From fbd4e9d239769afc46e42233f504dcc745016654 Mon Sep 17 00:00:00 2001 From: meganrm Date: Mon, 11 Mar 2024 15:10:05 -0700 Subject: [PATCH 1/3] import and render icons --- gatsby-config.js | 1 + package.json | 1 + src/components/DiseaseTable.tsx | 22 ++++++++- src/components/Layout.tsx | 2 +- src/img/cert-icon.svg | 6 +++ src/img/tube.svg | 8 ++++ yarn.lock | 79 +++++++++++++++++++++++++++++++-- 7 files changed, 113 insertions(+), 6 deletions(-) create mode 100644 src/img/cert-icon.svg create mode 100644 src/img/tube.svg diff --git a/gatsby-config.js b/gatsby-config.js index 4575e1a..9db4591 100644 --- a/gatsby-config.js +++ b/gatsby-config.js @@ -41,6 +41,7 @@ module.exports = { `gatsby-plugin-image`, "gatsby-plugin-sharp", "gatsby-transformer-sharp", + 'gatsby-plugin-react-svg', { resolve: "gatsby-transformer-remark", options: { diff --git a/package.json b/package.json index f9158db..515447e 100644 --- a/package.json +++ b/package.json @@ -15,6 +15,7 @@ "gatsby-plugin-netlify": "^5.0.0", "gatsby-plugin-purgecss": "^6.0.0", "gatsby-plugin-react-helmet": "^6.13.1", + "gatsby-plugin-react-svg": "^3.3.0", "gatsby-plugin-sass": "^6.13.1", "gatsby-plugin-sharp": "^5.13.1", "gatsby-remark-copy-linked-files": "^6.13.1", diff --git a/src/components/DiseaseTable.tsx b/src/components/DiseaseTable.tsx index a08cd08..3349867 100644 --- a/src/components/DiseaseTable.tsx +++ b/src/components/DiseaseTable.tsx @@ -1,10 +1,14 @@ import React from "react"; import { Table, Tag, Flex } from "antd"; +import Icon from "@ant-design/icons"; import Content from "./Content"; import { UnpackedDiseaseCellLine } from "../component-queries/DiseaseCellLines"; import { formatCellLineId } from "../utils"; +const Tube = require("../img/tube.svg"); +const CertificateIcon = require("../img/cert-icon.svg"); + import { tableTitle, container, @@ -13,6 +17,8 @@ import { clones, comingSoon, } from "../style/disease-table.module.css"; +import { WHITE } from "./Layout"; +import { Certificate } from "crypto"; interface DiseaseTableProps { diseaseName: string; @@ -92,7 +98,13 @@ const DiseaseTable = ({ } else { return ( - Obtain Line + + + Obtain Line + ); } @@ -110,7 +122,13 @@ const DiseaseTable = ({ href={certificate_of_analysis.publicURL} target="_blank" > - Cert. of Analysis + + + Cert. of Analysis + ) ); diff --git a/src/components/Layout.tsx b/src/components/Layout.tsx index 9f5ac4b..00f6ccb 100644 --- a/src/components/Layout.tsx +++ b/src/components/Layout.tsx @@ -11,7 +11,7 @@ import { container } from "../style/layout.module.css"; const OFF_WHITE = "#F2F2F2"; const DARK_BLUE = "#00215F"; -const WHITE = "#FFFFFF"; +export const WHITE = "#FFFFFF"; const LIGHT_BLUE = "#E5E9F1"; const DARK_GRAY = "#CBCBCC"; const LIGHT_GRAY = "#323233"; diff --git a/src/img/cert-icon.svg b/src/img/cert-icon.svg new file mode 100644 index 0000000..597790e --- /dev/null +++ b/src/img/cert-icon.svg @@ -0,0 +1,6 @@ + + + + + + diff --git a/src/img/tube.svg b/src/img/tube.svg new file