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-rw-r--r--bh20simplewebuploader/main.py86
1 files changed, 48 insertions, 38 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 3173d60..62b68d9 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -8,7 +8,7 @@ import os
import sys
import re
import string
-import yaml
+import ruamel.yaml as yaml
import pkg_resources
from flask import Flask, request, redirect, send_file, send_from_directory, render_template, jsonify
import os.path
@@ -16,6 +16,9 @@ import requests
import io
import arvados
from markupsafe import Markup
+from schema_salad.sourceline import add_lc_filename
+from schema_salad.schema import shortname
+from typing import MutableSequence, MutableMapping
ARVADOS_API = 'lugli.arvadosapi.com'
ANONYMOUS_TOKEN = '5o42qdxpxp5cj15jqjf7vnxx5xduhm4ret703suuoa3ivfglfh'
@@ -47,6 +50,8 @@ def type_to_heading(type_name):
Turn a type name like "sampleSchema" from the metadata schema into a human-readable heading.
"""
+ type_name = shortname(type_name)
+
print(type_name,file=sys.stderr)
# Remove camel case
decamel = re.sub('([A-Z])', r' \1', type_name)
@@ -78,7 +83,7 @@ def is_iri(string):
return string.startswith('http')
-def generate_form(schema, options):
+def generate_form(components, options):
"""
Linearize the schema into a list of dicts.
@@ -101,9 +106,6 @@ def generate_form(schema, options):
IRI.
"""
- # Get the list of form components, one of which is the root
- components = schema.get('$graph', [])
-
# Find the root
root_name = None
# And also index components by type name
@@ -131,14 +133,25 @@ def generate_form(schema, options):
# First make a heading, if we aren't the very root of the form
yield {'heading': type_to_heading(type_name)}
- for field_name, field_type in by_name.get(type_name, {}).get('fields', {}).items():
+ for field in by_name.get(type_name, {}).get('fields', []):
+ field_name = shortname(field["name"])
+ field_type = field["type"]
# For each field
ref_iri = None
docstring = None
- if not isinstance(field_type, str):
- # If the type isn't a string
+ optional = False
+ is_list = False
+
+ if isinstance(field_type, MutableSequence):
+ if field_type[0] == "null" and len(field_type) == 2:
+ optional = True
+ field_type = field_type[1]
+ else:
+ raise Exception("Can't handle it")
+
+ if isinstance(field_type, MutableMapping):
# It may have documentation
docstring = field_type.get('doc', None)
@@ -161,25 +174,13 @@ def generate_form(schema, options):
ref_iri = field_value
break
-
- # Now overwrite the field type with the actual type string
- field_type = field_type.get('type', '')
-
- # Decide if the field is optional (type ends in ?)
- optional = False
- if field_type.endswith('?'):
- # It's optional
- optional = True
- # Drop the ?
- field_type = field_type[:-1]
-
- # Decide if the field is a list (type ends in [])
- is_list = False
- if field_type.endswith('[]'):
- # It's a list
- is_list = True
- # Reduce to the normal type
- field_type = field_type[:-2]
+ if field_type["type"] == "array":
+ # Now replace the field type with the actual type string
+ is_list = True
+ field_type = field_type.get('items', '')
+ else:
+ field_type = field_type.get('type', '')
+ pass
if field_type in by_name:
# This is a subrecord. We need to recurse
@@ -227,15 +228,24 @@ def generate_form(schema, options):
return list(walk_fields(root_name))
-# At startup, we need to load the metadata schema from the uploader module, so we can make a form for it
-if os.path.isfile("bh20sequploader/bh20seq-schema.yml"):
- METADATA_SCHEMA = yaml.safe_load(open("bh20sequploader/bh20seq-schema.yml","r").read())
- METADATA_OPTION_DEFINITIONS = yaml.safe_load(open("bh20sequploader/bh20seq-options.yml","r").read())
-else:
- METADATA_SCHEMA = yaml.safe_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-schema.yml"))
- METADATA_OPTION_DEFINITIONS = yaml.safe_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-options.yml"))
-# print(METADATA_SCHEMA,file=sys.stderr)
-FORM_ITEMS = generate_form(METADATA_SCHEMA, METADATA_OPTION_DEFINITIONS)
+import schema_salad.schema
+def load_schema_generate_form():
+ # At startup, we need to load the metadata schema from the uploader module, so we can make a form for it
+ if os.path.isfile("bh20sequploader/bh20seq-schema.yml"):
+ METADATA_SCHEMA = yaml.round_trip_load(open("bh20sequploader/bh20seq-schema.yml","r").read())
+ METADATA_OPTION_DEFINITIONS = yaml.safe_load(open("bh20sequploader/bh20seq-options.yml","r").read())
+ else:
+ METADATA_SCHEMA = yaml.round_trip_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-schema.yml"))
+ METADATA_OPTION_DEFINITIONS = yaml.safe_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-options.yml"))
+
+ METADATA_SCHEMA["name"] = "bh20seq-schema.yml"
+ add_lc_filename(METADATA_SCHEMA, "bh20seq-schema.yml")
+ metaschema_names, _metaschema_doc, metaschema_loader = schema_salad.schema.get_metaschema()
+ schema_doc, schema_metadata = metaschema_loader.resolve_ref(METADATA_SCHEMA, "")
+
+ return generate_form(schema_doc, METADATA_OPTION_DEFINITIONS)
+
+FORM_ITEMS = load_schema_generate_form()
@app.route('/')
def send_home():
@@ -543,10 +553,10 @@ def status_page():
for s in (("passed", "/download"), ("pending", "#pending"), ("rejected", "#rejected")):
output.write("<p><a href='%s'>%s sequences QC %s</a></p>" % (s[1], status.get(s[0], 0), s[0]))
- output.write("<a id='pending'><h1>Pending</h1>")
+ output.write("<a id='pending'><h1>Pending</h1></a>")
pending_table(output, out)
- output.write("<a id='rejected'><h1>Rejected</h1>")
+ output.write("<a id='rejected'><h1>Rejected</h1></a>")
rejected_table(output, out)
return render_template('status.html', table=Markup(output.getvalue()), menu='STATUS')