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-rw-r--r--uploader/authorisation.py2
-rw-r--r--uploader/base_routes.py7
-rw-r--r--uploader/files/__init__.py1
-rw-r--r--uploader/phenotypes/models.py83
-rw-r--r--uploader/phenotypes/views.py382
-rw-r--r--uploader/population/rqtl2.py123
-rw-r--r--uploader/static/css/styles.css189
-rw-r--r--uploader/templates/base.html55
-rw-r--r--uploader/templates/phenotypes/add-phenotypes-raw-files.html2
-rw-r--r--uploader/templates/phenotypes/edit-phenotype.html332
-rw-r--r--uploader/templates/phenotypes/job-status.html8
-rw-r--r--uploader/templates/phenotypes/macro-display-resumable-elements.html60
-rw-r--r--uploader/templates/phenotypes/review-job-data.html101
-rw-r--r--uploader/templates/phenotypes/view-dataset.html66
-rw-r--r--uploader/templates/phenotypes/view-phenotype.html83
-rw-r--r--uploader/templates/populations/macro-display-population-card.html5
16 files changed, 1124 insertions, 375 deletions
diff --git a/uploader/authorisation.py b/uploader/authorisation.py
index ee8fe97..bd3454c 100644
--- a/uploader/authorisation.py
+++ b/uploader/authorisation.py
@@ -18,7 +18,7 @@ def require_login(function):
"""Check that the user is logged in and their token is valid."""
def __clear_session__(_no_token):
session.clear_session_info()
- flash("You need to be logged in.", "alert-danger")
+ flash("You need to be logged in.", "alert-danger big-alert")
return redirect("/")
return session.user_token().either(
diff --git a/uploader/base_routes.py b/uploader/base_routes.py
index 742a254..326086f 100644
--- a/uploader/base_routes.py
+++ b/uploader/base_routes.py
@@ -46,6 +46,13 @@ def jquery(filename):
appenv(), f"share/genenetwork2/javascript/jquery/{filename}")
+@base.route("/datatables/<path:filename>")
+def datatables(filename):
+ """Fetch DataTables files."""
+ return send_from_directory(
+ appenv(), f"share/genenetwork2/javascript/DataTables/{filename}")
+
+
@base.route("/node-modules/<path:filename>")
def node_modules(filename):
"""Fetch node-js modules."""
diff --git a/uploader/files/__init__.py b/uploader/files/__init__.py
index 60d2f3b..53c3176 100644
--- a/uploader/files/__init__.py
+++ b/uploader/files/__init__.py
@@ -1,3 +1,4 @@
+"""General files and chunks utilities."""
from .chunks import chunked_binary_read
from .functions import (fullpath,
save_file,
diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py
index 73b1cce..e1ec0c9 100644
--- a/uploader/phenotypes/models.py
+++ b/uploader/phenotypes/models.py
@@ -54,6 +54,20 @@ def phenotypes_count(conn: mdb.Connection,
return int(cursor.fetchone()["total_phenos"])
+def phenotype_publication_data(conn, phenotype_id) -> Optional[dict]:
+ """Retrieve the publication data for a phenotype if it exists."""
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute(
+ "SELECT DISTINCT pxr.PhenotypeId, pub.* FROM PublishXRef AS pxr "
+ "INNER JOIN Publication as pub ON pxr.PublicationId=pub.Id "
+ "WHERE pxr.PhenotypeId=%s",
+ (phenotype_id,))
+ res = cursor.fetchone()
+ if res is None:
+ return res
+ return dict(res)
+
+
def dataset_phenotypes(conn: mdb.Connection,
population_id: int,
dataset_id: int,
@@ -61,7 +75,7 @@ def dataset_phenotypes(conn: mdb.Connection,
limit: Optional[int] = None) -> tuple[dict, ...]:
"""Fetch the actual phenotypes."""
_query = (
- "SELECT pheno.*, pxr.Id, ist.InbredSetCode FROM Phenotype AS pheno "
+ "SELECT pheno.*, pxr.Id AS xref_id, ist.InbredSetCode FROM Phenotype AS pheno "
"INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId "
"INNER JOIN PublishFreeze AS pf ON pxr.InbredSetId=pf.InbredSetId "
"INNER JOIN InbredSet AS ist ON pf.InbredSetId=ist.Id "
@@ -73,31 +87,41 @@ def dataset_phenotypes(conn: mdb.Connection,
return tuple(dict(row) for row in cursor.fetchall())
-def __phenotype_se__(cursor: Cursor,
- species_id: int,
- population_id: int,
- dataset_id: int,
- xref_id: str) -> dict:
+def __phenotype_se__(cursor: Cursor, xref_id, dataids_and_strainids):
"""Fetch standard-error values (if they exist) for a phenotype."""
- _sequery = (
- "SELECT pxr.Id AS xref_id, pxr.DataId, str.Id AS StrainId, pse.error, nst.count "
- "FROM Phenotype AS pheno "
- "INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId "
- "INNER JOIN PublishSE AS pse ON pxr.DataId=pse.DataId "
- "INNER JOIN NStrain AS nst ON pse.DataId=nst.DataId "
- "INNER JOIN Strain AS str ON nst.StrainId=str.Id "
- "INNER JOIN StrainXRef AS sxr ON str.Id=sxr.StrainId "
- "INNER JOIN PublishFreeze AS pf ON sxr.InbredSetId=pf.InbredSetId "
- "INNER JOIN InbredSet AS iset ON pf.InbredSetId=iset.InbredSetId "
- "WHERE (str.SpeciesId, pxr.InbredSetId, pf.Id, pxr.Id)=(%s, %s, %s, %s)")
- cursor.execute(_sequery,
- (species_id, population_id, dataset_id, xref_id))
- return {(row["DataId"], row["StrainId"]): {
- "xref_id": row["xref_id"],
- "DataId": row["DataId"],
- "error": row["error"],
- "count": row["count"]
- } for row in cursor.fetchall()}
+ paramstr = ", ".join(["(%s, %s)"] * len(dataids_and_strainids))
+ flat = tuple(item for sublist in dataids_and_strainids for item in sublist)
+ cursor.execute("SELECT * FROM PublishSE WHERE (DataId, StrainId) IN "
+ f"({paramstr})",
+ flat)
+ debug_query(cursor, app.logger)
+ _se = {
+ (row["DataId"], row["StrainId"]): {
+ "DataId": row["DataId"],
+ "StrainId": row["StrainId"],
+ "error": row["error"]
+ }
+ for row in cursor.fetchall()
+ }
+
+ cursor.execute("SELECT * FROM NStrain WHERE (DataId, StrainId) IN "
+ f"({paramstr})",
+ flat)
+ debug_query(cursor, app.logger)
+ _n = {
+ (row["DataId"], row["StrainId"]): {
+ "DataId": row["DataId"],
+ "StrainId": row["StrainId"],
+ "count": row["count"]
+ }
+ for row in cursor.fetchall()
+ }
+
+ keys = set(tuple(_se.keys()) + tuple(_n.keys()))
+ return {
+ key: {"xref_id": xref_id, **_se.get(key,{}), **_n.get(key,{})}
+ for key in keys
+ }
def __organise_by_phenotype__(pheno, row):
"""Organise disparate data rows into phenotype 'objects'."""