mode 100644 index 0000000..eaf740d --- /dev/null +++ b/src/img/tube.svg @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/yarn.lock b/yarn.lock index d1bcb5a..c30e43c 100644 --- a/yarn.lock +++ b/yarn.lock @@ -5044,6 +5044,11 @@ better-opn@^2.1.1: dependencies: open "^7.0.3" +big.js@^3.1.3: + version "3.2.0" + resolved "https://registry.yarnpkg.com/big.js/-/big.js-3.2.0.tgz#a5fc298b81b9e0dca2e458824784b65c52ba588e" + integrity sha512-+hN/Zh2D08Mx65pZ/4g5bsmNiZUuChDiQfTUQ7qJr4/kuopCr88xZsAXv6mBoZEsUI4OuGHlX59qE94K2mMW8Q== + big.js@^5.2.2: version "5.2.2" resolved "https://registry.yarnpkg.com/big.js/-/big.js-5.2.2.tgz#65f0af382f578bcdc742bd9c281e9cb2d7768328" @@ -6486,7 +6491,7 @@ css.escape@^1.5.1: resolved "https://registry.yarnpkg.com/css.escape/-/css.escape-1.5.1.tgz#42e27d4fa04ae32f931a4b4d4191fa9cddee97cb" integrity sha512-YUifsXXuknHlUsmlgyY0PKzgPOr7/FjCePfHNt0jxm83wHZi44VDMQ7/fGNkjY3/jV1MC+1CmZbaHzugyeRtpg== -css@^2.0.0: +css@2.2.4, css@^2.0.0: version "2.2.4" resolved 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+gatsby-plugin-react-svg@^3.3.0: + version "3.3.0" + resolved "https://registry.yarnpkg.com/gatsby-plugin-react-svg/-/gatsby-plugin-react-svg-3.3.0.tgz#1dad8594ecd6ffd86e5ff45e1b9365367c999c44" + integrity sha512-kFPElMFu1QCkiFCm1pSrVkOHAeafU6wkD0qCVPs7nL/Txh5KFh0aOO6Feiwvfre1Jo+Eg3lwCuGmgsy9L+4pDg== + dependencies: + svg-react-loader "^0.4.6" + gatsby-plugin-sass@^6.13.1: version "6.13.1" resolved "https://registry.yarnpkg.com/gatsby-plugin-sass/-/gatsby-plugin-sass-6.13.1.tgz#13fa6a4b95aee7c1bf3e69c017ae9c8e1a0abf49" @@ -11493,6 +11510,11 @@ json2mq@^0.2.0: dependencies: string-convert "^0.2.0" +json5@^0.5.0: + version "0.5.1" + resolved "https://registry.yarnpkg.com/json5/-/json5-0.5.1.tgz#1eade7acc012034ad84e2396767ead9fa5495821" + integrity sha512-4xrs1aW+6N5DalkqSVA8fxh458CXvR99WU8WLKmq4v8eWAL86Xo3BVqyd3SkA9wEVjCMqyvvRRkshAdOnBp5rw== + json5@^1.0.1, json5@^1.0.2: version "1.0.2" resolved "https://registry.yarnpkg.com/json5/-/json5-1.0.2.tgz#63d98d60f21b313b77c4d6da18bfa69d80e1d593" @@ -11811,6 +11833,15 @@ loader-runner@^4.2.0: resolved "https://registry.yarnpkg.com/loader-runner/-/loader-runner-4.3.0.tgz#c1b4a163b99f614830353b16755e7149ac2314e1" integrity sha512-3R/1M+yS3j5ou80Me59j7F9IMs4PXs3VqRrm0TU3AbKPxlmpoY1TNscJV/oGJXo8qCatFGTfDbY6W6ipGOYXfg== +loader-utils@1.1.0: + version "1.1.0" + resolved "https://registry.yarnpkg.com/loader-utils/-/loader-utils-1.1.0.tgz#c98aef488bcceda2ffb5e2de646d6a754429f5cd" + integrity sha512-gkD9aSEG9UGglyPcDJqY9YBTUtCLKaBK6ihD2VP1d1X60lTfFspNZNulGBBbUZLkPygy4LySYHyxBpq+VhjObQ== + dependencies: + big.js "^3.1.3" + emojis-list "^2.0.0" + json5 "^0.5.0" + loader-utils@^1.2.3: version "1.4.2" resolved "https://registry.yarnpkg.com/loader-utils/-/loader-utils-1.4.2.tgz#29a957f3a63973883eb684f10ffd3d151fec01a3" @@ -12004,7 +12035,7 @@ lodash.uniq@^4.5.0: resolved "https://registry.yarnpkg.com/lodash.uniq/-/lodash.uniq-4.5.0.tgz#d0225373aeb652adc1bc82e4945339a842754773" integrity