metadata_edits: Add "POST /<dataset_id>/traits/<name>/update"

2 files changed, 135 insertions, 127 deletions

diff --git a/wqflask/wqflask/metadata_edits.py b/wqflask/wqflask/metadata_edits.py
index 94e2710b..bab1fa71 100644
--- a/wqflask/wqflask/metadata_edits.py
+++ b/wqflask/wqflask/metadata_edits.py
@@ -1,11 +1,13 @@
 import MySQLdb
 import os
 import json
+import datetime
 import difflib
 
 
 from collections import namedtuple
-from flask import Blueprint, current_app, render_template, request
+from flask import (Blueprint, current_app, redirect,
+                   flash, g, render_template, request)
 from itertools import groupby
 
 from wqflask.decorators import edit_access_required
@@ -21,6 +23,9 @@ from gn3.db.phenotypes import Probeset
 from gn3.db.phenotypes import Publication
 from gn3.db.phenotypes import PublishXRef
 from gn3.db.phenotypes import probeset_mapping
+from gn3.commands import run_cmd
+from gn3.db.traits import get_trait_csv_sample_data
+from gn3.db.traits import update_sample_data
 
 
 metadata_edit = Blueprint('metadata_edit', __name__)
@@ -125,6 +130,7 @@ def display_phenotype_metadata(dataset_id: str, name: str):
         publish_xref=_d.get("publish_xref"),
         phenotype=_d.get("phenotype"),
         publication=_d.get("publication"),
+        dataset_id=dataset_id,
         resource_id=request.args.get("resource-id"),
         version=os.environ.get("GN_VERSION"),
     )
@@ -145,3 +151,131 @@ def display_probeset_metadata(name: str):
         resource_id=request.args.get("resource-id"),
         version=os.environ.get("GN_VERSION"),
     )
+
+
+@metadata_edit.route("/<dataset_id>/traits/<name>/update", methods=("POST",))
+@edit_access_required
+def update_phenotype(dataset_id: str, name: str):
+    conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
+                           user=current_app.config.get("DB_USER"),
+                           passwd=current_app.config.get("DB_PASS"),
+                           host=current_app.config.get("DB_HOST"))
+    data_ = request.form.to_dict()
+    TMPDIR = current_app.config.get("TMPDIR")
+    author = (g.user_session.record.get(b"user_id",
+                                        b"").decode("utf-8") or
+              g.user_session.record.get("user_id", ""))
+    phenotype_id = str(data_.get('phenotype-id'))
+    if 'file' not in request.files:
+        flash("No sample-data has been uploaded", "warning")
+    else:
+        file_ = request.files['file']
+        SAMPLE_DATADIR = os.path.join(TMPDIR, "sample-data")
+        if not os.path.exists(SAMPLE_DATADIR):
+            os.makedirs(SAMPLE_DATADIR)
+        if not os.path.exists(os.path.join(SAMPLE_DATADIR,
+                                           "diffs")):
+            os.makedirs(os.path.join(SAMPLE_DATADIR,
+                                     "diffs"))
+        if not os.path.exists(os.path.join(SAMPLE_DATADIR,
+                                           "updated")):
+            os.makedirs(os.path.join(SAMPLE_DATADIR,
+                                     "updated"))
+        current_time = str(datetime.datetime.now().isoformat())
+        new_file_name = (os.path.join(TMPDIR,
+                                      "sample-data/updated/",
+                                      (f"{author}."
+                                       f"{name}.{phenotype_id}."
+                                       f"{current_time}.csv")))
+        uploaded_file_name = (os.path.join(
+            TMPDIR,
+            "sample-data/updated/",
+            (f"updated.{author}."
+             f"{request.args.get('resource-id')}."
+             f"{current_time}.csv")))
+        file_.save(new_file_name)
+        publishdata_id = ""
+        lines = []
+        with open(new_file_name, "r") as f:
+            lines = f.read()
+            first_line = lines.split('\n', 1)[0]
+            publishdata_id = first_line.split("Id:")[-1].strip()
