--- a/cravat_annotate/cravat_annotate.py	Wed Jul 18 10:25:55 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,128 +0,0 @@
-import requests
-import json
-import sys
-import re
-import argparse
-from __future__ import print_function
-
-
-# The endpoint that CravatQuerys are submitted to
-endpoint = 'http://www.cravat.us/CRAVAT/rest/service/query'
-
-
-# newline and delimiter values used in the output file
-delimiter = "\t"
-newline = "\n"
-
-
-# Defualt indices for intepretting a cravat file's row of data in to a CravatQuery
-cr_mapping = {
-	'chromosome': 1,
-	'position': 2,
-	'strand': 3,
-	'reference': 4,
-	'alternate': 5
-}
-
-
-# The neccessary attributes neeeded to submit a query.
-query_keys = [
-	'chromosome', 'position', 'strand', 'reference', 'alternate'
-]
-
-
-# Expected response keys from server. Ordered in list so that galaxy output has uniform column ordering run-to-run.
-# If cravat server returns additional keys, they are appended to and included in output.
-ordered_keys = [
-	"Chromosome", "Position", "Strand", "Reference base(s)", "Alternate base(s)",
-	"HUGO symbol", "S.O. transcript", "Sequence ontology protein change", "Sequence ontology",
-	"S.O. all transcripts", "gnomAD AF", "gnomAD AF (African)", "gnomAD AF (Amrican)",
-	"gnomAD AF (Ashkenazi Jewish)", "gnomAD AF (East Asian)", "gnomAD AF (Finnish)",
-	"gnomAD AF (Non-Finnish European)", "gnomAD AF (Other)", "gnomAD AF (South Asian)",
-	"1000 Genomes AF", "ESP6500 AF (average)", "ESP6500 AF (European American)",
-	"ESP6500 AF (African American)", "COSMIC transcript", "COSMIC protein change", 
-	"COSMIC variant count [exact nucleotide change]", "cosmic_site_nt", "CGL driver class",
-	"TARGET", "dbSNP", "cgc_role", "cgc_inheritance", "cgc_tumor_type_somatic",
-	"cgc_tumor_type_germline", "ClinVar", "ClinVar disease identifier", "ClinVar XRef",
-	"GWAS Phenotype (GRASP)", "GWAS PMID (GRASP)", "Protein 3D variant"
-]
-
-
-def get_args():
-    parser = argparse.ArgumentParser()
-    parser.add_argument('--input',
-                            '-i',
-                            required = True,
-                            help='Input path to a cravat file for querying',)
-    parser.add_argument('--output',
-                            '-o',
-                            default = None,
-                            help = 'Output path to write results from query')
-    return parser.parse_args()
-
-
-def format_chromosome(chrom):
-	""" : Ensure chromosome entry is propely formatted for use as querying attribute. """
-	if chrom[0:3] == 'chr':
-		return chrom
-	return 'chr' + str(chrom)
-
-
-def get_query_string(row):
-	""" : From a row dict, return a query string for the Cravat server.
-		: The row dict is cravat headeres associated to their values of that row.
-	"""
-	return '_'.join([ row['chromosome'], row['position'], row['strand'], row['reference'], row['alternate'] ])
-
-
-def query(in_path, out_path):
-	""" : From a Cravat the file at in_path, query each line on the Cravat server.
-		: Write the response values to file at out_path.
-	"""
-	with open(in_path, 'r') as in_file, \
-	open(out_path, 'w') as out_file:
-		for line in in_file:
-			try:
-				line = line.strip().split('\t')
-				# row is dict of cravat col headers assioted values in this line
-				row = { header: line[index] for header, index in cr_mapping.items() }
-				row['chromosome'] = format_chromosome(row['chromosome'])
-				query_string = get_query_string(row)
-				call = requests.get(endpoint, params={ 'mutation': query_string })
-				if call.status_code != 200 or call.text == "":
-					raise requests.RequestException('Bad server response for query="{}". Respone code: "{}", Response Text: "{}"'
-						.format(query_string, call.status_code, call.text))
-				json_response = json.loads(call.text)
-				# See if server returned additional json key-vals not expected in ordered_keys
-				for key in json_response:
-					if key not in ordered_keys:
-						ordered_keys.append(key)
-				# Write key in order of ordered_keys to standardize order of output columns
-				wrote = False
-				for key in ordered_keys:
-					if key in json_response:
-						val = json_response[key]
-					else:
-						val = None
-					# Standardize format for  numeric values
-					try:
-						val = float(val)
-						val = format(val, ".4f")
-					except:
-						pass
-					if wrote:
-						out_file.write(delimiter)
-					out_file.write(str(val))
-					wrote = True
-				out_file.write(newline)		
-			except Exception as e:
-				print(e, file=sys.stderr)
-				continue
-
-
-if __name__ == "__main__":
-	cli_args = get_args()
-	if cli_args.output == None:
-		base, _ = os.path.split(cli_args.input)
-		cli_args.output = os.path.join(base, "cravat_converted.txt") 
-	query(cli_args.input, cli_args.output)

--- a/cravat_annotate/cravat_annotate.xml	Wed Jul 18 10:25:55 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-<tool id="cravat_query" name="CRAVAT Query" version="1.0.0">
-    <description>Queries CRAVAT for cancer annotation</description>
-  <command interpreter="python">cravat_annotate.py -i $input -o $output</command>
-  
-  <inputs>
-    <param format="tabular" name="input" type="data" label="Source file"/>
-  </inputs>
-  
-  <outputs>
-    <data format="tabular" name="output" />
-  </outputs>
-
-  <tests>
-    <test>
-      <param name="input" value="input_call.txt"/>
-      <output name="output" file="Galaxy23-[CRAVAT_Query_on_data_22].tabular"/>
-    </test>
-  </tests>
-
-  <help>
-    This tool queries CRAVAT for cancer annotation.