@@ -117,6 +141,7 @@ def __organise_by_phenotype__(pheno, row):
**(_pheno["data"] if bool(_pheno) else {}),
(row["DataId"], row["StrainId"]): {
"DataId": row["DataId"],
+ "StrainId": row["StrainId"],
"mean": row["mean"],
"Locus": row["Locus"],
"LRS": row["LRS"],
@@ -170,11 +195,9 @@ def phenotype_by_id(
**_pheno,
"data": tuple(__merge_pheno_data_and_se__(
_pheno["data"],
- __phenotype_se__(cursor,
- species_id,
- population_id,
- dataset_id,
- xref_id)).values())
+ __phenotype_se__(
+ cursor, xref_id, tuple(_pheno["data"].keys()))
+ ).values())
}
if bool(_pheno) and len(_pheno.keys()) > 1:
raise Exception(
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
index 400baa6..ddec54c 100644
--- a/uploader/phenotypes/views.py
+++ b/uploader/phenotypes/views.py
@@ -3,12 +3,14 @@ import sys
import uuid
import json
import datetime
+from typing import Any
from pathlib import Path
from zipfile import ZipFile
-from functools import wraps
+from functools import wraps, reduce
from logging import INFO, ERROR, DEBUG, FATAL, CRITICAL, WARNING
from redis import Redis
+from pymonad.either import Left
from requests.models import Response
from MySQLdb.cursors import DictCursor
from gn_libs.mysqldb import database_connection
@@ -44,11 +46,15 @@ from .models import (dataset_by_id,
phenotypes_count,
save_new_dataset,
dataset_phenotypes,
- datasets_by_population)
+ datasets_by_population,
+ phenotype_publication_data)
phenotypesbp = Blueprint("phenotypes", __name__)
render_template = make_template_renderer("phenotypes")
+_FAMILIES_WITH_SE_AND_N_ = (
+ "Reference Populations (replicate average, SE, N)",)
+
@phenotypesbp.route("/phenotypes", methods=["GET"])
@require_login
def index():
@@ -191,12 +197,10 @@ def view_dataset(# pylint: disable=[unused-argument]
phenotype_count=phenotypes_count(
conn, population["Id"], dataset["Id"]),
phenotypes=enumerate_sequence(
- dataset_phenotypes(conn,
- population["Id"],
- dataset["Id"],
- offset=start_at,
- limit=count),
- start=start_at+1),
+ dataset_phenotypes(
+ conn,
+ population["Id"],
+ dataset["Id"])),
start_from=start_at,
count=count,
activelink="view-dataset")
@@ -220,16 +224,31 @@ def view_phenotype(# pylint: disable=[unused-argument]
):
"""View an individual phenotype from the dataset."""
def __render__(privileges):
+ phenotype = phenotype_by_id(conn,
+ species["SpeciesId"],
+ population["Id"],
+ dataset["Id"],
+ xref_id)
+ def __non_empty__(value) -> bool:
+ if isinstance(value, str):
+ return value.strip() != ""
+ return bool(value)
+
return render_template(
"phenotypes/view-phenotype.html",
species=species,
population=population,
dataset=dataset,
- phenotype=phenotype_by_id(conn,
- species["SpeciesId"],
- population["Id"],
- dataset["Id"],
- xref_id),
+ xref_id=xref_id,
+ phenotype=phenotype,
+ has_se=any(bool(item.get("error")) for item in phenotype["data"]),
+ publish_data={
+ key.replace("_", " "): val
+ for key,val in
+ (phenotype_publication_data(conn, phenotype["Id"]) or {}).items()
+ if (key in ("PubMed_ID", "Authors", "Title", "Journal")
+ and __non_empty__(val))
+ },
privileges=(privileges
### For demo! Do not commit this part
+ ("group:resource:edit-resource",
@@ -362,7 +381,7 @@ def process_phenotypes_individual_files(error_uri):
return error_uri
filepath = save_file(
- _sentfile, Path(app.config["UPLOAD_FOLDER"]))
+ _sentfile, Path(app.config["UPLOAD_FOLDER"]), hashed=False)
zfile.write(
Path(app.config["UPLOAD_FOLDER"], filepath),
arcname=filepath.name)
@@ -411,8 +430,7 @@ def add_phenotypes(species: dict, population: dict, dataset: dict, **kwargs):# p
"December"),
current_month=today.strftime("%B"),
current_year=int(today.strftime("%Y")),
- families_with_se_and_n=(
- "Reference Populations (replicate average, SE, N)",),
+ families_with_se_and_n=_FAMILIES_WITH_SE_AND_N_,
use_bundle=use_bundle,
activelink="add-phenotypes")
@@ -502,3 +520,335 @@ def job_status(
metadata=jobs.job_files_metadata(
rconn, jobs.jobsnamespace(), job['jobid']),
activelink="add-phenotypes")
+
+
+@phenotypesbp.route(
+ "<int:species_id>/populations/<int:population_id>/phenotypes/datasets"
+ "/<int:dataset_id>/job/<uuid:job_id>/review",
+ methods=["GET"])
+@require_login
+@with_dataset(
+ species_redirect_uri="species.populations.phenotypes.index",
+ population_redirect_uri="species.populations.phenotypes.select_population",
+ redirect_uri="species.populations.phenotypes.list_datasets")
+def review_job_data(
+ species: dict,
+ population: dict,
+ dataset: dict,
+ job_id: uuid.UUID,
+ **kwargs
+):# pylint: disable=[unused-argument]
+ """Review data one more time before entering it into the database."""
+ with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
+ try:
+ job = jobs.job(rconn, jobs.jobsnamespace(), str(job_id))
+ except jobs.JobNotFound as _jnf:
+ job = None
+
+ def __metadata_by_type__(by_type, item):
+ filetype = item[1]["filetype"]
+ return {
+ **by_type,
+ filetype: (by_type.get(filetype, tuple())
+ + ({"filename": item[0], **item[1]},))
+ }
+ metadata: dict[str, Any] = reduce(
+ __metadata_by_type__,
+ (jobs.job_files_metadata(
+ rconn, jobs.jobsnamespace(), job['jobid'])
+ if job else {}).items(),
+ {})
+
+ def __desc__(filetype):
+ match filetype:
+ case "phenocovar":
+ desc = "phenotypes"
+ case "pheno":
+ desc = "phenotypes data"
+ case "phenose":
+ desc = "phenotypes standard-errors"
+ case "phenonum":
+ desc = "phenotypes samples"
+ case _:
+ desc = f"unknown file type '{filetype}'."
+
+ return desc
+
+ def __summarise__(filetype, files):
+ return {
+ "filetype": filetype,
+ "number-of-files": len(files),
+ "total-data-rows": sum(
+ int(afile["linecount"]) - 1 for afile in files),
+ "description": __desc__(filetype)
+ }
+
+ summary = {
+ filetype: __summarise__(filetype, meta)
+ for filetype,meta in metadata.items()
+ }
+ return render_template("phenotypes/review-job-data.html",
+ species=species,
+ population=population,
+ dataset=dataset,
+ job_id=job_id,
+ job=job,
+ summary=summary,
+ activelink="add-phenotypes")
+
+
+def update_phenotype_metadata(conn, metadata: dict):
+ """Update a phenotype's basic metadata values."""
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute("SELECT * FROM Phenotype WHERE Id=%(phenotype-id)s",
+ metadata)
+ res = {
+ **{
+ _key: _val for _key,_val in {
+ key.lower().replace("_", "-"): value
+ for key, value in (cursor.fetchone() or {}).items()
+ }.items()
+ if _key in metadata.keys()
+ },
+ "phenotype-id": metadata.get("phenotype-id")
+ }
+ if res == metadata:
+ return False
+
+ cursor.execute(
+ "UPDATE Phenotype SET "
+ "Pre_publication_description=%(pre-publication-description)s, "
+ "Post_publication_description=%(post-publication-description)s, "
+ "Original_description=%(original-description)s, "
+ "Units=%(units)s, "
+ "Pre_publication_abbreviation=%(pre-publication-abbreviation)s, "
+ "Post_publication_abbreviation=%(post-publication-abbreviation)s "
+ "WHERE Id=%(phenotype-id)s",
+ metadata)
+ return cursor.rowcount
+
+
+def update_phenotype_values(conn, values):
+ """Update a phenotype's data values."""
+ with conn.cursor() as cursor:
+ cursor.executemany(
+ "UPDATE PublishData SET value=%(new)s "
+ "WHERE Id=%(data_id)s AND StrainId=%(strain_id)s",
+ tuple(item for item in values if item["new"] is not None))
+ cursor.executemany(
+ "DELETE FROM PublishData "
+ "WHERE Id=%(data_id)s AND StrainId=%(strain_id)s",
+ tuple(item for item in values if item["new"] is None))
+ return len(values)
+ return 0
+
+
+def update_phenotype_se(conn, serrs):
+ """Update a phenotype's standard-error values."""