+        with open(new_file_name, "w") as f:
+            f.write(lines.split("\n\n")[-1])
+        csv_ = get_trait_csv_sample_data(conn=conn,
+                                         trait_name=str(name),
+                                         phenotype_id=str(phenotype_id))
+        with open(uploaded_file_name, "w") as f_:
+            f_.write(csv_.split("\n\n")[-1])
+        r = run_cmd(cmd=("csvdiff "
+                         f"'{uploaded_file_name}' '{new_file_name}' "
+                         "--format json"))
+        diff_output = (f"{TMPDIR}/sample-data/diffs/"
+                       f"{author}.{request.args.get('resource-id')}."
+                       f"{current_time}.json")
+        with open(diff_output, "w") as f:
+            dict_ = json.loads(r.get("output"))
+            dict_.update({
+                "author": author,
+                "publishdata_id": publishdata_id,
+                "dataset_id": data_.get("dataset-name"),
+                "timestamp": datetime.datetime.now().strftime(
+                    "%Y-%m-%d %H:%M:%S")
+            })
+            f.write(json.dumps(dict_))
+        flash("Sample-data has been successfully uploaded", "success")
+    # Run updates:
+    phenotype_ = {
+        "pre_pub_description": data_.get("pre-pub-desc"),
+        "post_pub_description": data_.get("post-pub-desc"),
+        "original_description": data_.get("orig-desc"),
+        "units": data_.get("units"),
+        "pre_pub_abbreviation": data_.get("pre-pub-abbrev"),
+        "post_pub_abbreviation": data_.get("post-pub-abbrev"),
+        "lab_code": data_.get("labcode"),
+        "submitter": data_.get("submitter"),
+        "owner": data_.get("owner"),
+        "authorized_users": data_.get("authorized-users"),
+    }
+    updated_phenotypes = update(
+        conn, "Phenotype",
+        data=Phenotype(**phenotype_),
+        where=Phenotype(id_=data_.get("phenotype-id")))
+    diff_data = {}
+    if updated_phenotypes:
+        diff_data.update({"Phenotype": diff_from_dict(old={
+            k: data_.get(f"old_{k}") for k, v in phenotype_.items()
+            if v is not None}, new=phenotype_)})
+    publication_ = {
+        "abstract": data_.get("abstract"),
+        "authors": data_.get("authors"),
+        "title": data_.get("title"),
+        "journal": data_.get("journal"),
+        "volume": data_.get("volume"),
+        "pages": data_.get("pages"),
+        "month": data_.get("month"),
+        "year": data_.get("year")
+    }
+    updated_publications = update(
+        conn, "Publication",
+        data=Publication(**publication_),
+        where=Publication(id_=data_.get("pubmed-id",
+                                        data_.get("old_id_"))))
+    if updated_publications:
+        diff_data.update({"Publication": diff_from_dict(old={
+            k: data_.get(f"old_{k}") for k, v in publication_.items()
+            if v is not None}, new=publication_)})
+    if diff_data:
+        diff_data.update({"dataset_id": name})
+        diff_data.update({"resource_id": request.args.get('resource-id')})
+        diff_data.update({"author": author})
+        diff_data.update({"timestamp": datetime.datetime.now().strftime(
+            "%Y-%m-%d %H:%M:%S")})
+        insert(conn,
+               table="metadata_audit",
+               data=MetadataAudit(dataset_id=name,
+                                  editor=author,
+                                  json_data=json.dumps(diff_data)))
+        flash(f"Diff-data: \n{diff_data}\nhas been uploaded", "success")
+    return redirect(f"/datasets/{dataset_id}/traits/{name}/edit"
+                    f"?resource-id={request.args.get('resource-id')}")
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 08c88a25..963e48b7 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -416,132 +416,6 @@ def submit_trait_form():
         version=GN_VERSION)
 
