6 files changed, 117 insertions, 26 deletions
diff --git a/gn3/api/async_commands.py b/gn3/api/async_commands.py
new file mode 100644
index 0000000..c0cf4bb
--- /dev/null
+++ b/gn3/api/async_commands.py
@@ -0,0 +1,16 @@
+"""Endpoints and functions concerning commands run in external processes."""
+import redis
+from flask import jsonify, Blueprint
+
+async_commands = Blueprint("async_commands", __name__)
+
+@async_commands.route("/state/<command_id>")
+def command_state(command_id):
+    """Respond with the current state of command identified by `command_id`."""
+    with redis.Redis(decode_responses=True) as rconn:
+        state = rconn.hgetall(name=command_id)
+        if not state:
+            return jsonify(
+                status=404,
+                error="The command id provided does not exist.")
+        return jsonify(dict(state.items()))
diff --git a/gn3/api/correlation.py b/gn3/api/correlation.py
index 46121f8..7eb7cd6 100644
--- a/gn3/api/correlation.py
+++ b/gn3/api/correlation.py
@@ -1,13 +1,21 @@
 """Endpoints for running correlations"""
+import sys
+from functools import reduce
+
+import redis
 from flask import jsonify
 from flask import Blueprint
 from flask import request
+from flask import current_app
 
-from gn3.computations.correlations import compute_all_sample_correlation
-from gn3.computations.correlations import compute_all_lit_correlation
-from gn3.computations.correlations import compute_tissue_correlation
-from gn3.computations.correlations import map_shared_keys_to_values
+from gn3.settings import SQL_URI
+from gn3.commands import queue_cmd, compose_pcorrs_command
 from gn3.db_utils import database_connector
+from gn3.responses.pcorrs_responses import build_response
+from gn3.computations.correlations import map_shared_keys_to_values
+from gn3.computations.correlations import compute_tissue_correlation
+from gn3.computations.correlations import compute_all_lit_correlation
+from gn3.computations.correlations import compute_all_sample_correlation
 
 correlation = Blueprint("correlation", __name__)
 
@@ -58,17 +66,15 @@ def compute_lit_corr(species=None, gene_id=None):
     might be needed for actual computing of the correlation results
     """
 
-    conn, _cursor_object = database_connector()
-    target_traits_gene_ids = request.get_json()
-    target_trait_gene_list = list(target_traits_gene_ids.items())
+    with database_connector() as conn:
+        target_traits_gene_ids = request.get_json()
+        target_trait_gene_list = list(target_traits_gene_ids.items())
 
-    lit_corr_results = compute_all_lit_correlation(
-        conn=conn, trait_lists=target_trait_gene_list,
-        species=species, gene_id=gene_id)
+        lit_corr_results = compute_all_lit_correlation(
+            conn=conn, trait_lists=target_trait_gene_list,
+            species=species, gene_id=gene_id)
 
-    conn.close()
-
-    return jsonify(lit_corr_results)
+        return jsonify(lit_corr_results)
 
 
 @correlation.route("/tissue_corr/<string:corr_method>", methods=["POST"])
@@ -83,3 +89,44 @@ def compute_tissue_corr(corr_method="pearson"):
                                          corr_method=corr_method)
 