+ with conn.cursor() as cursor:
+ cursor.executemany(
+ "INSERT INTO PublishSE(DataId, StrainId, error) "
+ "VALUES(%(data_id)s, %(strain_id)s, %(new)s) "
+ "ON DUPLICATE KEY UPDATE error=VALUES(error)",
+ tuple(item for item in serrs if item["new"] is not None))
+ cursor.executemany(
+ "DELETE FROM PublishSE "
+ "WHERE DataId=%(data_id)s AND StrainId=%(strain_id)s",
+ tuple(item for item in serrs if item["new"] is None))
+ return len(serrs)
+ return 0
+
+
+def update_phenotype_n(conn, counts):
+ """Update a phenotype's strain counts."""
+ with conn.cursor() as cursor:
+ cursor.executemany(
+ "INSERT INTO NStrain(DataId, StrainId, count) "
+ "VALUES(%(data_id)s, %(strain_id)s, %(new)s) "
+ "ON DUPLICATE KEY UPDATE count=VALUES(count)",
+ tuple(item for item in counts if item["new"] is not None))
+ cursor.executemany(
+ "DELETE FROM NStrain "
+ "WHERE DataId=%(data_id)s AND StrainId=%(strain_id)s",
+ tuple(item for item in counts if item["new"] is None))
+ return len(counts)
+
+ return 0
+
+
+def update_phenotype_data(conn, data: dict):
+ """Update the numeric data for a phenotype."""
+ def __organise_by_dataid_and_strainid__(acc, current):
+ _key, dataid, strainid = current[0].split("::")
+ _keysrc, _keytype = _key.split("-")
+ newkey = f"{dataid}::{strainid}"
+ newitem = acc.get(newkey, {})
+ newitem[_keysrc] = newitem.get(_keysrc, {})
+ newitem[_keysrc][_keytype] = current[1]
+ return {**acc, newkey: newitem}
+
+ def __separate_items__(acc, row):
+ key, val = row
+ return ({
+ **acc[0],
+ key: {
+ **val["value"],
+ "changed?": (not val["value"]["new"] == val["value"]["original"])
+ }
+ }, {
+ **acc[1],
+ key: {
+ **val["se"],
+ "changed?": (not val["se"]["new"] == val["se"]["original"])
+ }
+ },{
+ **acc[2],
+ key: {
+ **val["n"],
+ "changed?": (not val["n"]["new"] == val["n"]["original"])
+ }
+ })
+
+ values, serrs, counts = tuple(
+ tuple({
+ "data_id": row[0].split("::")[0],
+ "strain_id": row[0].split("::")[1],
+ "new": row[1]["new"]
+ } for row in item)
+ for item in (
+ filter(lambda val: val[1]["changed?"], item.items())# type: ignore[arg-type]
+ for item in reduce(# type: ignore[var-annotated]
+ __separate_items__,
+ reduce(__organise_by_dataid_and_strainid__,
+ data.items(),
+ {}).items(),
+ ({}, {}, {}))))
+
+ return (update_phenotype_values(conn, values),
+ update_phenotype_se(conn, serrs),
+ update_phenotype_n(conn, counts))
+
+
+@phenotypesbp.route(
+ "<int:species_id>/populations/<int:population_id>/phenotypes/datasets"
+ "/<int:dataset_id>/phenotype/<int:xref_id>/edit",
+ methods=["GET", "POST"])
+@require_login
+@with_dataset(
+ species_redirect_uri="species.populations.phenotypes.index",
+ population_redirect_uri="species.populations.phenotypes.select_population",
+ redirect_uri="species.populations.phenotypes.list_datasets")
+def edit_phenotype_data(# pylint: disable=[unused-argument]
+ species: dict,
+ population: dict,
+ dataset: dict,
+ xref_id: int,
+ **kwargs
+):
+ """Edit the data for a particular phenotype."""
+ def __render__(**kwargs):
+ processed_kwargs = {
+ **kwargs,
+ "privileges": (kwargs.get("privileges", tuple())
+ ### For demo! Do not commit this part
+ + ("group:resource:edit-resource",
+ "group:resource:delete-resource",)
+ ### END: For demo! Do not commit this part
+ )
+ }
+ return render_template(
+ "phenotypes/edit-phenotype.html",
+ species=species,
+ population=population,
+ dataset=dataset,
+ xref_id=xref_id,
+ families_with_se_and_n=_FAMILIES_WITH_SE_AND_N_,
+ **processed_kwargs,
+ activelink="edit-phenotype")
+
+ with database_connection(app.config["SQL_URI"]) as conn:
+ if request.method == "GET":
+ def __fetch_phenotype__(privileges):
+ phenotype = phenotype_by_id(conn,
+ species["SpeciesId"],
+ population["Id"],
+ dataset["Id"],
+ xref_id)
+ if phenotype is None:
+ msg = ("Could not find the phenotype with cross-reference ID"
+ f" '{xref_id}' from dataset '{dataset['FullName']}' "
+ f" from the '{population['FullName']}' population of "
+ f" species '{species['FullName']}'.")
+ return Left({"privileges": privileges, "phenotype-error": msg})
+ return {"privileges": privileges, "phenotype": phenotype}
+
+ def __fetch_publication_data__(**kwargs):
+ pheno = kwargs["phenotype"]
+ return {
+ **kwargs,
+ "publication_data": phenotype_publication_data(
+ conn, pheno["Id"])
+ }
+
+ def __fail__(failure_object):
+ # process the object
+ return __render__(failure_object=failure_object)
+
+ return oauth2_post(
+ "/auth/resource/phenotypes/individual/linked-resource",
+ json={
+ "species_id": species["SpeciesId"],
+ "population_id": population["Id"],
+ "dataset_id": dataset["Id"],
+ "xref_id": xref_id
+ }
+ ).then(
+ lambda resource: tuple(
+ privilege["privilege_id"] for role in resource["roles"]
+ for privilege in role["privileges"])
+ ).then(
+ __fetch_phenotype__
+ ).then(
+ lambda args: __fetch_publication_data__(**args)
+ ).either(__fail__, lambda args: __render__(**args))
+
+ ## POST
+ _change = False
+ match request.form.get("submit", "invalid-action"):
+ case "update basic metadata":
+ _change = update_phenotype_metadata(conn, {
+ key: value.strip() if bool(value.strip()) else None
+ for key, value in request.form.items()
+ if key not in ("submit",)
+ })
+ msg = "Basic metadata was updated successfully."
+ case "update data":
+ _update = update_phenotype_data(conn, {
+ key: value.strip() if bool(value.strip()) else None
+ for key, value in request.form.items()
+ if key not in ("submit",)
+ })
+ msg = (f"{_update[0]} value rows, {_update[1]} standard-error "
+ f"rows and {_update[2]} 'N' rows were updated.")
+ _change = any(item != 0 for item in _update)
+ case "update publication":
+ flash("NOT IMPLEMENTED: Would update publication data.", "alert-success")
+ case _:
+ flash("Invalid phenotype editing action.", "alert-danger")
+
+ if _change:
+ flash(msg, "alert-success")
+ return redirect(url_for(
+ "species.populations.phenotypes.view_phenotype",
+ species_id=species["SpeciesId"],
+ population_id=population["Id"],
+ dataset_id=dataset["Id"],
+ xref_id=xref_id))
+
+ flash("No change was made by the user.", "alert-info")
+ return redirect(url_for(
+ "species.populations.phenotypes.edit_phenotype_data",
+ species_id=species["SpeciesId"],
+ population_id=population["Id"],
+ dataset_id=dataset["Id"],
+ xref_id=xref_id))
diff --git a/uploader/population/rqtl2.py b/uploader/population/rqtl2.py
index 436eca0..044cdd4 100644
--- a/uploader/population/rqtl2.py
+++ b/uploader/population/rqtl2.py
@@ -11,13 +11,11 @@ from typing import Union, Callable, Optional
import MySQLdb as mdb
from redis import Redis
from MySQLdb.cursors import DictCursor
-from werkzeug.utils import secure_filename
from gn_libs.mysqldb import database_connection
from flask import (
flash,
escape,
request,
- jsonify,
url_for,
redirect,
Response,
@@ -191,127 +189,6 @@ def trigger_rqtl2_bundle_qc(
return jobid
-def chunk_name(uploadfilename: str, chunkno: int) -> str:
- """Generate chunk name from original filename and chunk number"""
- if uploadfilename == "":
- raise ValueError("Name cannot be empty!")
