Update submission functions (#80)

* update submissions

* update tests

src/cport/modules/cons_ppisp.py

@@ -59,8 +59,9 @@ def submit(self):
         input_form.set(name="submitter", value=str(self.chain_id))
         input_form.set(name="emailAddr", value="[email protected]")
         input_form.set(name="pChain", value=self.chain_id)
-        input_form.set(name="userfile", value=self.pdb_file)
-        browser.submit_selected()
+        with open(self.pdb_file, "rb") as file_obj:
+            input_form.set(name="userfile", value=file_obj)
+            browser.submit_selected()
 
         # https://regex101.com/r/FBgZFE/1
         processing_url = re.findall(r"<a href=\"(.*)\">this link<", str(browser.page))[

src/cport/modules/csm_potential.py

@@ -53,7 +53,7 @@ def submit(self):
         req = requests.post(CSM_POTENTIAL_URL, files=data)
 
         response = req.json()
-        if response["job_id"]:
+        if "job_id" in response:
             # successful submission
             job_id = response["job_id"]
         else:

src/cport/modules/ispred4.py

@@ -52,12 +52,14 @@ def submit(self):
         browser.open(ISPRED4_URL)
 
         input_form = browser.select_form(nr=0)
-        input_form.set(name="structure", value=self.pdb_file)
         input_form.set(name="ispred_chain", value=self.chain_id)
         input_form.set(
             name="ispred_rsath", value="0.20"
         )  # this is the default value, could be changed for analysis later
-        browser.submit_selected()
+        with open(self.pdb_file, "rb") as file_obj:
+            input_form.set(name="structure", value=file_obj)
+            # input_form.set(name="structure", value=self.pdb_file)
+            browser.submit_selected()
 
         # https://regex101.com/r/KFLLil/1
         job_id = re.findall(r"Jobid:.*?;\">(.*?)</div>", str(browser.page))[0]
@@ -143,7 +145,6 @@ def download_result(download_link):
 
         """
         temp_file = tempfile.NamedTemporaryFile(delete=False)
-        # trunk-ignore(bandit/B310)
         request.urlretrieve(download_link, temp_file.name)
         return temp_file.name
 

src/cport/modules/meta_ppisp.py

@@ -63,8 +63,9 @@ def submit(self):
         input_form.set(name="submitter", value=str(self.chain_id))
         input_form.set(name="emailAddr", value="[email protected]")
         input_form.set(name="pChain", value=self.chain_id)
-        input_form.set(name="userfile", value=self.pdb_file)
-        browser.submit_selected()
+        with open(self.pdb_file, "rb") as file_obj:
+            input_form.set(name="userfile", value=file_obj)
+            browser.submit_selected()
 
         # https://regex101.com/r/FBgZFE/1
         processing_url = re.findall(r"<a href=\"(.*)\">this link<", str(browser.page))[

src/cport/modules/predus2.py

@@ -68,8 +68,9 @@ def submit(self):
         browser.open(PREDUS2_URL, verify=False)
 
         input_form = browser.select_form(nr=0)
-        input_form.set(name="userfile", value=filename)
-        browser.submit_selected()
+        with open(filename, "rb") as file_obj:
+            input_form.set(name="userfile", value=file_obj)
+            browser.submit_selected()
 
         # finds the submission url from the many links present on the page
         # https://regex101.com/r/Do6b51/1

src/cport/modules/scannet.py

@@ -52,10 +52,11 @@ def submit(self):
         browser.open(SCANNET_URL, verify=False)
 
         input_form = browser.select_form(nr=0)
-        input_form.set(name="PDBfile", value=self.pdb_file)
         input_form.set(name="email", value="[email protected]")
         input_form.set(name="chain", value=self.chain_id)
-        browser.submit_selected()
+        with open(self.pdb_file, "rb") as file_obj:
+            input_form.set(name="PDBfile", value=file_obj)
+            browser.submit_selected()
 
         browser.follow_link(browser.links()[7])
         processing_url = browser.get_url()

src/cport/modules/sppider.py

@@ -49,9 +49,9 @@ def submit(self):
         browser.open(SPPIDER_URL)
 
         sppider_form = browser.select_form()
-        sppider_form.set(name="PDBFileName", value=self.pdb_file)
-
-        browser.submit_selected()
+        with open(self.pdb_file, "rb") as file_obj:
+            sppider_form.set(name="PDBFileName", value=file_obj)
+            browser.submit_selected()
 
         sppider_links = browser.links()
         browser.follow_link(sppider_links[0])

tests/test_cons_ppisp.py

@@ -16,9 +16,9 @@ def cons_ppisp():
     yield ConsPPISP("tests/test_data/1PPE.pdb", "E")
 