sha512-xfBaXQd9ryd9dlSDvnvI0lvxfLJlYAZzXomUYzLKtUeOQvOP5piqAWuGtrhWeqaXK9hhoM/iyJc5AV+XfsX3HQ== -lodash@4.17.21, lodash@^4.0.1, lodash@^4.17.10, lodash@^4.17.11, lodash@^4.17.12, lodash@^4.17.15, lodash@^4.17.19, lodash@^4.17.20, lodash@^4.17.21, lodash@^4.17.4, lodash@~4.17.0: +lodash@4.17.21, lodash@^4.0.0, lodash@^4.0.1, lodash@^4.17.10, lodash@^4.17.11, lodash@^4.17.12, lodash@^4.17.15, lodash@^4.17.19, lodash@^4.17.20, lodash@^4.17.21, lodash@^4.17.4, lodash@~4.17.0: version "4.17.21" resolved "https://registry.yarnpkg.com/lodash/-/lodash-4.17.21.tgz#679591c564c3bffaae8454cf0b3df370c3d6911c" integrity sha512-v2kDEe57lecTulaDIuNTPy3Ry4gLGJ6Z1O3vE1krgXZNrsQ+LFTGHVxVjcXPs17LhbZVGedAJv8XZ1tvj5FvSg== @@ -14886,6 +14917,11 @@ radix3@^1.1.0: resolved "https://registry.yarnpkg.com/radix3/-/radix3-1.1.0.tgz#9745df67a49c522e94a33d0a93cf743f104b6e0d" integrity sha512-pNsHDxbGORSvuSScqNJ+3Km6QAVqk8CfsCBIEoDgpqLrkD2f3QM4I7d1ozJJ172OmIcoUcerZaNWqtLkRXTV3A== +ramda@0.21.0: + version "0.21.0" + resolved "https://registry.yarnpkg.com/ramda/-/ramda-0.21.0.tgz#a001abedb3ff61077d4ff1d577d44de77e8d0a35" + integrity sha512-HGd5aczYKQXGILB+abY290V7Xz62eFajpa6AtMdwEmQSakJmgSO7ks4eI3HdR34j+X2Vz4Thp9VAJbrCAMbO2w== + random-bytes@~1.0.0: version "1.0.0" resolved "https://registry.yarnpkg.com/random-bytes/-/random-bytes-1.0.0.tgz#4f68a1dc0ae58bd3fb95848c30324db75d64360b" @@ -16362,6 +16398,11 @@ rw@^1.3.3: resolved "https://registry.yarnpkg.com/rw/-/rw-1.3.3.tgz#3f862dfa91ab766b14885ef4d01124bfda074fb4" integrity sha512-PdhdWy89SiZogBLaw42zdeqtRJ//zFd2PgQavcICDUgJT5oW10QCRKbJ6bg4r0/UY2M6BWd5tkxuGFRvCkgfHQ== +rx@4.1.0: + version "4.1.0" + resolved "https://registry.yarnpkg.com/rx/-/rx-4.1.0.tgz#a5f13ff79ef3b740fe30aa803fb09f98805d4782" + integrity sha512-CiaiuN6gapkdl+cZUr67W6I8jquN4lkak3vtIsIWCl4XIPP8ffsoyN6/+PuGXnQy8Cu8W2y9Xxh31Rq4M6wUug== + rxjs@^6.4.0, rxjs@^6.6.0, rxjs@^6.6.2: version "6.6.7" resolved "https://registry.yarnpkg.com/rxjs/-/rxjs-6.6.7.tgz#90ac018acabf491bf65044235d5863c4dab804c9" @@ -16475,7 +16516,7 @@ sass@^1.70.0: immutable "^4.0.0" source-map-js ">=0.6.2 <2.0.0" -sax@^1.2.4, sax@~1.3.0: +sax@>=0.6.0, sax@^1.2.4, sax@~1.3.0: version "1.3.0" resolved "https://registry.yarnpkg.com/sax/-/sax-1.3.0.tgz#a5dbe77db3be05c9d1ee7785dbd3ea9de51593d0" integrity sha512-0s+oAmw9zLl1V1cS9BtZN7JAd0cW5e0QH4W3LWEK6a4LaLEA2OTpGYWDY+6XasBLtz6wkm3u1xRw95mRuJ59WA== @@ -17514,6 +17555,18 @@ supports-preserve-symlinks-flag@^1.0.0: resolved "https://registry.yarnpkg.com/supports-preserve-symlinks-flag/-/supports-preserve-symlinks-flag-1.0.0.tgz#6eda4bd344a3c94aea376d4cc31bc77311039e09" integrity sha512-ot0WnXS9fgdkgIcePe6RHNk1WA8+muPa6cSjeR3V8K27q9BB1rTE3R1p7Hv0z1ZyAc8s6Vvv8DIyWf681MAt0w== +svg-react-loader@^0.4.6: + version "0.4.6" + resolved "https://registry.yarnpkg.com/svg-react-loader/-/svg-react-loader-0.4.6.tgz#b263efb3e3d2fff4c682a729351aba5f185051a1" + integrity sha512-HVEypjWQsQuJdBIPzXGxpmQsQts7QwfQuYgK1rah6BVCMoLNSCh/ESKVNd7/tHq8DkWYHHTyaUMDA1FjqZYrgA== + dependencies: + css "2.2.4" + loader-utils "1.1.0" + ramda "0.21.0" + rx "4.1.0" + traverse "0.6.6" + xml2js "0.4.17" + svgo@^2.7.0: version "2.8.0" resolved "https://registry.yarnpkg.com/svgo/-/svgo-2.8.0.tgz#4ff80cce6710dc2795f0c7c74101e6764cfccd24" @@ -17895,6 +17948,11 @@ tr46@~0.0.3: resolved "https://registry.yarnpkg.com/tr46/-/tr46-0.0.3.tgz#8184fd347dac9cdc185992f3a6622e14b9d9ab6a" integrity sha512-N3WMsuqV66lT30CrXNbEjx4GEwlow3v6rr4mCcv6prnfwhS01rkgyFdjPNBYd9br7LpXV1+Emh01fHnq2Gdgrw== +traverse@0.6.6: + version "0.6.6" + resolved "https://registry.yarnpkg.com/traverse/-/traverse-0.6.6.tgz#cbdf560fd7b9af632502fed40f918c157ea97137" + integrity sha512-kdf4JKs8lbARxWdp7RKdNzoJBhGUcIalSYibuGyHJbmk40pOysQ0+QPvlkCOICOivDWU2IJo2rkrxyTK2AH4fw== + traverse@^0.6.6: version "0.6.8" resolved "https://registry.yarnpkg.com/traverse/-/traverse-0.6.8.tgz#5e5e0c41878b57e4b73ad2f3d1e36a715ea4ab15" @@ -19185,6 +19243,21 @@ xml-utils@^1.0.2: resolved "https://registry.yarnpkg.com/xml-utils/-/xml-utils-1.7.0.tgz#333ce391d8918f872aaf98d2cf90f9ef9b82bd0f" integrity sha512-bWB489+RQQclC7A9OW8e5BzbT8Tu//jtAOvkYwewFr+Q9T9KDGvfzC1lp0pYPEQPEoPQLDkmxkepSC/2gIAZGw== +xml2js@0.4.17: + version "0.4.17" + resolved "https://registry.yarnpkg.com/xml2js/-/xml2js-0.4.17.tgz#17be93eaae3f3b779359c795b419705a8817e868" + integrity sha512-1O7wk/NTQN0UEOItIYTxK4qP4sMUVU60MbF4Nj0a8jd6eebMXOicVI/KFOEsYKKH4uBpx6XG9ZGZctXK5rtO5Q== + dependencies: + sax ">=0.6.0" + xmlbuilder "^4.1.0" + +xmlbuilder@^4.1.0: + version "4.2.1" + resolved "https://registry.yarnpkg.com/xmlbuilder/-/xmlbuilder-4.2.1.tgz#aa58a3041a066f90eaa16c2f5389ff19f3f461a5" + integrity sha512-oEePiEefhQhAeUnwRnIBLBWmk/fsWWbQ53EEWsRuzECbQ3m5o/Esmq6H47CYYwSLW+Ynt0rS9hd0pd2ogMAWjg== + dependencies: + lodash "^4.0.0" + xmlhttprequest-ssl@~2.0.0: version "2.0.0" resolved "https://registry.yarnpkg.com/xmlhttprequest-ssl/-/xmlhttprequest-ssl-2.0.0.tgz#91360c86b914e67f44dce769180027c0da618c67" From 8c45a78846d5c138fadc66e3cc6591480cb95094 Mon Sep 17 00:00:00 2001 From: meganrm Date: Mon, 11 Mar 2024 15:48:15 -0700 Subject: [PATCH 2/3] add instructions --- ADMIN.md | 38 ++++++++++++++++++++++++++++++++++++++ README.md | 6 ++++++ 2 files changed, 44 insertions(+) create mode 100644 ADMIN.md diff --git a/ADMIN.md b/ADMIN.md new file mode 100644 index 0000000..1c95b84 --- /dev/null +++ b/ADMIN.md @@ -0,0 +1,38 @@ +## Adding new Disease Cell Lines through the admin CMS + +### Relational dependancies + +`Disease cell lines` reference: + 1. `Modeled diseases` + 2. `Cell lines` + +`Modeled diseases` reference + 1. `Gene names` + +`Cell lines` reference + 1. `Gene names` + + + +1. **Login to the Admin CMS**: Open your web browser and navigate to the admin CMS URL. Use github to sign in. + +2. **Before you start**: Before you add a new cell line you need to make sure you have already added: + 1. **the disease** the cell line is modeling. If you it is not yet in the database, go to the section on