- if chunkno < 1:
- raise ValueError("Chunk number must be greater than zero")
- return f"{secure_filename(uploadfilename)}_part_{chunkno:05d}"
-
-
-def chunks_directory(uniqueidentifier: str) -> Path:
- """Compute the directory where chunks are temporarily stored."""
- if uniqueidentifier == "":
- raise ValueError("Unique identifier cannot be empty!")
- return Path(app.config["UPLOAD_FOLDER"], f"tempdir_{uniqueidentifier}")
-
-
-@rqtl2.route(("<int:species_id>/populations/<int:population_id>/rqtl2/"
- "/rqtl2-bundle-chunked"),
- methods=["GET"])
-@require_login
-def upload_rqtl2_bundle_chunked_get(# pylint: disable=["unused-argument"]
- species_id: int,
- population_id: int
-):
- """
- Extension to the `upload_rqtl2_bundle` endpoint above that provides a way
- for testing whether all the chunks have been uploaded and to assist with
- resuming a failed expression-data.
- """
- fileid = request.args.get("resumableIdentifier", type=str) or ""
- filename = request.args.get("resumableFilename", type=str) or ""
- chunk = request.args.get("resumableChunkNumber", type=int) or 0
- if not(fileid or filename or chunk):
- return jsonify({
- "message": "At least one required query parameter is missing.",
- "error": "BadRequest",
- "statuscode": 400
- }), 400
-
- if Path(chunks_directory(fileid),
- chunk_name(filename, chunk)).exists():
- return "OK"
-
- return jsonify({
- "message": f"Chunk {chunk} was not found.",
- "error": "NotFound",
- "statuscode": 404
- }), 404
-
-
-def __merge_chunks__(targetfile: Path, chunkpaths: tuple[Path, ...]) -> Path:
- """Merge the chunks into a single file."""
- with open(targetfile, "ab") as _target:
- for chunkfile in chunkpaths:
- with open(chunkfile, "rb") as _chunkdata:
- _target.write(_chunkdata.read())
-
- chunkfile.unlink()
- return targetfile
-
-
-@rqtl2.route(("<int:species_id>/population/<int:population_id>/rqtl2/upload/"
- "/rqtl2-bundle-chunked"),
- methods=["POST"])
-@require_login
-def upload_rqtl2_bundle_chunked_post(species_id: int, population_id: int):
- """
- Extension to the `upload_rqtl2_bundle` endpoint above that allows large
- files to be uploaded in chunks.
-
- This should hopefully speed up uploads, and if done right, even enable
- resumable uploads
- """
- _totalchunks = request.form.get("resumableTotalChunks", type=int) or 0
- _chunk = request.form.get("resumableChunkNumber", default=1, type=int)
- _uploadfilename = request.form.get(
- "resumableFilename", default="", type=str) or ""
- _fileid = request.form.get(
- "resumableIdentifier", default="", type=str) or ""
- _targetfile = Path(app.config["UPLOAD_FOLDER"], _fileid)
-
- if _targetfile.exists():
- return jsonify({
- "message": (
- "A file with a similar unique identifier has previously been "
- "uploaded and possibly is/has being/been processed."),
- "error": "BadRequest",
- "statuscode": 400
- }), 400
-
- try:
- # save chunk data
- chunks_directory(_fileid).mkdir(exist_ok=True, parents=True)
- request.files["file"].save(Path(chunks_directory(_fileid),
- chunk_name(_uploadfilename, _chunk)))
-
- # Check whether upload is complete
- chunkpaths = tuple(
- Path(chunks_directory(_fileid), chunk_name(_uploadfilename, _achunk))
- for _achunk in range(1, _totalchunks+1))
- if all(_file.exists() for _file in chunkpaths):
- # merge_files and clean up chunks
- __merge_chunks__(_targetfile, chunkpaths)
- chunks_directory(_fileid).rmdir()
- jobid = trigger_rqtl2_bundle_qc(
- species_id, population_id, _targetfile, _uploadfilename)
- return url_for(
- "expression-data.rqtl2.rqtl2_bundle_qc_status", jobid=jobid)
- except Exception as exc:# pylint: disable=[broad-except]
- msg = "Error processing uploaded file chunks."
- app.logger.error(msg, exc_info=True, stack_info=True)
- return jsonify({
- "message": msg,
- "error": type(exc).__name__,
- "error-description": " ".join(str(arg) for arg in exc.args),
- "error-trace": traceback.format_exception(exc)
- }), 500
-
- return "OK"
-
-
@rqtl2.route("/upload/species/rqtl2-bundle/qc-status/<uuid:jobid>",
methods=["GET", "POST"])
@require_login
diff --git a/uploader/static/css/styles.css b/uploader/static/css/styles.css
index f482c1b..a1107d5 100644
--- a/uploader/static/css/styles.css
+++ b/uploader/static/css/styles.css
@@ -1,161 +1,134 @@
+* {
+ box-sizing: border-box;
+}
+
body {
margin: 0.7em;
- box-sizing: border-box;
display: grid;
- grid-template-columns: 1fr 6fr;
- grid-template-rows: 5em 100%;
+ grid-template-columns: 1fr 9fr;
grid-gap: 20px;
font-family: Georgia, Garamond, serif;
font-style: normal;
+ font-size: 20px;
}
#header {
- grid-column: 1/3;
- width: 100%;
- /* background: cyan; */
- padding-top: 0.5em;
- border-radius: 0.5em;
+ /* Place it in the parent element */
+ grid-column-start: 1;
+ grid-column-end: 3;
+
+ /* Define layout for the children elements */
+ display: grid;
+ grid-template-columns: 8fr 2fr;
+ /* Content styling */
background-color: #336699;
- border-color: #080808;
color: #FFFFFF;
- background-image: none;
+ border-radius: 3px;
}
-#header .header {
- font-size: 2em;
- display: inline-block;
- text-align: start;
-}
+#header #header-text {
+ /* Place it in the parent element */
+ grid-column-start: 1;
+ grid-column-end: 2;
-#header .header-nav {
- display: inline-block;
- color: #FFFFFF;
+ /* Content styling */
+ font-size: 1.7em;
+ padding-left: 1em;
}
-#header .header-nav li {
- border-width: 1px;
- border-color: #FFFFFF;
- vertical-align: middle;
- margin: 0.2em;
- border-style: solid;
- border-width: 2px;
- border-radius: 0.5em;
- text-align: center;
+#header #header-nav {
+ /* Place it in the parent element */
+ grid-column-start: 2;
+ grid-column-end: 3;
}
-#header .header-nav a {
+#header #header-nav .nav li a {
+ /* Content styling */
color: #FFFFFF;
- text-decoration: none;
+ background: #4477AA;
+ border: solid 5px #336699;
+ border-radius: 5px;
+ font-size: 0.7em;
+ text-align: center;
}
#nav-sidebar {
- grid-column: 1/2;
- /* background: #e5e5ff; */
- padding-top: 0.5em;
- border-radius: 0.5em;
- font-size: 1.2em;
+ /* Place it in the parent element */
+ grid-column-start: 1;
+ grid-column-end: 2;
}
-#main {
- grid-column: 2/3;
- width: 100%;
- /* background: gray; */
+#nav-sidebar .nav li a:hover {
border-radius: 0.5em;
}
-.pagetitle {
- padding-top: 0.5em;
- /* background: pink; */
+#nav-sidebar .nav .activemenu {
+ border-style: solid;
border-radius: 0.5em;
- /* background-color: #6699CC; */
- /* background-color: #77AADD; */
- background-color: #88BBEE;
-}
-
-.pagetitle h1 {
- text-align: start;
- text-transform: capitalize;
- padding-left: 0.25em;
-}
-
-.pagetitle .breadcrumb {
- background: none;
-}
-
-.pagetitle .breadcrumb .active a {
- color: #333333;
+ border-color: #AAAAAA;
+ background-color: #EFEFEF;
}
-.pagetitle .breadcrumb a {
- color: #666666;
-}
+#main {
+ /* Place it in the parent element */
+ grid-column-start: 2;
+ grid-column-end: 3;
-.main-content {
- font-size: 1.275em;
+ /* Define layout for the children elements */
+ display: grid;
+ grid-template-columns: 1fr;
+ grid-template-rows: 4em 100%;
+ grid-gap: 1em;
}
-.breadcrumb {
- text-transform: capitalize;
