Merge old scripts

lib/argosDataDumper_v1.0.py

@@ -0,0 +1,25 @@
+import getpass
+import json
+import os
+import requests
+
+basename = "https://hive3.biochemistry.gwu.edu/"
+
+def apiLogin():
+   global cookies
+
+   user = input("\nEnter your username on HIVE3 (email address): ")
+   password  = getpass.getpass()
+   loginParams = {'api': '0', 'cmdr': 'login', 'login': user, 'pswd': password}
+   response = requests.get(basename, params=loginParams)
+   if response.text != '':
+      print(response.text)
+      apiLogin()  # Try again
+   else:
+      cookies = response.cookies
+
+apiLogin()
+
+
+
+

lib/argosPuller.sh

@@ -0,0 +1,24 @@
+#!/bin/bash
+
+if [ "$#" -eq 0 ]
+then
+        echo "No arguments supplied"
+        exit 1
+fi
+
+for FILE in /software/argosdb/dataset-maker/recipes/*.json;
+do
+        query=$(printf "%s\n" "${FILE##*/}" | sed -r 's/(.*[0-9]{6})_.*/\1/' | tr '[:lower:]' '[:upper:]' $sample);
+        echo $query;
+        if [[ ! -e ~/api/data/$query.json ]]; then
+                touch ~/api/data/"$query".json;
+        fi;
+        curl -X 'POST' \
+                'https://api.argosdb.org/dataset/detail' \
+                -H 'accept: application/json' \
+                -H 'Content-Type: application/json' \
+                -d '{
+                    "bcoid": "'"$query"'",
+                    "dataversion": "'"$1"'"
+                }' > ~/api/data/"$query".json;
+done

lib/numberOfSanityErrors.py

@@ -0,0 +1,15 @@
+# Redirect the output of Robel's dataset-maker/check-dataset-sanity.py to a file and run this script on it to get a count of how many errors there are by table.
+
+import json
+
+with open ("dataset-sanity-log-10.24.2024", "r") as inFile:
+    myObj = json.load(inFile)
+
+myList = []
+
+for key in myObj:
+    values = myObj[key]
+    for value in values:
+        myList.append(value)
+    print (key + ", Number of errors: " + str(len(myList)))
+

lib/sample.json

@@ -0,0 +1,3 @@
+{
+        "my_first_key" : "my_first_value"
+}

lib/shell/argosPuller.sh

@@ -0,0 +1,39 @@
+#!/bin/bash
+
+if [ "$#" -eq 0 ]
+then
+        echo "No version supplied; usage: ./argosPuller.sh <version>"
+        exit 1
+fi
+
+for FILE in /software/argosdb/dataset-maker/recipes/*.json;
+do
+        query=$(printf "%s\n" "${FILE##*/}" | sed -r 's/(.*[0-9]{6})_.*/\1/' | tr '[:lower:]' '[:upper:]' $sample);
+        echo $query;
+        if [[ ! -e ~/api/data/$query.json ]]; then
+                touch ~/api/data/"$query".json;
+        fi;
+        curl -X 'POST' \
+                'https://api.argosdb.org/dataset/detail' \
+                -H 'accept: application/json' \
+                -H 'Content-Type: application/json' \
+                -d '{
+                    "bcoid": "'"$query"'",
+                    "dataversion": "'"$1"'"
+                }' > ~/api/data/"$query".json;
+done
+
+echo "Finished downlaoding data from ARGOS API. Attempting to push data sets to HIVE 3..."
+read -p "Enter your login for HIVE 3: " user
+read -sp "Enter your password" pass
+#This needs a check to make sure it logged in properly and retry input if not.
+curl -k -c ~/hive3.cookie "https://hive3.biochemistry.gwu.edu/dna.cgi?cmdr=login&login=${user}&pswd=${pass}"
+
+for DATASET in ~/api/data/*.json;
+do
+        curl -v -b  ~/hive3.cookie  -X POST -F "content=@${DATASET}" -F 'cmd=objSetFile' -F 'raw=1'  -F 'bin=0' -F 'type=u-file' -F 'filename=_.json' -F 'name=ArgosDataSetFile'  -F 'ext=json'  'https://hive3.biochemistry.gwu.edu/dna.cgi';
+done
+
+
+
+

lib/shell/hive3pushTest.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+echo "Finished downlaoding data from ARGOS API. Attempting to push data sets to HIVE 3...\n"
+read -p "Enter your login for HIVE 3: " user
+read -p "Enter your password" pass
+curl -k -c ~/hive3.cookie "https://hive3.biochemistry.gwu.edu/dna.cgi?cmdr=login&login=${user}&pswd=${pass}"
+
+# Log into HIVE 3:
+# curl -k -c ~/hive3.cookie 'https://hive3.biochemistry.gwu.edu/dna.cgi?cmdr=login&login=argos@argos.org&pswd=qQ123123'
+# Remember to get input from user for login/pass!!!
+
+for DATASET in ~/scripts/*.json;
+#for DATASET in ~/api/data/*.json;
+do
+        curl -v -b  ~/hive3.cookie  -X POST -F "content=@${DATASET}" -F 'cmd=objSetFile' -F 'raw=1'  -F 'bin=0' -F 'type=u-file' -F 'filename=_.json' -F 'name=apiTestFile'  -F 'ext=json'  'https://hive3.biochemistry.gwu.edu/dna.cgi';
+done
+#        curl -v -b  ~/hive3.cookie  -X POST -F 'content=@/home/vboxuser/scripts/test.json' -F 'cmd=objSetFile' -F 'raw=1'  -F 'bin=0' -F 'type=u-file' -F 'filename=_.json' -F 'name=apiTestFile'  -F 'ext=json'  'https://hive3.biochemistry.gwu.edu/dna.cgi';
+
+# The @content tag is where you specify the file.
+