adding a disease and then continue here. + 2. **the parental/base cell line**. If it is not yet in the database, go to the section on adding a cell line and then continue here. + +3. **Add New Disease Cell Line**: Look for a button or link labeled 'Add New', 'Create New', 'New Disease Cell Line' or similar. Click on it to start the process of adding a new disease cell line. + +4. **Enter Disease Cell Line Details**: You will likely be presented with a form to fill out with the details of the new disease cell line. This might include fields like 'Name', 'Description', 'Associated Diseases', 'Research Notes', etc. Fill out all the necessary fields with the correct information. + +5. **Save the New Disease Cell Line**: Once you've filled out all the necessary information, look for a button or link labeled 'Save', 'Create', 'Submit', or similar. Click on it to save the new disease cell line. + +6. **Verify the New Disease Cell Line**: After saving, you should be redirected to a page showing all disease cell lines, including the new one. Verify that all the information is correct. If there are any errors, look for an 'Edit' button or link to go back and correct any mistakes. + +Remember, the exact steps and labels might vary depending on the specifics of your CMS. If you have any trouble, refer to your CMS's documentation or contact your CMS's support team. + +## Adding new Disease through the admin CMS +1. **Before you start**: Before you add a new disease you need to make sure you have already added **the gene** the disease model is based on. If you it is not yet in the database, go to the section on adding a gene and then continue here. + +## Adding new Gene through the admin CMS +1. Click on **Gene and structures names** and click on "New Gene and structure name" or select it from the "Quick add" menu +2. Add the gene symbol and gene name \ No newline at end of file diff --git a/README.md b/README.md index d555225..7c48ace 100644 --- a/README.md +++ b/README.md @@ -29,3 +29,9 @@ Media Libraries have been included in this starter as a default. Contributions are always welcome, no matter how large or small. Before contributing, please read the [code of conduct](CODE_OF_CONDUCT.md). + +## Development +See [contributing guide](CONTRIBUTING.md) + +## Changes to the content +see [admin guide](ADMIN.md) \ No newline at end of file From 8cd66d8adc5aafe5c7b1ac6c6b8b1f2967f65568 Mon Sep 17 00:00:00 2001 From: Megan Riel-Mehan Date: Mon, 11 Mar 2024 15:54:40 -0700 Subject: [PATCH 3/3] Update ADMIN.md --- ADMIN.md | 22 ++++++++++++++-------- 1 file changed, 14 insertions(+), 8 deletions(-) diff --git a/ADMIN.md b/ADMIN.md index 1c95b84..05b0a26 100644 --- a/ADMIN.md +++ b/ADMIN.md @@ -3,15 +3,19 @@ ### Relational dependancies `Disease cell lines` reference: + 1. `Modeled diseases` 2. `Cell lines` `Modeled diseases` reference + 1. `Gene names` `Cell lines` reference + 1. `Gene names` +![Untitled](https://github.com/allen-cell-animated/cell-catalog/assets/5170636/7625a706-1c26-437d-850a-9ea494ee5a81) 