-}
+#main #pagetitle {
+ /* Place it in the parent element */
+ grid-column-start: 1;
+ grid-column-end: 3;
-dd {
- margin-left: 3em;
- font-size: 0.88em;
- padding-bottom: 1em;
+ /* Content-styling */
+ border-radius: 3px;
+ background-color: #88BBEE;
}
-input[type="submit"], .btn {
+#main #pagetitle .title {
+ font-size: 1.4em;
text-transform: capitalize;
+ padding-left: 0.5em;
}
-.card {
- margin-top: 0.3em;
- border-width: 1px;
- border-style: solid;
- border-radius: 0.3em;
- border-color: #AAAAAA;
- padding: 0.5em;
-}
+#main #all-content {
+ /* Place it in the parent element */
+ grid-column-start: 1;
+ grid-column-end: 3;
-.activemenu {
- border-style: solid;
- border-radius: 0.5em;
- border-color: #AAAAAA;
- background-color: #EFEFEF;
-}
-
-.danger {
- color: #A94442;
- border-color: #DCA7A7;
- background-color: #F2DEDE;
-}
-
-.heading {
- border-bottom: solid #EEBB88;
+ /* Define layout for the children elements */
+ display: grid;
+ grid-template-columns: 7fr 3fr; /* For a maximum screen width of 1366 pixels */
+ grid-gap: 1.5em;
}
-.subheading {
- padding: 1em 0 0.1em 0.5em;
- border-bottom: solid #88BBEE;
+#main #all-content .row {
+ margin: 0 2px;
}
-form {
- margin-top: 0.3em;
- background: #E5E5FF;
- padding: 0.5em;
- border-radius:0.5em;
+#main #all-content #main-content {
+ background: #FFFFFF;
+ max-width: 950px;
}
-form .form-control {
- background-color: #EAEAFF;
+#pagetitle .breadcrumb {
+ background: none;
+ text-transform: capitalize;
+ font-size: 0.75em;
}
-.sidebar-content .card .card-title {
- font-size: 1.5em;
+#pagetitle .breadcrumb .active a {
+ color: #333333;
}
-.sidebar-content .card-text table tbody td:nth-child(1) {
- font-weight: bolder;
+#pagetitle .breadcrumb a {
+ color: #666666;
}
diff --git a/uploader/templates/base.html b/uploader/templates/base.html
index 3a8ef16..c37e1f3 100644
--- a/uploader/templates/base.html
+++ b/uploader/templates/base.html
@@ -23,25 +23,24 @@
</head>
<body>
- <header id="header" class="container-fluid">
- <div class="row">
- <span class="header col-lg-9">GeneNetwork Data Quality Control and Upload</span>
- <nav class="header-nav col-lg-3">
- <ul class="nav justify-content-end">
- <li>
- {%if user_logged_in()%}
- <a href="{{url_for('oauth2.logout')}}"
- title="Log out of the system">{{user_email()}} &mdash; Log Out</a>
- {%else%}
- <a href="{{authserver_authorise_uri()}}"
- title="Log in to the system">Log In</a>
- {%endif%}
- </li>
- </ul>
- </nav>
+ <header id="header">
+ <span id="header-text">GeneNetwork Data Quality Control and Upload</span>
+ <nav id="header-nav">
+ <ul class="nav justify-content-end">
+ <li>
+ {%if user_logged_in()%}
+ <a href="{{url_for('oauth2.logout')}}"
+ title="Log out of the system">{{user_email()}} &mdash; Log Out</a>
+ {%else%}
+ <a href="{{authserver_authorise_uri()}}"
+ title="Log in to the system">Log In</a>
+ {%endif%}
+ </li>
+ </ul>
+ </nav>
</header>
- <aside id="nav-sidebar" class="container-fluid">
+ <aside id="nav-sidebar">
<ul class="nav flex-column">
<li {%if activemenu=="home"%}class="activemenu"{%endif%}>
<a href="/" >Home</a></li>
@@ -90,10 +89,10 @@
</ul>
</aside>
- <main id="main" class="main container-fluid">
+ <main id="main" class="main">
- <div class="pagetitle row">
- <h1>GN Uploader: {%block pagetitle%}{%endblock%}</h1>
+ <div id="pagetitle" class="pagetitle">
+ <span class="title">GN Uploader: {%block pagetitle%}{%endblock%}</span>
<nav>
<ol class="breadcrumb">
<li {%if activelink is not defined or activelink=="home"%}
@@ -108,14 +107,12 @@
</nav>
</div>
- <div class="row">
- <div class="container-fluid">
- <div class="col-md-8 main-content">
- {%block contents%}{%endblock%}
- </div>
- <div class="sidebar-content col-md-4">
- {%block sidebarcontents%}{%endblock%}
- </div>
+ <div id="all-content">
+ <div id="main-content">
+ {%block contents%}{%endblock%}
+ </div>
+ <div id="sidebar-content">
+ {%block sidebarcontents%}{%endblock%}
</div>
</div>
</main>
@@ -127,7 +124,5 @@
filename='js/bootstrap.min.js')}}"></script>
<script type="text/javascript" src="/static/js/misc.js"></script>
{%block javascript%}{%endblock%}
-
</body>
-
</html>
diff --git a/uploader/templates/phenotypes/add-phenotypes-raw-files.html b/uploader/templates/phenotypes/add-phenotypes-raw-files.html
index d9a8424..7f8d8b0 100644
--- a/uploader/templates/phenotypes/add-phenotypes-raw-files.html
+++ b/uploader/templates/phenotypes/add-phenotypes-raw-files.html
@@ -600,10 +600,12 @@
console.log("SUCCESS DATA: ", data);
console.log("SUCCESS STATUS: ", textstatus);
console.log("SUCCESS jqXHR: ", jqxhr);
+ window.location.assign(window.location.origin + data["redirect-to"]);
},
});
return false;
}
+ return false;
};
var uploadSuccess = (file_input_name) => {
diff --git a/uploader/templates/phenotypes/edit-phenotype.html b/uploader/templates/phenotypes/edit-phenotype.html
new file mode 100644
index 0000000..32c903f
--- /dev/null
+++ b/uploader/templates/phenotypes/edit-phenotype.html
@@ -0,0 +1,332 @@
+{%extends "phenotypes/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "populations/macro-display-population-card.html" import display_population_card%}
+
+{%block title%}Phenotypes{%endblock%}
+
+{%block pagetitle%}Phenotypes{%endblock%}
+
+{%block lvl4_breadcrumbs%}
+<li {%if activelink=="edit-phenotype"%}
+ class="breadcrumb-item active"
+ {%else%}
+ class="breadcrumb-item"
+ {%endif%}>
+ <a href="{{url_for('species.populations.phenotypes.edit_phenotype_data',
+ species_id=species.SpeciesId,
+ population_id=population.Id,
+ dataset_id=dataset.Id,
+ xref_id=xref_id)}}">View Datasets</a>
+</li>
+{%endblock%}
+
+{%block contents%}
+{{flash_all_messages()}}
+
+<div class="row">
+ <h2 class="heading">edit phenotype data</h2>
+ <p>The forms provided in this page help you update the data for the
+ phenotypes, and the publication information for the phenotype,
+ respectively.</p>
+</div>
+
+<div class="row">
+ <h3 class="subheading">Basic metadata</h3>
+ <form name="frm-phenotype-basic-metadata"
+ class="form-horizontal"
+ method="POST"
+ action="{{url_for(
+ 'species.populations.phenotypes.edit_phenotype_data',
+ species_id=species.SpeciesId,
+ population_id=population.Id,
+ dataset_id=dataset.Id,
+ xref_id=xref_id)}}">
+ <input type="hidden" name="phenotype-id" value="{{phenotype.Id}}" />
+ <div class="form-group">
+ <label for="txt-pre-publication-description"
+ class="control-label col-sm-2">Pre-Publication Description</label>
+ <div class="col-sm-10">
+ <input type="text"
+ id="txt-pre-publication-description"
+ name="pre-publication-description"
+ class="form-control"
+ value="{{phenotype['Pre_publication_description'] or ''}}" />
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-pre-publication-abbreviation"
+ class="control-label col-sm-2">Pre-Publication Abbreviation</label>
+ <div class="col-sm-10">
+ <input type="text"
+ id="txt-pre-publication-abbreviation"
+ name="pre-publication-abbreviation"
+ class="form-control"
+ value="{{phenotype['Pre_publication_abbreviation'] or ''}}" />
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-post-publication-description"
