From fa4260ad08b7aefaea3ea7b64f87ddc221c57cc3 Mon Sep 17 00:00:00 2001
From: Adam Novak
Date: Mon, 20 Apr 2020 11:27:30 -0700
Subject: Put back Intersex with the closest PATO equivalent
These options still disagree with the doc string in the schema.---
bh20sequploader/bh20seq-options.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/bh20sequploader/bh20seq-options.yml b/bh20sequploader/bh20seq-options.yml
index da47e1a..7320ecf 100644
--- a/bh20sequploader/bh20seq-options.yml
+++ b/bh20sequploader/bh20seq-options.yml
@@ -13,6 +13,7 @@ host_age_unit:
host_sex:
Male: http://purl.obolibrary.org/obo/PATO_0000384
Female: http://purl.obolibrary.org/obo/PATO_0000383
+ Intersex: http://purl.obolibrary.org/obo/PATO_0001340
sample_sequencing_technology:
Illumina NextSeq 500: http://www.ebi.ac.uk/efo/EFO_0009173
--
cgit v1.2.3
From b8804933e540aa9231b4a3c406553d7df9d97e0e Mon Sep 17 00:00:00 2001
From: Adam Novak
Date: Mon, 20 Apr 2020 11:30:09 -0700
Subject: Make doc not contradict option list
---
bh20sequploader/bh20seq-schema.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index 64008f2..bbcafc8 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -24,7 +24,7 @@ $graph:
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_000115
host_sex:
- doc: Sex of the host as defined in NCIT, IRI expected (http://purl.obolibrary.org/obo/NCIT_C20197 (Male), http://purl.obolibrary.org/obo/NCIT_C27993 (Female), http://purl.obolibrary.org/obo/NCIT_C45908 (Intersex), or http://purl.obolibrary.org/obo/NCIT_C17998 (Unknown))
+ doc: Sex of the host, IRI expected
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/PATO_0000047
--
cgit v1.2.3
From adf76b6c85da9277921cfe4c45df764310d29737 Mon Sep 17 00:00:00 2001
From: Adam Novak
Date: Mon, 20 Apr 2020 11:43:47 -0700
Subject: Nicer headings for xxx2 fields and float support
---
bh20simplewebuploader/main.py | 25 +++++++++++++++++++------
bh20simplewebuploader/templates/form.html | 2 +-
2 files changed, 20 insertions(+), 7 deletions(-)
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 8c5c18c..e31f18b 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -46,8 +46,11 @@ def name_to_label(field_name):
"""
Turn a filed name like "host_health_status" from the metadata schema into a human-readable label.
"""
-
- return string.capwords(field_name.replace('_', ' '))
+
+ # May end in a number, which should be set off by a space
+ set_off_number = re.sub('([0-9])$', r' \1', field_name)
+
+ return string.capwords(set_off_number.replace('_', ' '))
def is_iri(string):
"""
@@ -66,10 +69,16 @@ def generate_form(schema, options):
Each dict either has a 'heading' (in which case we put a heading for a
form section in the template) or an 'id', 'label', 'type', and 'required'
- (in which case we make a form field in the template). Non-heading dicts
- with type 'select' will have an 'options' field, with a list of (name,
- value) tuples, and represent a form dropdown element. Non-heading dicts may
- have a human-readable 'docstring' field describing them.
+ (in which case we make a form field in the template).
+
+ Non-heading dicts with type 'select' will have an 'options' field, with a
+ list of (name, value) tuples, and represent a form dropdown element.
+
+ Non-heading dicts with type 'number' may have a 'step', which, if <1 or
+ 'any', allows the number to be a float.
+
+ Non-heading dicts may have a human-readable 'docstring' field describing
+ them.
Takes the deserialized metadata schema YAML, and also a deserialized YAML
of option values. The option values are keyed on (unscoped) field name in
@@ -177,6 +186,10 @@ def generate_form(schema, options):
record['type'] = 'text' # HTML input type
elif field_type == 'int':
record['type'] = 'number'
+ elif field_type == 'float':
+ record['type'] = 'number'
+ # Choose a reasonable precision for the control
+ record['step'] = '0.0001'
else:
raise NotImplementedError('Unimplemented field type {} in {} in metadata schema'.format(field_type, type_name))
yield record
diff --git a/bh20simplewebuploader/templates/form.html b/bh20simplewebuploader/templates/form.html
index 6993cf5..02ae84d 100644
--- a/bh20simplewebuploader/templates/form.html
+++ b/bh20simplewebuploader/templates/form.html
@@ -238,7 +238,7 @@
{% endfor %}
{% else %}
-
+
{% endif %}
{% endif %}
{% if loop.index == loop.length %}
--
cgit v1.2.3
From 3bd4ac02ded5af9a666ad7e99ebf6891bc339636 Mon Sep 17 00:00:00 2001
From: Adam Novak
Date: Mon, 20 Apr 2020 11:44:18 -0700
Subject: Support any number of series fields
---
bh20simplewebuploader/main.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index e31f18b..34dc354 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -48,7 +48,7 @@ def name_to_label(field_name):
"""
# May end in a number, which should be set off by a space
- set_off_number = re.sub('([0-9])$', r' \1', field_name)
+ set_off_number = re.sub('([0-9]+)$', r' \1', field_name)
return string.capwords(set_off_number.replace('_', ' '))
--
cgit v1.2.3
From f38b9c6f22b82327df9648938a5a4bcf863d8c41 Mon Sep 17 00:00:00 2001
From: Adam Novak
Date: Mon, 20 Apr 2020 11:52:47 -0700
Subject: Use a date picker for any string 'date'
---
bh20simplewebuploader/main.py | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 34dc354..ceab8a6 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -183,7 +183,13 @@ def generate_form(schema, options):
# Make a tuple for each one
record['options'].append((name, value))
elif field_type == 'string':
- record['type'] = 'text' # HTML input type
+ if field_name.endswith('date'):
+ # Use a date picker to generate a good string.
+ # Comes back YYYY-MM-DD.
+ record['type'] = 'date'
+ else:
+ # Normal text string
+ record['type'] = 'text'
elif field_type == 'int':
record['type'] = 'number'
elif field_type == 'float':
--
cgit v1.2.3