 
-@pytest.mark.skip("Cannot guarantee that the cons-PPISP server is up")
-def test_submit():
-    pass
+def test_submit(cons_ppisp):
+    summary_url = cons_ppisp.submit()
+    assert isinstance(summary_url, str)
 
 
 def test_retrieve_prediction_link(cons_ppisp):

tests/test_csm_potential.py

@@ -16,9 +16,10 @@ def csm_potential():
     yield CsmPotential("tests/test_data/1PPE.pdb", "E")
 
 
-@pytest.mark.skip("Cannot guarantee that the CSM-Potential server is up")
-def test_submit():
-    pass
+@pytest.mark.skip("CSM-Potential is not working")
+def test_submit(csm_potential):
+    summary_url = csm_potential.submit()
+    assert isinstance(summary_url, str)
 
 
 def test_parse_prediction(csm_potential, precalc_result):

tests/test_ispred4.py

@@ -17,9 +17,9 @@ def ispred4():
     yield Ispred4("tests/test_data/1PPE.pdb", "E")
 
 
-@pytest.mark.skip("Cannot guarantee that the ISPRED4 server is up")
-def test_submit():
-    pass
+def test_submit(ispred4):
+    summary_url = ispred4.submit()
+    assert isinstance(summary_url, str)
 
 
 def test_retrieve_prediction_link(ispred4):

tests/test_meta_ppisp.py

@@ -16,9 +16,9 @@ def meta_ppisp():
     yield MetaPPISP("tests/test_data/1PPE.pdb", "E")
 
 
-@pytest.mark.skip("Cannot guarantee that the meta-PPISP server is up")
-def test_submit():
-    pass
+def test_submit(meta_ppisp):
+    summary_url = meta_ppisp.submit()
+    assert isinstance(summary_url, str)
 
 
 def test_retrieve_prediction_link(meta_ppisp):

tests/test_predictprotein.py

@@ -16,9 +16,9 @@ def predictprotein():
     yield Predictprotein("tests/test_data/1PPE.pdb", "E")
 
 
-@pytest.mark.skip("Cannot guarantee that the Predict Protein server is up")
-def test_submit():
-    pass
+def test_submit(predictprotein):
+    summary_url = predictprotein.submit()
+    assert isinstance(summary_url, str)
 
 
 def test_parse_prediction(predictprotein, precalc_result):

tests/test_predus2.py

@@ -16,9 +16,9 @@ def predus2():
     yield Predus2("tests/test_data/1PPE.pdb", "E")
 
 
-@pytest.mark.skip("Cannot guarantee that the PredUs2 server is up")
-def test_submit():
-    pass
+def test_submit(predus2):
+    summary_url = predus2.submit()
+    assert isinstance(summary_url, str)
 
 
 def test_retrieve_prediction_link(predus2):

tests/test_psiver.py

@@ -16,9 +16,9 @@ def psiver():
     yield Psiver("tests/test_data/1PPE.pdb", "E")
 
 
-@pytest.mark.skip("Cannot guarantee that the PSIVER server is up")
-def test_submit():
-    pass
+def test_submit(psiver):
+    summary_url = psiver.submit()
+    assert isinstance(summary_url, str)
 
 
 def test_retrieve_prediction_link(psiver):

tests/test_scannet.py

@@ -16,9 +16,10 @@ def scannet():
     yield ScanNet("tests/test_data/1PPE.pdb", "A")
 
 
-@pytest.mark.skip("Cannot guarantee that the cons-PPISP server is up")
-def test_submit():
-    pass
+@pytest.mark.skip("server is down")
+def test_submit(scannet):
+    summary_url = scannet.submit()
+    assert isinstance(summary_url, str)
 
 
 def test_retrieve_prediction_link(scannet):

tests/test_scriber.py

@@ -16,9 +16,9 @@ def scriber():
     yield Scriber("tests/test_data/1PPE.pdb", "E")
 
 
-@pytest.mark.skip("Cannot guarantee that the Scriber server is up")
-def test_submit():
-    pass
+def test_submit(scriber):
+    summary_url = scriber.submit()
+    assert isinstance(summary_url, str)
 
 
 def test_retrieve_prediction_link(scriber):

tests/test_sppider.py

@@ -16,9 +16,9 @@ def sppider():
     yield Sppider("tests/test_data/1PPE.pdb", "E")
 
 
-@pytest.mark.skip("Cannot guarantee that the SPPIDER server is up")
-def test_submit():
-    pass
+def test_submit(sppider):
+    summary_url = sppider.submit()
+    assert isinstance(summary_url, str)
 
 
 def test_retrieve_prediction_link(sppider):

tests/test_whiscy.py

@@ -9,9 +9,10 @@ def whiscy():
     yield Whiscy("tests/test_data/1PPE.pdb", "E")
 
 
-@pytest.mark.skip("Cannot test the submission")
+@pytest.mark.skip("FIXME: Split into smaller tests")
 def test_submit(whiscy):
-    pass
+    summary_url = whiscy.submit()
+    assert isinstance(summary_url, str)
 
 
 def test_retrieve_prediction(whiscy):