+ class="control-label col-sm-2">Post-Publication Description</label>
+ <div class="col-sm-10">
+ <input type="text"
+ id="txt-post-publication-description"
+ name="post-publication-description"
+ class="form-control"
+ value="{{phenotype['Post_publication_description'] or ''}}" />
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-post-publication-abbreviation"
+ class="control-label col-sm-2">Post-Publication Abbreviation</label>
+ <div class="col-sm-10">
+ <input type="text"
+ id="txt-post-publication-abbreviation"
+ name="post-publication-abbreviation"
+ class="form-control"
+ value="{{phenotype['Post_publication_abbreviation'] or ''}}" />
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-original-description"
+ class="control-label col-sm-2">Original Description</label>
+ <div class="col-sm-10">
+ <input type="text"
+ id="txt-original-description"
+ name="original-description"
+ class="form-control"
+ value="{{phenotype['Original_description'] or ''}}" />
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-units"
+ class="control-label col-sm-2">units</label>
+ <div class="col-sm-10">
+ <input type="text"
+ id="txt-units"
+ name="units"
+ class="form-control"
+ required="required"
+ value="{{phenotype['Units']}}" />
+ </div>
+ </div>
+
+ <div class="form-group">
+ <div class="col-sm-offset-2 col-sm-10">
+ <input type="submit"
+ name="submit"
+ class="btn btn-primary"
+ value="update basic metadata">
+ </div>
+ </div>
+ </form>
+</div>
+
+
+<div class="row">
+ <h3 class="subheading">phenotype data</h3>
+ <form id="frm-edit-phenotype-data"
+ class="form-horizontal"
+ method="POST"
+ action="{{url_for(
+ 'species.populations.phenotypes.edit_phenotype_data',
+ species_id=species.SpeciesId,
+ population_id=population.Id,
+ dataset_id=dataset.Id,
+ xref_id=xref_id)}}">
+ <div style="max-height: 23.37em;overflow-y: scroll;">
+ <table class="table table-striped table-responsive table-form-table">
+ <thead style="position: sticky; top: 0;">
+ <tr>
+ <th>#</th>
+ <th>Sample</th>
+ <th>Value</th>
+ {%if population.Family in families_with_se_and_n%}
+ <th>Standard-Error</th>
+ <th>Number of Samples</th>
+ {%endif%}
+ </tr>
+ </thead>
+
+ <tbody>
+ {%for item in phenotype.data%}
+ <tr>
+ <td>{{loop.index}}</td>
+ <td>{{item.StrainName}}</td>
+ <td>
+ <input type="text"
+ name="value-new::{{item.DataId}}::{{item.StrainId}}"
+ value="{{item.value}}"
+ class="form-control" />
+ <input type="hidden"
+ name="value-original::{{item.DataId}}::{{item.StrainId}}"
+ value="{{item.value}}" /></td>
+ {%if population.Family in families_with_se_and_n%}
+ <td>
+ <input type="text"
+ name="se-new::{{item.DataId}}::{{item.StrainId}}"
+ value="{{item.error or ''}}"
+ data-original-value="{{item.error or ''}}"
+ class="form-control" />
+ <input type="hidden"
+ name="se-original::{{item.DataId}}::{{item.StrainId}}"
+ value="{{item.error or ''}}" /></td>
+ <td>
+ <input type="text"
+ name="n-new::{{item.DataId}}::{{item.StrainId}}"
+ value="{{item.count or ''}}"
+ data-original-value="{{item.count or "-"}}"
+ class="form-control" />
+ <input type="hidden"
+ name="n-original::{{item.DataId}}::{{item.StrainId}}"
+ value="{{item.count or ''}}" /></td>
+ {%endif%}
+ </tr>
+ {%endfor%}
+ </tbody>
+ </table>
+ </div>
+ <div class="form-group">
+ <div class="col-sm-offset-2 col-sm-10">
+ <input type="submit"
+ name="submit"
+ class="btn btn-primary"
+ value="update data" />
+ </div>
+ </div>
+ </form>
+</div>
+
+
+<div class="row">
+ <h3 class="subheading">publication information</h3>
+ <p>Use the form below to update the publication information for this
+ phenotype.</p>
+ <form id="frm-edit-phenotype-pub-data"
+ class="form-horizontal"
+ method="POST"
+ action="#">
+ <div class="form-group">
+ <label for="txt-pubmed-id" class="control-label col-sm-2">Pubmed ID</label>
+ <div class="col-sm-10">
+ <input id="txt-pubmed-id" name="pubmed-id" type="text"
+ class="form-control" />
+ <span class="form-text text-muted">
+ Enter your publication's PubMed ID.</span>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-publication-authors" class="control-label col-sm-2">Authors</label>
+ <div class="col-sm-10">
+ <input id="txt-publication-authors" name="publication-authors"
+ type="text" class="form-control" />
+ <span class="form-text text-muted">
+ Enter the authors.</span>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-publication-title" class="control-label col-sm-2">
+ Publication Title</label>
+ <div class="col-sm-10">
+ <input id="txt-publication-title" name="publication-title" type="text"
+ class="form-control" />
+ <span class="form-text text-muted">
+ Enter your publication's title.</span>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-publication-abstract" class="control-label col-sm-2">
+ Publication Abstract</label>
+ <div class="col-sm-10">
+ <textarea id="txt-publication-abstract" name="publication-abstract"
+ class="form-control" rows="10"></textarea>
+ <span class="form-text text-muted">
+ Enter the abstract for your publication.</span>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-publication-journal" class="control-label col-sm-2">Journal</label>
+ <div class="col-sm-10">
+ <input id="txt-publication-journal" name="journal" type="text"
+ class="form-control" />
+ <span class="form-text text-muted">
+ Enter the name of the journal where your work was published.</span>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-publication-volume" class="control-label col-sm-2">Volume</label>
+ <div class="col-sm-10">
+ <input id="txt-publication-volume" name="publication-volume" type="text"
+ class="form-control" />
+ <span class="form-text text-muted">
+ Enter the volume in the following format &hellip;</span>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-publication-pages" class="control-label col-sm-2">Pages</label>
+ <div class="col-sm-10">
+ <input id="txt-publication-pages" name="publication-pages" type="text"
+ class="form-control" />
+ <span class="form-text text-muted">
+ Enter the journal volume where your work was published.</span>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="select-publication-month" class="control-label col-sm-2">
+ Publication Month</label>
+ <div class="col-sm-10">
+ <select id="select-publication-month" name="publication-month"
+ class="form-control">
+ {%for month in monthnames%}
+ <option value="{{month | lower}}"
+ {%if current_month | lower == month | lower%}
+ selected="selected"
+ {%endif%}>{{month | capitalize}}</option>
+ {%endfor%}
+ </select>
+ <span class="form-text text-muted">
+ Select the month when the work was published.
+ <span class="text-danger">
+ This cannot be before, say 1600 and cannot be in the future!</span></span>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-publication-year" class="control-label col-sm-2">Publication Year</label>
+ <div class="col-sm-10">
+ <input id="txt-publication-year" name="publication-year" type="text"
+ class="form-control" value="{{current_year}}" />
+ <span class="form-text text-muted">
+ Enter the year your work was published.