-  </help>
-
-</tool>
-

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cravat_submit/cravat_submit.py	Wed Jul 18 10:32:36 2018 -0400
@@ -0,0 +1,103 @@
+import requests
+import json
+import time
+import urllib
+import sys
+import csv
+
+input_filename = sys.argv[1]
+input_select_bar = sys.argv[2]
+output_filename = sys.argv[3]
+
+# HACK: Input args corrections. 
+if input_select_bar == "None":
+    # The server represents an analyses of None as ""; however, submitting a blank string on command line throws off arg position
+    input_select_bar = ""
+    # The server represents the "Vest and Chasm" analyses as "VEST;CHASM; however, galaxy converts the semi-colon to an 'X'. Switch it back.
+elif input_select_bar == "VESTXCHASM":
+    input_select_bar = "VEST;CHASM" 
+
+write_header = True
+
+#plugs in params to given URL
+submit = requests.post('http://cravat.us/CRAVAT/rest/service/submit', files={'inputfile':open(input_filename)}, data={'email':'znylund@insilico.us.com', 'analyses': input_select_bar})   
+#,'analysis':input_select_bar,'functionalannotation': "on"})                   
+#Makes the data a json dictionary, takes out only the job ID
+jobid = json.loads(submit.text)['jobid']
+#out_file.write(jobid)    
+submitted = json.loads(submit.text)['status']
+#out_file.write('\t' + submitted)
+
+#loops until we find a status equal to Success, then breaks
+while True:
+    check = requests.get('http://staging.cravat.us/CRAVAT/rest/service/status', params={'jobid': jobid})
+    status = json.loads(check.text)['status']
+    resultfileurl = json.loads(check.text)['resultfileurl']
+    #out_file.write(str(status) + ', ')
+    if status == 'Success':
+        #out_file.write('\t' + resultfileurl)
+        break
+    else:
+        time.sleep(2)
+        
+#out_file.write('\n')
+
+#creates three files
+file_1 = time.strftime("%H:%M") + '_Z_Variant_Result.tsv'
+file_2 = time.strftime("%H:%M") + '_Z_Additional_Details.tsv'
+file_3 = time.strftime("%H:%M") + 'Combined_Variant_Results.tsv'
+
+
+#Download the two results
+urllib.urlretrieve("http://cravat.us/CRAVAT/results/" + jobid + "/" + "Variant.Result.tsv", file_1)
+urllib.urlretrieve("http://cravat.us/CRAVAT/results/" + jobid + "/" + "Variant_Additional_Details.Result.tsv", file_2)
+
+headers = []
+duplicates = []
+
+#opens the Variant Result file and the Variant Additional Details file as csv readers, then opens the output file (galaxy) as a writer
+with open(file_1) as tsvin_1, open(file_2) as tsvin_2, open(output_filename, 'wb') as tsvout:
+    tsvreader_1 = csv.reader(tsvin_1, delimiter='\t')
+    tsvreader_2 = csv.reader(tsvin_2, delimiter='\t')
+    tsvout = csv.writer(tsvout, delimiter='\t')
+         
+#loops through each row in the Variant Additional Details file         
+    for row in tsvreader_2:
+        #sets row_2 equal to the same row in Variant Result file
+        row_2 = tsvreader_1.next()
+        #checks if row is empty or if the first term contains '#'
+        if row == [] or row[0][0] == '#':
+            continue
+        #checks if the row begins with input line
+        if row[0] == 'Input line':
+            #Goes through each value in the headers list in VAD
+            for value in row:   
+                #Adds each value into headers 
+                headers.append(value)
+            #Loops through the Keys in VR
+            for value in row_2:
+                #Checks if the value is already in headers
+                if value in headers:
+                    continue
+                #else adds the header to headers
+                else:
+                    headers.append(value)
+                    
+            print headers
+            tsvout.writerow(headers)
+            
+            
+        else:
+            
+            cells = []
+            #Goes through each value in the next list
+            for value in row:
+                #adds it to cells
+                cells.append(value)
+            #Goes through each value from the VR file after position 11 (After it is done repeating from VAD file)
+            for value in row_2[11:]:
+                #adds in the rest of the values to cells
+                cells.append(value)
+                
+            print  cells
+            tsvout.writerow(cells)
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cravat_submit/cravat_submit.xml	Wed Jul 18 10:32:36 2018 -0400
@@ -0,0 +1,34 @@
+<tool id="cravat_submit" name="CRAVAT Submit, Check, and Retrieve" version="0.1.0">
+    <description>Submits, checks for, and retrieves data for cancer annotation</description>
+  <command interpreter="python">cravat_submit.py $input $dropdown $output</command>
+  
+  
+  <inputs>
+  
+    <param format="tabular" name="input" type="data" label="Source file"> </param>
+    <param format="tabular" name="dropdown" type="select" label="Analysis Program">
+      <option value="None">None</option>
+      <option value="VEST">VEST</option>
+      <option value="CHASM">CHASM</option>
+      <option value="VEST;CHASM">VEST and CHASM</option>
+    </param>
+    
+    
+  </inputs>
+  
+  <outputs>
+    <data format="tabular" name="output" />
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input" value="fa_gc_content_input.fa"/>
+      <output name="out_file1" file="fa_gc_content_output.txt"/>
+    </test>
+  </tests>
+
+  <help>
+ This tool submits, checks for, and retrieves data for cancer annotation.
+  </help>
+
+</tool>