From 20722c736eea3e850305b306f9e451d7b50747a6 Mon Sep 17 00:00:00 2001 From: Steven Kearnes Date: Tue, 14 Jan 2025 15:39:31 -0500 Subject: [PATCH 1/4] Add unmeasured amount fields --- .../full.pbtxt | 13 ++++++++ ord_interface/editor/html/reaction.html | 32 +++++++++++++++++-- ord_interface/editor/js/amounts.js | 16 ++++++++++ ord_interface/editor/js/utils.js | 1 + ord_interface/editor/py/serve.py | 4 +-- 5 files changed, 61 insertions(+), 5 deletions(-) diff --git a/ord_interface/editor/db/680b0d9fe649417cb092d790907bd5a5/full.pbtxt b/ord_interface/editor/db/680b0d9fe649417cb092d790907bd5a5/full.pbtxt index 0ede50e0..4f3ae53a 100644 --- a/ord_interface/editor/db/680b0d9fe649417cb092d790907bd5a5/full.pbtxt +++ b/ord_interface/editor/db/680b0d9fe649417cb092d790907bd5a5/full.pbtxt @@ -95,6 +95,19 @@ reactions { inputs { key: "5" value { + components { + identifiers { + type: SMILES + details: "6" + value: "5" + } + amount { + unmeasured { + type: SATURATED + details: "saturated" + } + } + } addition_order: 93 addition_time { value: 96.0 diff --git a/ord_interface/editor/html/reaction.html b/ord_interface/editor/html/reaction.html index 5877d766..279f86fc 100644 --- a/ord_interface/editor/html/reaction.html +++ b/ord_interface/editor/html/reaction.html @@ -220,7 +220,8 @@ - + + + + + + + +
reaction role
limiting reactant
amount
@@ -230,6 +231,12 @@ 		includes solutes
unmeasured?
details
@@ -340,7 +347,8 @@ reaction ID
includes workup
has derived amount
- + + amount
@@ -348,6 +356,12 @@ + + unmeasured? +
+ details
+ +
@@ -723,7 +737,8 @@ automated
details
- + + aliquot amount
@@ -731,6 +746,12 @@ + + unmeasured? +
+ details
+ +
@@ -886,6 +907,11 @@ + + unmeasured? +
+ details
+ diff --git a/ord_interface/editor/js/amounts.js b/ord_interface/editor/js/amounts.js index 84d74722..901cfd83 100644 --- a/ord_interface/editor/js/amounts.js +++ b/ord_interface/editor/js/amounts.js @@ -22,6 +22,7 @@ exports = { unload, }; +const asserts = goog.require('goog.asserts'); const utils = goog.require('ord.utils'); const Amount = goog.require('proto.ord.Amount'); @@ -31,6 +32,8 @@ const Moles = goog.require('proto.ord.Moles'); const MolesUnit = goog.require('proto.ord.Moles.MolesUnit'); const Volume = goog.require('proto.ord.Volume'); const VolumeUnit = goog.require('proto.ord.Volume.VolumeUnit'); +const UnmeasuredAmount = goog.require('proto.ord.UnmeasuredAmount'); +const UnmeasuredAmountType = goog.require('proto.ord.UnmeasuredAmount.UnmeasuredAmountType'); /** * Initializes the selector for an Amount section. @@ -149,6 +152,10 @@ function load(node, amount) { : null; utils.setOptionalBool($('.amount_includes_solutes.optional_bool', node), solutes); + } else if (amount.hasUnmeasured()) { + const unmeasured = amount.getUnmeasured(); + utils.setSelector($('.unmeasured_amount_type', node), unmeasured.getType()); + $('.unmeasured_amount_details', node).text(unmeasured.getDetails()); } } @@ -165,6 +172,8 @@ function unload(node) { const value = parseFloat($('.amount_value', node).text()); const precision = parseFloat($('.amount_precision', node).text()); const units = $('.amount_units', node).val(); + const unmeasuredType = utils.getSelectorText($('.unmeasured_amount_type', node)[0]); + const unmeasuredDetails = $('.unmeasured_amount_details', node).text(); if (MassUnit[units]) { const message = new Mass(); if (!isNaN(value)) { @@ -206,6 +215,13 @@ function unload(node) { if (solutes !== null) { amount.setVolumeIncludesSolutes(solutes); } + } else if (unmeasuredDetails) { + const unmeasured = new UnmeasuredAmount(); + unmeasured.setType(UnmeasuredAmountType[unmeasuredType]); + unmeasured.setDetails(asserts.assertString(unmeasuredDetails)); + if (!utils.isEmptyMessage(unmeasured)) { + amount.setUnmeasured(unmeasured); + } } return amount; } diff --git a/ord_interface/editor/js/utils.js b/ord_interface/editor/js/utils.js index ffff6131..dcfde36c 100644 --- a/ord_interface/editor/js/utils.js +++ b/ord_interface/editor/js/utils.js @@ -561,6 +561,7 @@ async function compareDataset(fileName, dataset) { if (xhr.status === 200) { resolve(); } else { + console.log(xhr.response); reject(); } }; diff --git a/ord_interface/editor/py/serve.py b/ord_interface/editor/py/serve.py index d5a2050c..a7284d76 100644 --- a/ord_interface/editor/py/serve.py +++ b/ord_interface/editor/py/serve.py @@ -533,8 +533,8 @@ def compare(name): local_ascii = text_format.MessageToString(local) if remote_ascii != local_ascii: diff = difflib.context_diff(local_ascii.splitlines(), remote_ascii.splitlines(), n=10) - print(f"Datasets differ:\n{pprint.pformat(list(diff))}") - return "differs", 409 # "Conflict" + diff_text = pprint.pformat(list(diff)) + return diff_text, 409 # "Conflict" return "equals" From 8b25a08f7091cf1d9bcc20c12c48731af47c02fc