+ <span class="text-danger">
+ This cannot be before, say 1600 and cannot be in the future!</span>
+ </span>
+ </div>
+ </div>
+ <div class="form-group">
+ <div class="col-sm-offset-2 col-sm-10">
+ <input type="submit"
+ name="submit"
+ class="btn btn-primary not-implemented"
+ value="update publication" />
+ </div>
+ </div>
+ </form>
+</div>
+
+{%endblock%}
+
+{%block sidebarcontents%}
+{{display_population_card(species, population)}}
+{%endblock%}
diff --git a/uploader/templates/phenotypes/job-status.html b/uploader/templates/phenotypes/job-status.html
index 6f43d22..12963c1 100644
--- a/uploader/templates/phenotypes/job-status.html
+++ b/uploader/templates/phenotypes/job-status.html
@@ -62,8 +62,12 @@
{%if job.status in ("completed:success", "success")%}
<p>
{%if errors | length == 0%}
- <a href="#"
- class="not-implemented btn btn-primary"
+ <a href="{{url_for('species.populations.phenotypes.review_job_data',
+ species_id=species.SpeciesId,
+ population_id=population.Id,
+ dataset_id=dataset.Id,
+ job_id=job_id)}}"
+ class="btn btn-primary"
title="Continue to process data">Continue</a>
{%else%}
<span class="text-muted"
diff --git a/uploader/templates/phenotypes/macro-display-resumable-elements.html b/uploader/templates/phenotypes/macro-display-resumable-elements.html
new file mode 100644
index 0000000..b0bf1b5
--- /dev/null
+++ b/uploader/templates/phenotypes/macro-display-resumable-elements.html
@@ -0,0 +1,60 @@
+{%macro display_resumable_elements(id, title, help)%}
+<div id="{{id}}"
+ class="resumable-elements hidden"
+ style="background:#D4D4EE;border-radius: 5px;;padding: 1em;border-left: solid #B2B2CC 1px;border-bottom: solid #B2B2CC 2px;margin-top:0.3em;">
+ <strong style="line-height: 1.2em;">{{title | title}}</strong>
+
+ <span class="form-text text-muted">{{help | safe}}</span>
+
+ <div id="{{id}}-selected-files"
+ class="resumable-selected-files"
+ style="display:flex;flex-direction:row;flex-wrap: wrap;justify-content:space-around;gap:10px 20px;">
+ <div class="panel panel-info file-display-template hidden">
+ <div class="panel-heading filename">The Filename Goes Here!</div>
+ <div class="panel-body">
+ <ul>
+ <li>
+ <strong>Name</strong>:
+ <span class="filename">the file's name</span></li>
+
+ <li><strong>Size</strong>: <span class="filesize">0 MB</span></li>
+
+ <li>
+ <strong>Unique Identifier</strong>:
+ <span class="fileuniqueid">brrr</span></li>
+
+ <li>
+ <strong>Mime</strong>:
+ <span class="filemimetype">text/csv</span></li>
+ </ul>
+ </div>
+ </div>
+ </div>
+
+ <a id="{{id}}-browse-button"
+ class="resumable-browse-button btn btn-info"
+ href="#"
+ style="margin-left: 80%;">Browse</a>
+
+ <div id="{{id}}-progress-bar" class="progress hidden">
+ <div class="progress-bar"
+ role="progress-bar"
+ aria-valuenow="60"
+ aria-valuemin="0"
+ aria-valuemax="100"
+ style="width: 0%;">
+ Uploading: 60%
+ </div>
+ </div>
+
+ <div id="{{id}}-cancel-resume-buttons">
+ <a id="{{id}}-resume-button"
+ class="resumable-resume-button btn btn-info hidden"
+ href="#">resume upload</a>
+
+ <a id="{{id}}-cancel-button"
+ class="resumable-cancel-button btn btn-danger hidden"
+ href="#">cancel upload</a>
+ </div>
+</div>
+{%endmacro%}
diff --git a/uploader/templates/phenotypes/review-job-data.html b/uploader/templates/phenotypes/review-job-data.html
new file mode 100644
index 0000000..7bc8c62
--- /dev/null
+++ b/uploader/templates/phenotypes/review-job-data.html
@@ -0,0 +1,101 @@
+{%extends "phenotypes/base.html"%}
+{%from "cli-output.html" import cli_output%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "macro-table-pagination.html" import table_pagination%}
+{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%}
+
+{%block extrameta%}
+{%if not job%}
+<meta http-equiv="refresh"
+ content="20; url={{url_for('species.populations.phenotypes.view_dataset', species_id=species.SpeciesId,
+ population_id=population.Id,
+ dataset_id=dataset.Id)}}" />
+{%endif%}
+{%endblock%}
+
+{%block title%}Phenotypes{%endblock%}
+
+{%block pagetitle%}Phenotypes{%endblock%}
+
+{%block lvl4_breadcrumbs%}
+<li {%if activelink=="add-phenotypes"%}
+ class="breadcrumb-item active"
+ {%else%}
+ class="breadcrumb-item"
+ {%endif%}>
+ <a href="{{url_for('species.populations.phenotypes.add_phenotypes',
+ species_id=species.SpeciesId,
+ population_id=population.Id,
+ dataset_id=dataset.Id)}}">View Datasets</a>
+</li>
+{%endblock%}
+
+{%block contents%}
+
+{%if job%}
+<div class="row">
+ <h3 class="heading">Data Review</h3>
+ <p>The &#x201C;<strong>{{dataset.FullName}}</strong>&#x201D; dataset from the
+ &#x201C;<strong>{{population.FullName}}</strong>&#x201D; population of the
+ species &#x201C;<strong>{{species.SpeciesName}} ({{species.FullName}})</strong>&#x201D;
+ will be updated as follows:</p>
+
+ {%for ftype in ("phenocovar", "pheno", "phenose", "phenonum")%}
+ {%if summary.get(ftype, False)%}
+ <ul>
+ <li>A total of {{summary[ftype]["number-of-files"]}} files will be processed
+ adding {%if ftype == "phenocovar"%}(possibly){%endif%}
+ {{summary[ftype]["total-data-rows"]}} new
+ {%if ftype == "phenocovar"%}
+ phenotypes
+ {%else%}
+ {{summary[ftype]["description"]}} rows
+ {%endif%}
+ to the database.
