self):
headers = self.headers
url = self.api_url
block1 = {
"metadata": {
"authors": [],
"version": "0.0.0",
"tags": {}
},
"options": [],
"components": [],
"rules": {},
"notes": {},
"sequence": {
"url":
"/some/location",
"annotations": [{
"id": str(uuid4()),
"description": "bla bla",
"tags": {},
"sequence": "ACGT",
"start": 5,
"end": 58,
"strand": "-"
}]
}
}
res = POST(url + "block", data=json(block1), headers=headers)
id1 = res.json()['id']
self.assertTrue(res.status_code == 200)
self.assertTrue(len(id1) == 36)
block2 = {
"metadata": {
"authors": [],
"version": "0.0.0",
"tags": {}
},
"options": [],
"components": [],
"rules": {},
"notes": {}
}
res = POST(url + "block", data=json(block2), headers=headers)
id2 = res.json()['id']
self.assertTrue(res.status_code == 200)
self.assertTrue(len(id2) == 36)
block3 = {
"metadata": {
"authors": [],
"version": "0.0.0",
"tags": {}
},
"components": [id1, id2],
"options": [],
"rules": {},
"notes": {}
}
block4 = {
"metadata": {
"authors": [],
"version": "0.0.0",
"tags": {}
},
"options": [id1, id2],
"components": [],
"rules": {},
"notes": {}
}
res = POST(url + "block", data=json(block3), headers=headers)
id3 = res.json()['id']
self.assertTrue(res.status_code == 200)
self.assertTrue(len(id3) == 36)
res = POST(url + "block", data=json(block4), headers=headers)
id4 = res.json()['id']
self.assertTrue(res.status_code == 200)
self.assertTrue(len(id4) == 36)
proj1 = {
"metadata": {
"authors": [],
"version": "0.0.0",
"tags": {}
},
"components": [id3, id4],
"settings": {}
}
res = POST(url + "project", data=json(proj1), headers=headers)
pid1 = res.json()['id']
self.assertTrue(res.status_code == 200)
self.assertTrue(len(pid1) == 36)
proj1["settings"] = {"SBOLv-version": "1.2.0"}
res = PUT(url + "project/" + pid1, data=json(proj1), headers=headers)
pid1 = res.json()['id']
self.assertTrue(res.status_code == 200)
self.assertTrue(len(pid1) == 36)
res = GET(url + "project/" + pid1,
params={"tree": True},
headers=headers)
self.assertTrue(res.status_code == 200)
res = res.json()
self.assertTrue(len(res['components']) == 5)
self.assertTrue(len(res['components']['leaves']) == 3)
data1 = '{rateLimit{cost limit remaining resetAt}}'
chain = Chain("search")\
(type = Type("REPOSITORY"), query = "a sort:forks", first = 100)\
.get("repositoryCount")\
.get(Chain("pageInfo")\
.get("endCursor"))\
.nodes\
.on("Repository")\
.get("forkCount")\
.get(Chain("watchers")\
(last = 1).\
get("totalCount"))\
.get(Chain("stargazers")\
(last = 1).\
get("totalCount"))
print("chain = ", chain.to_dict())
logger.info(generate_query(data))
generate_query(data)
resp = Post("https://api.github.com/graphql",
json=generate_query(data1),
headers=header)
print(chain.to_dict())
resp = Post("https://api.github.com/graphql",
json=chain.to_dict(),
headers=header)
logger.info(resp.json())
def test_block_creation(self):
headers = self.headers
url = self.api_url
block1 = {
"metadata": {
"authors": [],
"version": "0.0.0",
"tags": {} },
"options":[],
"components":[],
"rules": {},
"notes": {},
"sequence": {
"url": "/some/location",
"annotations": [
{
"id": str(uuid4()),
"description" : "bla bla",
"tags" : {},
"sequence" : "ACGT",
"start" : 5,
"end" : 58,
"strand" : "-"
}
]
}
}
res = POST(url + "block", data = json(block1), headers=headers)
id1 = res.json()['id']
self.assertTrue(res.status_code==200)
self.assertTrue(len(id1)==36)
block2 = {
"metadata": {
"authors": [],
"version": "0.0.0",
"tags": {}
},
"options":[],
"components":[],
"rules": {},
"notes": {}
}
res = POST(url + "block", data = json(block2), headers=headers)
id2 = res.json()['id']
self.assertTrue(res.status_code==200)
self.assertTrue(len(id2)==36)
block3 = {
"metadata": {
"authors": [],
"version": "0.0.0",
"tags": {}
},
"components": [
id1,
id2
],
"options":[],
"rules": {},
"notes": {}
}
block4 = {
"metadata": {
"authors": [],
"version": "0.0.0",
"tags": {}
},
"options": [
id1,
id2
],
"components":[],
"rules": {},
"notes": {}
}
res = POST(url + "block", data = json(block3), headers=headers)
id3 = res.json()['id']
self.assertTrue(res.status_code==200)
self.assertTrue(len(id3)==36)
res = POST(url + "block", data = json(block4), headers=headers)
id4 = res.json()['id']
self.assertTrue(res.status_code==200)
self.assertTrue(len(id4)==36)
proj1 = {
"metadata": {
"authors": [],
"version": "0.0.0",
"tags": {}
},
"components": [
id3,
id4
],
"settings": {}
}
res = POST(url + "project", data = json(proj1), headers=headers)
pid1 = res.json()['id']
self.assertTrue(res.status_code==200)
self.assertTrue(len(pid1)==36)
proj1["settings"] = { "SBOLv-version": "1.2.0" }
res = PUT(url + "project/" + pid1, data = json(proj1), headers=headers)
pid1 = res.json()['id']
self.assertTrue(res.status_code==200)
self.assertTrue(len(pid1)==36)
res = GET(url + "project/" + pid1, params = {"tree":True}, headers=headers)
self.assertTrue(res.status_code==200)
res = res.json()
self.assertTrue(len(res['components'])==5)
self.assertTrue(len(res['components']['leaves'])==3)