Merge pull request #7 from DCBIA-OrthoLab/master

Release version 1.1.0

CMakeLists.txt

@@ -2,14 +2,18 @@ cmake_minimum_required(VERSION 2.8.9)
 
 project(DatabaseInteractor)
 
+set(DatabaseInteractor_VERSION_MAJOR 1)
+set(DatabaseInteractor_VERSION_MINOR 1)
+set(DatabaseInteractor_VERSION_PATCH 0)
+
 #-----------------------------------------------------------------------------
 # Extension meta-information
 set(EXTENSION_HOMEPAGE "http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/DatabaseInteractor")
 set(EXTENSION_CATEGORY "Web System Tools")
 set(EXTENSION_CONTRIBUTORS "Clement Mirabel (University of Michigan), Juan Carlos Prieto (UNC)")
 set(EXTENSION_DESCRIPTION "This extension can interact with online data in a database and local folders.")
-set(EXTENSION_ICONURL "https://www.slicer.org/wiki/File:DatabaseInteractor_Logo.png")
-set(EXTENSION_SCREENSHOTURLS "https://www.slicer.org/wiki/File:FullView_DatabaseInteractor.png")
+set(EXTENSION_ICONURL "https://www.slicer.org/w/images/7/7f/DatabaseInteractor_Logo.png")
+set(EXTENSION_SCREENSHOTURLS "https://www.slicer.org/w/images/1/1f/FullView_DatabaseInteractor.png")
 set(EXTENSION_DEPENDS "NA") # Specified as a space separated string, a list or 'NA' if any
 
 #-----------------------------------------------------------------------------

DatabaseInteractor/.gitignore

@@ -0,0 +1,3 @@
+.DS_Store
+*.pyc
+

DatabaseInteractor/ClusterpostLib.py

@@ -0,0 +1,184 @@
+import os,sys
+#sys.path.append(os.path.join(os.path.dirname(os.path.abspath(__file__)),'requests/'))
+import requests
+import vtk, qt, ctk, slicer
+from slicer.ScriptedLoadableModule import *
+
+import json
+
+class ClusterpostLib():
+    def __init__(self, parent=None):
+        if parent:
+            parent.title = " "
+        self.server = ""
+        self.verify = False
+        self.auth = {}
+        self.user = None
+
+    def setServerUrl(self, server):
+        self.server = server
+
+    def setVerifyHttps(self, verify):
+        self.verify = verify
+
+
+    def getUser(self):
+        if(self.user == None):
+
+            r = requests.get(url=self.server + "/auth/user",
+                auth=self.auth,
+                verify=False)
+
+            self.user = r.json()
+        return self.user
+
+    def userLogin(self, user):
+
+        r = requests.post(url=self.server + "/auth/login",
+            json=user,
+            verify=self.verify)
+
+        self.auth = JWTAuth(r.json()["token"])
+
+    def setToken(self, token):
+        self.auth = JWTAuth(token)
+
+
+    def getExecutionServers(self):
+        r = requests.get(url=self.server + "/executionserver",
+            auth=self.auth,
+            verify=self.verify)
+
+        return r.json()
+
+
+    def createJob(self, job):
+        r = requests.post(url=self.server + "/dataprovider",
+            auth=self.auth,
+            verify=self.verify,
+            json=job)
+
+        return r.json()
+
+    def addAttachment(self, jobid, filename):
+
+        basefn = os.path.basename(filename)
+        data = open(filename, 'rb')
+
+        r = requests.put(url=self.server + "/dataprovider/" + jobid + "/" + basefn,
+            auth=self.auth,
+            verify=self.verify,
+            headers={"Content-Type": "application/octet-stream"},
+            data=data)
+
+        data.close()
+
+        return r.json()
+
+    def getAttachment(self, jobid, name, filename="", responseType=None):
+
+        stream=filename!=""
+
+        r = requests.get(url=self.server + "/dataprovider/" + jobid + "/" + name,
+            auth=self.auth,
+            verify=self.verify,
+            stream=stream,
+            headers={
+                'responseType': responseType,
+                'Content-Type': 'application/octet-stream'
+            })
+
+        if(stream):
+            with open(filename, 'wb') as fd:
+                for chunk in r.iter_content(chunk_size=2048):
+                    fd.write(chunk)
+
+        return r
+
+    def executeJob(self, jobid, force=False):
+        r = requests.post(url=self.server + "/executionserver/" + jobid,
+            auth=self.auth,
+            verify=self.verify,
+            json={"force":force})
+
+        return r.json()
+
+    def getJobs(self, executable=None, jobstatus=None, email=None):
+
+        payload={}
+
+        if(executable):
+            payload["executable"] = executable
+
+        if(jobstatus):
+            payload["jobstatus"] = jobstatus
+
+        if(email):
+            payload["email"] = email
+
+        r = requests.get(url=self.server + "/dataprovider/user",
+            auth=self.auth,
+            verify=self.verify,
+            params=payload)
+
+        return r.json()
+
+    def getJob(self, id):
+        r = requests.get(url=self.server + "/dataprovider/" + id,
+            auth=self.auth,
+            verify=self.verify)
+
+        return r.json()
+
+    def createAndSubmitJob(self, job, files):
+        res = self.createJob(job)
+
+        jobid = res["id"]
+
+        for file in files:
+            self.addAttachment(jobid, file)
+
+        return self.executeJob(jobid)
+
+    def getJobsDone(self, outdir):
+        res = self.getJobs(jobstatus="DONE")
+        for job in res:
+            outputs = job["outputs"]
+
+            jobname = job["_id"]
+
+            key = "name"
+
+            if(key in job):
+                jobname = job["name"]
+
+            outputdir = os.path.join(outdir, jobname)
+
+            if(not os.path.exists(outputdir)):
+                os.mkdir(outputdir)
+
+            for output in outputs:
+                if(output["type"] == "file"):
+                    self.getAttachment(job["_id"], output["name"], os.path.join(outputdir, output["name"]), "blob")
+
+    def updateJobStatus(self, jobid, status):
+        res = self.getJob(jobid)
+        res["jobstatus"] = {
+            "status": status
+        }
+        r = requests.put(url=self.server + "/dataprovider",
+            auth=self.auth,
+            verify=self.verify,
+            data=json.dumps(res))
+
+        return r.json()
+
+
+class JWTAuth(requests.auth.AuthBase):
+    def __init__(self, token):
+        self.token = token
+
+    def __call__(self, r):
+    # Implement my authentication
+        r.headers['Authorization'] = 'Bearer ' + self.token
+        return r