+ </li>
+ </ul>
+ {%endif%}
+ {%endfor%}
+
+ <a href="#" class="not-implemented btn btn-primary">continue</a>
+</div>
+{%else%}
+<div class="row">
+ <h4 class="subheading">Invalid Job</h3>
+ <p class="text-danger">
+ Could not find a job with the ID: <strong>{{job_id}}.</p>
+ <p>You will be redirected in
+ <span id="countdown-element" class="text-info">20</span> second(s)</p>
+ <p class="text-muted">
+ <small>
+ If you are not redirected, please
+ <a href="{{url_for(
+ 'species.populations.phenotypes.view_dataset',
+ species_id=species.SpeciesId,
+ population_id=population.Id,
+ dataset_id=dataset.Id)}}">click here</a> to continue
+ </small>
+ </p>
+</div>
+{%endif%}
+{%endblock%}
+
+{%block sidebarcontents%}
+{{display_pheno_dataset_card(species, population, dataset)}}
+{%endblock%}
+
+
+{%block javascript%}
+<script type="text/javascript">
+ $(document).ready(function() {
+ var countdown = 20;
+ var countdown_element = $("#countdown-element");
+ if(countdown_element.length === 1) {
+ intv = window.setInterval(function() {
+ countdown = countdown - 1;
+ countdown_element.html(countdown);
+ }, 1000);
+ }
+ });
+</script>
+{%endblock%}
diff --git a/uploader/templates/phenotypes/view-dataset.html b/uploader/templates/phenotypes/view-dataset.html
index 66de5d8..4e1be6b 100644
--- a/uploader/templates/phenotypes/view-dataset.html
+++ b/uploader/templates/phenotypes/view-dataset.html
@@ -5,6 +5,11 @@
{%block title%}Phenotypes{%endblock%}
+{%block css%}
+<link rel="stylesheet"
+ href="{{url_for('base.datatables', filename='css/jquery.dataTables.css')}}" />
+{%endblock%}
+
{%block pagetitle%}Phenotypes{%endblock%}
{%block lvl4_breadcrumbs%}
@@ -56,12 +61,7 @@
<div class="row">
<h2>Phenotype Data</h2>
-
- <p>This dataset has a total of {{phenotype_count}} phenotypes.</p>
-
- {{table_pagination(start_from, count, phenotype_count, url_for('species.populations.phenotypes.view_dataset', species_id=species.SpeciesId, population_id=population.Id, dataset_id=dataset.Id), "phenotypes")}}
-
- <table class="table">
+ <table id="tbl-phenotypes-list" class="table">
<thead>
<tr>
<th>#</th>
@@ -70,23 +70,7 @@
</tr>
</thead>
- <tbody>
- {%for pheno in phenotypes%}
- <tr>
- <td>{{pheno.sequence_number}}</td>
- <td><a href="{{url_for('species.populations.phenotypes.view_phenotype',
- species_id=species.SpeciesId,
- population_id=population.Id,
- dataset_id=dataset.Id,
- xref_id=pheno['pxr.Id'])}}"
- title="View phenotype details">
- {{pheno.InbredSetCode}}_{{pheno["pxr.Id"]}}</a></td>
- <td>{{pheno.Post_publication_description or pheno.Pre_publication_abbreviation or pheno.Original_description}}</td>
- </tr>
- {%else%}
- <tr><td colspan="5"></td></tr>
- {%endfor%}
- </tbody>
+ <tbody></tbody>
</table>
</div>
{%endblock%}
@@ -94,3 +78,39 @@
{%block sidebarcontents%}
{{display_population_card(species, population)}}
{%endblock%}
+
+
+{%block javascript%}
+<script src="{{url_for('base.datatables',
+ filename='js/jquery.dataTables.js')}}"></script>
+<script type="text/javascript">
+ $(function() {
+ $("#tbl-phenotypes-list").DataTable({
+ responsive: true,
+ data: {{phenotypes | tojson}},
+ columns: [
+ {data: "sequence_number"},
+ {
+ data: function(pheno) {
+ var spcs_id = {{species.SpeciesId}};
+ var pop_id = {{population.Id}};
+ var dtst_id = {{dataset.Id}};
+ return `<a href="/species/${spcs_id}` +
+ `/populations/${pop_id}` +
+ `/phenotypes/datasets/${dtst_id}` +
+ `/phenotype/${pheno.xref_id}` +
+ `" target="_blank">` +
+ `${pheno.InbredSetCode}_${pheno.xref_id}` +
+ `</a>`;
+ }
+ },
+ {data: function(pheno) {
+ return (pheno.Post_publication_description ||
+ pheno.Original_description ||
+ pheno.Pre_publication_description);
+ }}
+ ]
+ });
+ });
+</script>
+{%endblock%}
diff --git a/uploader/templates/phenotypes/view-phenotype.html b/uploader/templates/phenotypes/view-phenotype.html
index 99bb8e5..21ac501 100644
--- a/uploader/templates/phenotypes/view-phenotype.html
+++ b/uploader/templates/phenotypes/view-phenotype.html
@@ -16,7 +16,7 @@
species_id=species.SpeciesId,
population_id=population.Id,
dataset_id=dataset.Id,
- xref_id=xref_id)}}">View Datasets</a>
+ xref_id=xref_id)}}">View Phenotype</a>
</li>
{%endblock%}
@@ -34,51 +34,58 @@
<td>{{phenotype.Post_publication_description or phenotype.Pre_publication_abbreviation or phenotype.Original_description}}
</tr>
<tr>
- <td><strong>Cross-Reference ID</strong></td>
- <td>{{phenotype.xref_id}}</td>
- </tr>
- <tr>
- <td><strong>Collation</strong></td>
+ <td><strong>Database</strong></td>
<td>{{dataset.FullName}}</td>
</tr>
<tr>
<td><strong>Units</strong></td>
<td>{{phenotype.Units}}</td>
</tr>
+ {%for key,value in publish_data.items()%}
+ <tr>
+ <td><strong>{{key}}</strong></td>
+ <td>{{value}}</td>
+ </tr>
+ {%else%}
+ <tr>
+ <td colspan="2" class="text-muted">
+ <span class="glyphicon glyphicon-exclamation-sign"></span>
+ No publication data found.
+ </td>
+ </tr>
+ {%endfor%}
</tbody>
</table>
+ </div>
+</div>
- <form action="#edit-delete-phenotype"
- method="POST"
- id="frm-delete-phenotype">
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id" value="{{population.Id}}" />
- <input type="hidden" name="dataset_id" value="{{dataset.Id}}" />
- <input type="hidden" name="phenotype_id" value="{{phenotype.Id}}" />
-
- <div class="btn-group btn-group-justified">
- <div class="btn-group">
- {%if "group:resource:edit-resource" in privileges%}
- <input type="submit"
- title="Edit the values for the phenotype. This is meant to be used when you need to update only a few values."
- class="btn btn-primary not-implemented"
- value="edit" />
- {%endif%}
- </div>
- <div class="btn-group"></div>
- <div class="btn-group">
- {%if "group:resource:delete-resource" in privileges%}
- <input type="submit"
- title="Delete the entire phenotype. This is useful when you need to change data for most or all of the fields for this phenotype."
- class="btn btn-danger not-implemented"
- value="delete" />
- {%endif%}
- </div>
- </div>
- </form>
+{%if "group:resource:edit-resource" in privileges
+or "group:resource:delete-resource" in privileges%}
+<div class="row">
+ <div class="btn-group btn-group-justified">
+ <div class="btn-group">
+ {%if "group:resource:edit-resource" in privileges%}
+ <a href="{{url_for('species.populations.phenotypes.edit_phenotype_data',
+ species_id=species.SpeciesId,
+ population_id=population.Id,
+ dataset_id=dataset.Id,
+ xref_id=xref_id)}}"
+ title="Edit the values for the phenotype. This is meant to be used when you need to update only a few values."
+ class="btn btn-primary">Edit</a>
+ {%endif%}
+ </div>
+ <div class="btn-group"></div>
+ <div class="btn-group">
+ {%if "group:resource:delete-resource" in privileges%}
+ <a href="#"
+ title="Delete the entire phenotype. This is useful when you need to change data for most or all of the fields for this phenotype."
+ class="btn btn-danger not-implemented"
+ disabled="disabled">delete</a>
+ {%endif%}
+ </div>
</div>
</div>
+{%endif%}
<div class="row">
<div class="panel panel-default">
@@ -90,9 +97,10 @@
<th>#</th>
<th>Sample</th>
<th>Value</th>
- <th>Symbol</th>
+ {%if has_se%}
<th>SE</th>
<th>N</th>
+ {%endif%}
</tr>
</thead>
@@ -102,9 +110,10 @@
<td>{{loop.index}}</td>
<td>{{item.StrainName}}</td>
<td>{{item.value}}</td>
- <td>{{item.Symbol or "-"}}</td>
+ {%if has_se%}
<td>{{item.error or "-"}}</td>
<td>{{item.count or "-"}}</td>
+ {%endif%}
</tr>
{%endfor%}
</tbody>
diff --git a/uploader/templates/populations/macro-display-population-card.html b/uploader/templates/populations/macro-display-population-card.html
index 79f7925..16b477f 100644
--- a/uploader/templates/populations/macro-display-population-card.html
+++ b/uploader/templates/populations/macro-display-population-card.html
@@ -33,11 +33,6 @@
<td>Family</td>
<td>{{population.Family}}</td>
</tr>
-
- <tr>
- <td>Description</td>
- <td>{{(population.Description or "")[0:500]}}&hellip;</td>
- </tr>
</tbody>
</table>
</div>
generated by cgit v1.2.3 (git 2.46.2) at 2025-02-02 07:34:39 +0000