diff options
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | .guix-channel | 8 | ||||
| -rwxr-xr-x | .guix-shell | 7 | ||||
| -rw-r--r-- | .guix/modules/gn-guile.scm | 34 | ||||
| -rw-r--r-- | README.md | 138 | ||||
| -rw-r--r-- | doc/git-markdown-editor.md | 117 | ||||
| -rw-r--r-- | doc/gn-guile.md | 1 | ||||
| -rwxr-xr-x | gn-guile.sh | 3 | ||||
| -rw-r--r-- | gn/db/sources/wikidata.scm | 29 | ||||
| -rw-r--r-- | gn/db/sparql.scm | 3 | ||||
| l---------[-rw-r--r--] | guix.scm | 72 | ||||
| -rwxr-xr-x | scripts/lmdb-publishdata-export.scm | 229 | ||||
| -rw-r--r-- | web/.guix-shell | 8 | ||||
| -rw-r--r-- | web/css/gn-template-style.css | 39 | ||||
| -rw-r--r-- | web/templates/genenetwork.scm | 18 | ||||
| -rw-r--r-- | web/view/view.scm | 4 | ||||
| -rw-r--r-- | web/webserver.scm | 34 |
17 files changed, 526 insertions, 219 deletions
@@ -2,3 +2,4 @@ BXD.* pheno.txt GWA.json K.json +.aider* diff --git a/.guix-channel b/.guix-channel new file mode 100644 index 0000000..6e0982a --- /dev/null +++ b/.guix-channel @@ -0,0 +1,8 @@ +(channel + (version 0) + (directory ".guix/modules") + (dependencies + (channel + (name guix-bioinformatics) + (url "https://git.genenetwork.org/guix-bioinformatics") + (branch "master"))))
\ No newline at end of file diff --git a/.guix-shell b/.guix-shell deleted file mode 100755 index bc81e06..0000000 --- a/.guix-shell +++ /dev/null @@ -1,7 +0,0 @@ -#!/bin/bash -# -# . .guix-shell -- guile -L . --fresh-auto-compile --listen=1970 - -echo "Create a shell to run tools." - -guix shell -L ~/guix-bioinformatics -C -D -F --network coreutils guile guile-dbi guile-dbd-mysql guile-fibers guile-json guile-gnutls guile-readline guile-redis openssl nss-certs gemma parallel tar xz python python-lmdb python-cffi guile-gcrypt guile-hashing time gemma-gn2 $* diff --git a/.guix/modules/gn-guile.scm b/.guix/modules/gn-guile.scm new file mode 100644 index 0000000..03f2b14 --- /dev/null +++ b/.guix/modules/gn-guile.scm @@ -0,0 +1,34 @@ +;; To use this file to build HEAD of gn-guile: +;; +;; guix build -f guix.scm +;; +;; To get a development container +;; +;; guix shell -C -D -f guix.scm +;; + +(define-module (gn-guile) + #:use-module ((gn packages guile) #:select (gn-guile) #:prefix gn:) + #:use-module (guix gexp) + #:use-module (guix utils) + #:use-module (guix packages) + #:use-module (guix git-download)) + +(define %source-dir (dirname (dirname (current-source-directory)))) + +(define vcs-file? + (or (git-predicate %source-dir) + (const #t))) + +(define-public gn-guile + (package + (inherit gn:gn-guile) + (source + (local-file "../.." + "gn-guile-checkout" + #:recursive? #t + #:select? vcs-file?)))) + +;; Add definition for tests should you need it, here. + +gn-guile @@ -2,6 +2,17 @@ This directory provides a Guile web service incl. the new REST API. It is used in conjunction with the Python web services and (very much) WIP. +## Run + +1. **Navigate to the Web Directory and Start the Server** + +Running the web server is documented in [guix script](./web/.guix-shell). + +``` +curl http://127.0.0.1:8091/version +"4.0.0" +``` + # Documentation Start with this file and then the documentation in [doc](./doc/gn-guile.md). @@ -17,130 +28,22 @@ git clone tux02.genenetwork.org:/home/git/public/gn-guile GNU Guile allows you to develop against a live running web server using emacs-geiser. To try this fire up the web server from the `web` directory as ```sh -cd web -unset GUIX_PROFILE -. .guix-shell -- guile -L .. --listen=1970 -e main ./webserver.scm 8091 -``` - -Note the leading dot. The .guix-shell is defined in `gn-guile/web` and loads required packages using GNU Guix. -If you are on Debian you may need to unset GUIX_PROFILE