1. **Login to the Admin CMS**: Open your web browser and navigate to the admin CMS URL. Use github to sign in. @@ -20,19 +24,21 @@ 1. **the disease** the cell line is modeling. If you it is not yet in the database, go to the section on adding a disease and then continue here. 2. **the parental/base cell line**. If it is not yet in the database, go to the section on adding a cell line and then continue here. -3. **Add New Disease Cell Line**: Look for a button or link labeled 'Add New', 'Create New', 'New Disease Cell Line' or similar. Click on it to start the process of adding a new disease cell line. - -4. **Enter Disease Cell Line Details**: You will likely be presented with a form to fill out with the details of the new disease cell line. This might include fields like 'Name', 'Description', 'Associated Diseases', 'Research Notes', etc. Fill out all the necessary fields with the correct information. +3. **Add New Disease Cell Line**: Click the button "Add new disease cell line" -5. **Save the New Disease Cell Line**: Once you've filled out all the necessary information, look for a button or link labeled 'Save', 'Create', 'Submit', or similar. Click on it to save the new disease cell line. +4. **Enter Disease Cell Line Details**: If this cell line is not ready to be on the website, leave the status as is. -6. **Verify the New Disease Cell Line**: After saving, you should be redirected to a page showing all disease cell lines, including the new one. Verify that all the information is correct. If there are any errors, look for an 'Edit' button or link to go back and correct any mistakes. - -Remember, the exact steps and labels might vary depending on the specifics of your CMS. If you have any trouble, refer to your CMS's documentation or contact your CMS's support team. +5. **Save the New Disease Cell Line**: From the "Publish" dropdown click "Publish now" ## Adding new Disease through the admin CMS 1. **Before you start**: Before you add a new disease you need to make sure you have already added **the gene** the disease model is based on. If you it is not yet in the database, go to the section on adding a gene and then continue here. +## Adding new Normal Cell Line through the admin CMS +1. **Before you start**: Before you add a new disease you need to make sure you have already added **the gene** the disease model is based on. If you it is not yet in the database, go to the section on adding a gene and then continue here. + +2. **Add new Normal Cell Line**: Go to the cell line section, click the button "Add new cell line" +5. **Save the Normal Cell Line**: From the "Publish" dropdown click "Publish now" + ## Adding new Gene through the admin CMS 1. Click on **Gene and structures names** and click on "New Gene and structure name" or select it from the "Quick add" menu -2. Add the gene symbol and gene name \ No newline at end of file +2. Add the gene symbol and gene name