     return jsonify(results)
+
+@correlation.route("/partial", methods=["POST"])
+def partial_correlation():
+    """API endpoint for partial correlations."""
+    def trait_fullname(trait):
+        return f"{trait['dataset']}::{trait['trait_name']}"
+
+    def __field_errors__(args):
+        def __check__(acc, field):
+            if args.get(field) is None:
+                return acc + (f"Field '{field}' missing",)
+            return acc
+        return __check__
+
+    def __errors__(request_data, fields):
+        errors = tuple()
+        if request_data is None:
+            return ("No request data",)
+
+        return reduce(__field_errors__(request_data), fields, errors)
+
+    args = request.get_json()
+    request_errors = __errors__(
+        args, ("primary_trait", "control_traits", "target_db", "method"))
+    if request_errors:
+        return build_response({
+            "status": "error",
+            "messages": request_errors,
+            "error_type": "Client Error"})
+    return build_response({
+        "status": "success",
+        "results": queue_cmd(
+            conn=redis.Redis(),
+            cmd=compose_pcorrs_command(
+                trait_fullname(args["primary_trait"]),
+                tuple(
+                    trait_fullname(trait) for trait in args["control_traits"]),
+                args["method"], args["target_db"],
+                int(args.get("criteria", 500))),
+            job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
+            env = {"PYTHONPATH": ":".join(sys.path), "SQL_URI": SQL_URI})})
diff --git a/gn3/api/ctl.py b/gn3/api/ctl.py
new file mode 100644
index 0000000..ac33d63
--- /dev/null
+++ b/gn3/api/ctl.py
@@ -0,0 +1,24 @@
+"""module contains endpoints for ctl"""
+
+from flask import Blueprint
+from flask import request
+from flask import jsonify
+
+from gn3.computations.ctl import call_ctl_script
+
+ctl = Blueprint("ctl", __name__)
+
+
+@ctl.route("/run_ctl", methods=["POST"])
+def run_ctl():
+    """endpoint to run ctl
+    input: request form object
+    output:json object enum::(response,error)
+
+    """
+    ctl_data = request.json
+
+    (cmd_results, response) = call_ctl_script(ctl_data)
+    return (jsonify({
+        "results": response
+    }), 200) if response is not None else (jsonify({"error": str(cmd_results)}), 401)
diff --git a/gn3/api/general.py b/gn3/api/general.py
index 69ec343..e0bfc81 100644
--- a/gn3/api/general.py
+++ b/gn3/api/general.py
@@ -7,7 +7,7 @@ from flask import request
 
 from gn3.fs_helpers import extract_uploaded_file
 from gn3.commands import run_cmd
-
+from gn3.db import datasets
 
 general = Blueprint("general", __name__)
 
@@ -68,3 +68,8 @@ def run_r_qtl(geno_filestr, pheno_filestr):
     cmd = (f"Rscript {rqtl_wrapper} "
            f"{geno_filestr} {pheno_filestr}")
     return jsonify(run_cmd(cmd)), 201
+
+@general.route("/dataset/<accession_id>")
+def dataset_metadata(accession_id):
+    """Return info as JSON for dataset with ACCESSION_ID."""
+    return jsonify(datasets.dataset_metadata(accession_id))
diff --git a/gn3/api/heatmaps.py b/gn3/api/heatmaps.py
index 633a061..80c8ca8 100644
--- a/gn3/api/heatmaps.py
+++ b/gn3/api/heatmaps.py
@@ -24,15 +24,14 @@ def clustered_heatmaps():
         return jsonify({
             "message": "You need to provide at least two trait names."
         }), 400
-    conn, _cursor = database_connector()
-    def parse_trait_fullname(trait):
-        name_parts = trait.split(":")
-        return "{dataset_name}::{trait_name}".format(
-            dataset_name=name_parts[1], trait_name=name_parts[0])
-    traits_fullnames = [parse_trait_fullname(trait) for trait in traits_names]
+    with database_connector() as conn:
+        def parse_trait_fullname(trait):
+            name_parts = trait.split(":")
+            return f"{name_parts[1]}::{name_parts[0]}"
+        traits_fullnames = [parse_trait_fullname(trait) for trait in traits_names]
 
-    with io.StringIO() as io_str:
-        figure = build_heatmap(traits_fullnames, conn, vertical=vertical)
-        figure.write_json(io_str)
-        fig_json = io_str.getvalue()
-    return fig_json, 200
+        with io.StringIO() as io_str:
+            figure = build_heatmap(traits_fullnames, conn, vertical=vertical)
+            figure.write_json(io_str)
+            fig_json = io_str.getvalue()
+        return fig_json, 200
diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
index 85b2460..70ebe12 100644
--- a/gn3/api/rqtl.py
+++ b/gn3/api/rqtl.py
@@ -25,7 +25,7 @@ run the rqtl_wrapper script and return the results as JSON
         raise FileNotFoundError
 
     # Split kwargs by those with values and boolean ones that just convert to True/False
-    kwargs = ["model", "method", "nperm", "scale", "control_marker"]
+    kwargs = ["covarstruct", "model", "method", "nperm", "scale", "control_marker"]
     boolean_kwargs = ["addcovar", "interval", "pstrata", "pairscan"]
     all_kwargs = kwargs + boolean_kwargs