first. - -Next fire up emacs with `emacs-geiser-guile` and connect to the running web server with `M-x geiser-connect` and the port `1970`. Now you can not only inspect procedures, but also update any prodedure on the live server using `C-M-x` and get updated output from the webserver! - -# Tools - -Some tooling and scripts that run independently are stored in `./scripts`. - -Here’s the entire markdown content combined into a single, copyable file: - - -# Gn-Markdown - -Gn-Markdown is an API endpoint to edit, parse, and commit markdown files for gn-docs. - -## How to Test the APIs - -1. **Navigate to the Web Directory and Start the Server** - -```sh -cd web -export REPO_PATH=<repo_path> -. .guix-shell -- guile -L .. --listen=1970 -e main ./webserver.scm 8091 +guix shell --container --network --file=guix.scm -- guile -L . --fresh-auto-compile --listen=1970 -e main web/webserver.scm 8091 ``` -2. **Test Endpoints** - -The main endpoints provided are `/edit` and `/commit`. More endpoints may be added in the future. - -## Edit (GET) +The `--container` option runs the code in an isolated container, and the `--network` option connects that container's networking to the host to allow you to access the running service. -This is a GET request to retrieve a file's details. Make sure you pass a valid file_path as search_query (the path should be relative to the repo) +## Welcome to the world of interactive Lisp programming -**Request Example:** +Next fire up emacs with `emacs-geiser-guile` and connect to the running web server with `M-x geiser-connect` and the port `1970`. Now you can not only inspect procedures, but also update any prodedure on the live server using `C-M-x` on code, call and get updated output from the webserver! No need to save/reload files and all that. -```bash - -curl -G -d "file_path=test.md" localhost:8091/edit - -``` +Note that you may have to try different versions of guile+emacs to succeed. -**Expected Success Response:** - -```json -{ -"file_path": "test.md", -"content": "Test for new user\n test 2 for line\n test 3 for new line\n ## real markdown two test\n", -"hash": "ecd96f27c45301279150fbda411544687db1aa45" -} -``` - -**Expected Error Response (Status 400):** - -```json -{ -"error": <error_type>, -"msg": <error_reason> -} -``` - -## Commit (POST) - -This is a POST request to commit changes to a file. - -**Request URL:** - -```bash - -curl -X POST http://127.0.0.1:8091/commit \ --H 'Content-Type: application/json' \ --d '{ -"content": "make test commit", -"filename": "test.md", -"email": "test@gmail.com", -"username": "test", -"commit_message": "init commit", -"prev_commit": "7cbfc40d98b49a64e98e7cd562f373053d0325bd" -}' - -``` - - - -**Expected Response for success:** - -```json -{ -"status": "201", -"message": "Committed file successfully", -"content": "Test for new user\n test 2 for line\n test 3 for new line\n ## real markdown two test\n", -"commit_sha": "47df3b7f13a935d50cc8b40e98ca9e513cba104c", -"commit_message": "commit by genetics" -} - -``` - -**If No Changes to File:** - -```json -{ -"status": "200", -"message": "Nothing to commit, working tree clean", -"commit_sha": "ecd96f27c45301279150fbda411544687db1aa45" -} -``` - -**Expected Error Response:** +# Tools -```json -{ -"error": "system-error", -"msg": "Commits do not match. Please pull in the latest changes for the current commit *ecd96f27c45301279150fbda411544687db1aa45* and previous commits." -} -``` +Some tooling and scripts that run independently are stored in `./scripts`. -## Notes -This is meant to be used as api endpoint only to edit any local repo; Clients are expected to handle other service e.g User Interface, authentication # Development @@ -148,6 +51,11 @@ This is meant to be used as api endpoint only to edit any local repo; Clients ar git remote add gn git.genenetwork.org:/home/git/public/gn-guile ``` +# Topics + +* More on [gn-guile](./doc/gn-guile.md) +* Markdown editor with git backend see [markdown](./doc/git-markdown-editor.md). + # LICENSE This software is published by the GeneNetwork team under the AGPL3. See [LICENSE](LICENSE.txt). diff --git a/doc/git-markdown-editor.md b/doc/git-markdown-editor.md new file mode 100644 index 0000000..f286284 --- /dev/null +++ b/doc/git-markdown-editor.md @@ -0,0 +1,117 @@ +# Gn-Markdown + +Gn-Markdown is an API endpoint to edit, parse, and commit markdown files for gn-docs. + +## How to Test the APIs + +1. **Navigate to the Web Directory and Start the Server** + +Running the web server is documented in [guix script](./web/.guix-shell). + +``` +curl http://127.0.0.1:8091/version +"4.0.0" +``` + +```sh +cd web +export CURRENT_REPO_PATH=<path-to-git-repo-with-files> +export CGIT_REPO_PATH=<path-to-git-bare-repo> +. .guix-shell -- guile -L .. --listen=1970 -e main ./webserver.scm 8091 +``` + + + +2. **Test Endpoints** + +The main endpoints provided are `/edit` and `/commit`. More endpoints may be added in the future. + +## Edit (GET) + +This is a GET request to retrieve a file's details. Make sure you pass a valid file_path as search_query (the path should be relative to the repo) + +**Request Example:** + +```bash + +curl -G -d "file_path=test.md" localhost:8091/edit + +``` + +**Expected Success Response:** + +```json +{ +"file_path": "test.md", +"content": "Test for new user\n test 2 for line\n test 3 for new line\n ## real markdown two test\n", +"hash": "ecd96f27c45301279150fbda411544687db1aa45" +} +``` + +**Expected Error Response (Status 400):** + +```json +{ +"error": <error_type>, +"msg": <error_reason> +} +``` + +## Commit (POST) + +This is a POST request to commit changes to a file. + +**Request URL:** + +```bash + +curl -X POST http://127.0.0.1:8091/commit \ +-H 'Content-Type: application/json' \ +-d '{ +"content": "make test commit", +"filename": "test.md", +"email": "test@gmail.com", +"username": "test", +"commit_message": "init commit", +"prev_commit": "7cbfc40d98b49a64e98e7cd562f373053d0325bd" +}' + +``` + + + +**Expected Response for success:** + +```json +{ +"status": "201", +"message": "Committed file successfully", +"content": "Test for new user\n test 2 for line\n test 3 for new line\n ## real markdown two test\n", +"commit_sha": "47df3b7f13a935d50cc8b40e98ca9e513cba104c", +"commit_message": "commit by genetics" +} + +``` + +**If No Changes to File:** + +```json +{ +"status": "200", +"message": "Nothing to commit, working tree clean", +"commit_sha": "ecd96f27c45301279150fbda411544687db1aa45" +} +``` + +**Expected Error Response:** + +```json +{ +"error": "system-error", +"msg": "Commits do not match. Please pull in the latest changes for the current commit *ecd96f27c45301279150fbda411544687db1aa45* and previous commits." +} +``` + +## Notes + +This is meant to be used as api endpoint only to edit any local repo; Clients are expected to handle other service e.g User Interface, authentication diff --git a/doc/gn-guile.md b/doc/gn-guile.md index 7a86c13..9e84e23 100644 --- a/doc/gn-guile.md +++ b/doc/gn-guile.md @@ -4,4 +4,5 @@ The GeneNetwork Guile web server serves an exploratory REST API as well as HTML Topics are: +* [Markdown editor](./git-markdown-editor.md). * [Branding GN](./branding.md) diff --git a/gn-guile.sh b/gn-guile.sh new file mode 100755 index 0000000..9341b26 --- /dev/null +++ b/gn-guile.sh @@ -0,0 +1,3 @@ +#! @SHELL@ + +guile -e main web/webserver.scm "$@" diff --git a/gn/db/sources/wikidata.scm b/gn/db/sources/wikidata.scm new file mode 100644 index 0000000..7397426 --- /dev/null +++ b/gn/db/sources/wikidata.scm @@ -0,0 +1,29 @@ +#! + +Wikidata queries + +!