 
-@app.route("/trait/update", methods=["POST"])
-@edit_access_required
-def update_phenotype():
-    conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
-                           user=current_app.config.get("DB_USER"),
-                           passwd=current_app.config.get("DB_PASS"),
-                           host=current_app.config.get("DB_HOST"))
-    data_ = request.form.to_dict()
-    TMPDIR = current_app.config.get("TMPDIR")
-    author = g.user_session.record.get(b'user_name')
-    if 'file' not in request.files:
-        flash("No sample-data has been uploaded", "warning")
-    else:
-        file_ = request.files['file']
-        trait_name = str(data_.get('dataset-name'))
-        phenotype_id = str(data_.get('phenotype-id', 35))
-        SAMPLE_DATADIR = os.path.join(TMPDIR, "sample-data")
-        if not os.path.exists(SAMPLE_DATADIR):
-            os.makedirs(SAMPLE_DATADIR)
-        if not os.path.exists(os.path.join(SAMPLE_DATADIR,
-                                           "diffs")):
-            os.makedirs(os.path.join(SAMPLE_DATADIR,
-                                     "diffs"))
-        if not os.path.exists(os.path.join(SAMPLE_DATADIR,
-                                           "updated")):
-            os.makedirs(os.path.join(SAMPLE_DATADIR,
-                                     "updated"))
-        current_time = str(datetime.datetime.now().isoformat())
-        new_file_name = (os.path.join(TMPDIR,
-                                      "sample-data/updated/",
-                                      (f"{author.decode('utf-8')}."
-                                       f"{trait_name}.{phenotype_id}."
-                                       f"{current_time}.csv")))
-        uploaded_file_name = (os.path.join(
-            TMPDIR,
-            "sample-data/updated/",
-            (f"updated.{author.decode('utf-8')}."
-             f"{trait_name}.{phenotype_id}."
-             f"{current_time}.csv")))
-        file_.save(new_file_name)
-        publishdata_id = ""
-        lines = []
-        with open(new_file_name, "r") as f:
-            lines = f.read()
-            first_line = lines.split('\n', 1)[0]
-            publishdata_id = first_line.split("Id:")[-1].strip()
-        with open(new_file_name, "w") as f:
-            f.write(lines.split("\n\n")[-1])
-        csv_ = get_trait_csv_sample_data(conn=conn,
-                                         trait_name=str(trait_name),
-                                         phenotype_id=str(phenotype_id))
-        with open(uploaded_file_name, "w") as f_:
-            f_.write(csv_.split("\n\n")[-1])
-        r = run_cmd(cmd=("csvdiff "
-                         f"'{uploaded_file_name}' '{new_file_name}' "
-                         "--format json"))
-        diff_output = (f"{TMPDIR}/sample-data/diffs/"
-                       f"{trait_name}.{author.decode('utf-8')}."
-                       f"{phenotype_id}.{current_time}.json")
-        with open(diff_output, "w") as f:
-            dict_ = json.loads(r.get("output"))
-            dict_.update({
-                "author": author.decode('utf-8'),
-                "publishdata_id": publishdata_id,
-                "dataset_id": data_.get("dataset-name"),
-                "timestamp": datetime.datetime.now().strftime(
-                    "%Y-%m-%d %H:%M:%S")
-            })
-            f.write(json.dumps(dict_))
-        flash("Sample-data has been successfully uploaded", "success")
-    # Run updates:
-    phenotype_ = {
-        "pre_pub_description": data_.get("pre-pub-desc"),
-        "post_pub_description": data_.get("post-pub-desc"),
-        "original_description": data_.get("orig-desc"),
-        "units": data_.get("units"),
-        "pre_pub_abbreviation": data_.get("pre-pub-abbrev"),
-        "post_pub_abbreviation": data_.get("post-pub-abbrev"),
-        "lab_code": data_.get("labcode"),
-        "submitter": data_.get("submitter"),
-        "owner": data_.get("owner"),
-        "authorized_users": data_.get("authorized-users"),
-    }
-    updated_phenotypes = update(
-        conn, "Phenotype",
-        data=Phenotype(**phenotype_),
-        where=Phenotype(id_=data_.get("phenotype-id")))
-    diff_data = {}
-    if updated_phenotypes:
-        diff_data.update({"Phenotype": diff_from_dict(old={
-            k: data_.get(f"old_{k}") for k, v in phenotype_.items()
-            if v is not None}, new=phenotype_)})
-    publication_ = {
-        "abstract": data_.get("abstract"),
-        "authors": data_.get("authors"),
-        "title": data_.get("title"),
-        "journal": data_.get("journal"),
-        "volume": data_.get("volume"),
-        "pages": data_.get("pages"),
-        "month": data_.get("month"),
-        "year": data_.get("year")
-    }
-    updated_publications = update(
-        conn, "Publication",
-        data=Publication(**publication_),
-        where=Publication(id_=data_.get("pubmed-id",
-                                        data_.get("old_id_"))))
-    if updated_publications:
-        diff_data.update({"Publication": diff_from_dict(old={
-            k: data_.get(f"old_{k}") for k, v in publication_.items()
-            if v is not None}, new=publication_)})
-    if diff_data:
-        diff_data.update({"dataset_id": data_.get("dataset-name")})
-        diff_data.update({"author": author.decode('utf-8')})
-        diff_data.update({"timestamp": datetime.datetime.now().strftime(
-            "%Y-%m-%d %H:%M:%S")})
-        insert(conn,
-               table="metadata_audit",
-               data=MetadataAudit(dataset_id=data_.get("dataset-name"),
-                                  editor=author.decode("utf-8"),
-                                  json_data=json.dumps(diff_data)))
-        flash(f"Diff-data: \n{diff_data}\nhas been uploaded", "success")
-    return redirect(f"/trait/{data_.get('dataset-name')}"
-                    f"/edit/inbredset-id/{data_.get('inbred-set-id')}")
-
-
 @app.route("/probeset/update", methods=["POST"])
 def update_probeset():
     conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),