Mon Sep 17 00:00:00 2001 From: Steven Kearnes Date: Tue, 14 Jan 2025 15:42:04 -0500 Subject: [PATCH 2/4] format --- ord_interface/editor/js/amounts.js | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/ord_interface/editor/js/amounts.js b/ord_interface/editor/js/amounts.js index 901cfd83..a21ddb98 100644 --- a/ord_interface/editor/js/amounts.js +++ b/ord_interface/editor/js/amounts.js @@ -33,7 +33,8 @@ const MolesUnit = goog.require('proto.ord.Moles.MolesUnit'); const Volume = goog.require('proto.ord.Volume'); const VolumeUnit = goog.require('proto.ord.Volume.VolumeUnit'); const UnmeasuredAmount = goog.require('proto.ord.UnmeasuredAmount'); -const UnmeasuredAmountType = goog.require('proto.ord.UnmeasuredAmount.UnmeasuredAmountType'); +const UnmeasuredAmountType = + goog.require('proto.ord.UnmeasuredAmount.UnmeasuredAmountType'); /** * Initializes the selector for an Amount section. @@ -172,7 +173,8 @@ function unload(node) { const value = parseFloat($('.amount_value', node).text()); const precision = parseFloat($('.amount_precision', node).text()); const units = $('.amount_units', node).val(); - const unmeasuredType = utils.getSelectorText($('.unmeasured_amount_type', node)[0]); + const unmeasuredType = + utils.getSelectorText($('.unmeasured_amount_type', node)[0]); const unmeasuredDetails = $('.unmeasured_amount_details', node).text(); if (MassUnit[units]) { const message = new Mass(); From d7d7caf046dabc22a232a9ab2471657bb931201e Mon Sep 17 00:00:00 2001 From: Steven Kearnes Date: Tue, 14 Jan 2025 18:03:38 -0500 Subject: [PATCH 3/4] updates --- .../editor/db/680b0d9fe649417cb092d790907bd5a5/full.pbtxt | 8 ++++++++ ord_interface/editor/html/reaction.html | 4 ++-- ord_interface/editor/js/amounts.js | 8 +++++--- 3 files changed, 15 insertions(+), 5 deletions(-) diff --git a/ord_interface/editor/db/680b0d9fe649417cb092d790907bd5a5/full.pbtxt b/ord_interface/editor/db/680b0d9fe649417cb092d790907bd5a5/full.pbtxt index 4f3ae53a..e4e3ae28 100644 --- a/ord_interface/editor/db/680b0d9fe649417cb092d790907bd5a5/full.pbtxt +++ b/ord_interface/editor/db/680b0d9fe649417cb092d790907bd5a5/full.pbtxt @@ -405,6 +405,14 @@ reactions { target_ph: 89.0 is_automated: true } + workups { + amount { + unmeasured { + type: CATALYTIC + details: "catalytic" + } + } + } outcomes { reaction_time { value: 113.0 diff --git a/ord_interface/editor/html/reaction.html b/ord_interface/editor/html/reaction.html index 279f86fc..87505ef5 100644 --- a/ord_interface/editor/html/reaction.html +++ b/ord_interface/editor/html/reaction.html @@ -737,10 +737,10 @@ automated
details
- + aliquot amount - +
±
diff --git a/ord_interface/editor/js/amounts.js b/ord_interface/editor/js/amounts.js index a21ddb98..c29d020f 100644 --- a/ord_interface/editor/js/amounts.js +++ b/ord_interface/editor/js/amounts.js @@ -169,12 +169,12 @@ function unload(node) { const amount = new Amount(); // NOTE(kearnes): Take the closest amount section; there may be others // nested deeper (e.g. in ProductMeasurement fields under a ReactionProduct). - node = $('.amount', node).first(); + if (!$(node).hasClass("amount")) { + node = $('.amount', node).first(); + } const value = parseFloat($('.amount_value', node).text()); const precision = parseFloat($('.amount_precision', node).text()); const units = $('.amount_units', node).val(); - const unmeasuredType = - utils.getSelectorText($('.unmeasured_amount_type', node)[0]); const unmeasuredDetails = $('.unmeasured_amount_details', node).text(); if (MassUnit[units]) { const message = new Mass(); @@ -219,6 +219,8 @@ function unload(node) { } } else if (unmeasuredDetails) { const unmeasured = new UnmeasuredAmount(); + const unmeasuredType = + utils.getSelectorText($('.unmeasured_amount_type', node)[0]); unmeasured.setType(UnmeasuredAmountType[unmeasuredType]); unmeasured.setDetails(asserts.assertString(unmeasuredDetails)); if (!utils.isEmptyMessage(unmeasured)) { From bf0eee4541be098300b34a12235a09b1c0df2c02 Mon Sep 17 00:00:00 2001 From: Steven Kearnes Date: Tue, 14 Jan 2025 18:03:50 -0500 Subject: [PATCH 4/4] format --- ord_interface/editor/js/amounts.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ord_interface/editor/js/amounts.js b/ord_interface/editor/js/amounts.js index c29d020f..5afdad54 100644 --- a/ord_interface/editor/js/amounts.js +++ b/ord_interface/editor/js/amounts.js @@ -220,7 +220,7 @@ function unload(node) { } else if (unmeasuredDetails) { const unmeasured = new UnmeasuredAmount(); const unmeasuredType = - utils.getSelectorText($('.unmeasured_amount_type', node)[0]); + utils.getSelectorText($('.unmeasured_amount_type', node)[0]); unmeasured.setType(UnmeasuredAmountType[unmeasuredType]); unmeasured.setDetails(asserts.assertString(unmeasuredDetails)); if (!utils.isEmptyMessage(unmeasured)) {