Updating code to work for #666

services/projectr/install_bioc.sh

@@ -5,8 +5,7 @@ Rver="${Rmaj}.3.1"
 
 current_dir=$(pwd)
 
-# Install and build R (Using 'apt-get install' on Ubuntu Trusty installs version 3.0.2 of R)
-curl http://lib.stat.cmu.edu/R/CRAN/src/base/${Rmaj}/${Rver}.tar.gz | tar -C /opt -zx
+curl -s -L http://lib.stat.cmu.edu/R/CRAN/src/base/${Rmaj}/${Rver}.tar.gz | tar xzv -C /opt
 cd /opt/${Rver}
 /opt/${Rver}/configure --with-readline=no --enable-R-shlib --enable-BLAS-shlib --with-x=no || exit 1
 make || exit 1

services/projectr/main.py

@@ -1,5 +1,6 @@
 import os, sys
 import pandas as pd
+from io import StringIO
 from flask import Flask, abort, jsonify, request
 
 cloud_logging = False
@@ -38,7 +39,9 @@ def do_binary_projection(target_df, loading_df):
     """Perform projection based on the number of genes that were expressed in the cell or observation."""
     # Only applies with unweighted gene carts.
     tp_target_series = target_df.astype(bool).sum(axis=0).transpose()
-    return pd.DataFrame(data=tp_target_series, columns=loading_df.columns, index=tp_target_series.index)
+    # Need to convert data to list of lists to create a DataFrame.
+    # https://stackoverflow.com/questions/70854450/pandas-dataframe-shape-of-passed-values-is-5-1-indices-imply-5-2
+    return pd.DataFrame(data=[tp_target_series], columns=loading_df.columns, index=tp_target_series.index)
 
 def do_pca_projection(target_df, loading_df):
     """Perform projection of PCA loadings."""
@@ -66,6 +69,10 @@ def index():
     write_entry("projectr", "INFO", "Genecart ID: {}".format(genecart_id))
 
 
+    # pd.read_json gives a FutureWarning, and suggest to wrap the json in StringIO.
+    target = StringIO(target)
+    loadings = StringIO(loadings)
+
     target_df = pd.read_json(target, orient="split")
     loading_df = pd.read_json(loadings, orient="split")
 

services/projectr/requirements.txt

@@ -1,5 +1,5 @@
 Flask==3.0.0
 gunicorn==20.1.0
 rpy2==3.5.1 # 3.5.2 and up gives errors with rpy2py and py2rpy
-pandas==1.4.1
+pandas==2.2.1
 google-cloud-logging