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 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_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_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_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)