# + +(define-module (gn db sources wikidata) +) + +(define ps-encoded-by "ps:P702") +(define wdt-instance-of "wdt:P31") +(define wdt-in-taxon "wdt:P703") +(define wd-human "wd:Q15978631") +(define wd-mouse "wd:Q83310") +(define wd-rat "wd:Q184224") +(define wd-gene "wd:Q7187") + +(define (wikidata_query_geneids gene_name) + "Return the wikidata identifiers pointing to genes of listed species" + (string-append + "SELECT DISTINCT ?wikidata_id + WHERE { + ?wikidata_id " wdt-instance-of " " wd-gene "; + " wdt-in-taxon " ?species . + VALUES (?species) { (" wd-human " ) ( " wd-mouse" ) ( " wd-rat" ) } . + ?wikidata_id rdfs:label \"" gene_name "\"@en . + } +" + )) diff --git a/gn/db/sparql.scm b/gn/db/sparql.scm index b7d94f3..f03389b 100644 --- a/gn/db/sparql.scm +++ b/gn/db/sparql.scm @@ -2,7 +2,7 @@ Module for handling SPARQL primitives. -Note that GN queries should go into gn/data - this is currently not +Note that GN queries should go into gn/db/sources - this is currently not the case. !# @@ -18,6 +18,7 @@ the case. #:use-module (web request) #:use-module (web uri) #:use-module (gn cache memoize) + #:use-module (gn db sources wikidata) #:use-module (web gn-uri) #:export (memo-sparql-species @@ -1,71 +1 @@ -;; To use this file to build HEAD of gn-guile: -;; -;; guix build -f guix.scm -;; -;; To get a development container -;; -;; guix shell -C -D -f guix.scm -;; - -(use-modules - ((guix licenses) #:prefix license:) - (guix gexp) - (guix packages) - (guix git-download) - (guix build-system guile) - (gnu packages algebra) - (gnu packages base) - (gnu packages bash) - (gnu packages compression) - (gnu packages bioinformatics) - (gnu packages build-tools) - (gnu packages certs) - (gnu packages curl) - (gnu packages gcc) - (gnu packages guile) - (gnu packages guile-xyz) - (gnu packages llvm) - (gnu packages ninja) - (gnu packages parallel) - (gnu packages perl) - (gnu packages perl6) - (gnu packages pkg-config) - (gnu packages python) - (gnu packages tls) - (srfi srfi-1) - (ice-9 popen) - (ice-9 rdelim)) - -(define %source-dir (dirname (current-filename))) - -(define %git-commit - (read-string (open-pipe "git show HEAD | head -1 | cut -d ' ' -f 2" OPEN_READ))) - -(define-public gn-guile-git - (package - (name "gn-guile-git") - (version (git-version "4.0.0-" "HEAD" %git-commit)) - (source (local-file %source-dir #:recursive? #t)) - (build-system guile-build-system) - - (inputs - (list guile-3.0-latest bash-minimal perl - guile-dbi guile-dbd-mysql guile-fibers guile-gnutls guile-readline guile-redis openssl nss-certs gemma parallel)) - (propagated-inputs - (list guile-json-4)) - -#! - (arguments - `(#:compile-flags '("--r6rs" "-Wunbound-variable" "-Warity-mismatch") - #:modules ((guix build guile-build-system) - (guix build utils) - (srfi srfi-26) - (ice-9 ftw) - (json)))) -!# - (home-page "https://git.genenetwork.com/gn-guile") - (synopsis "Next generation GN code in guile") - (description "Use of guile.") - (license license:gpl3))) - -gn-guile-git +.guix/modules/gn-guile.scm
\ No newline at end of file diff --git a/scripts/lmdb-publishdata-export.scm b/scripts/lmdb-publishdata-export.scm new file mode 100755 index 0000000..8427112 --- /dev/null +++ b/scripts/lmdb-publishdata-export.scm @@ -0,0 +1,229 @@ +#! /usr/bin/env guile +!# +;; To run this script run: +;; +;; $ guix shell guile guile-hashing guile3-dbi guile3-dbd-mysql \ +;; guile-lmdb -- guile lmdb-publishdata-export.scm +;; conn.scm +;; +;; Example conn.scm: +;; ((sql-username . "webqtlout") +;; (sql-password . "xxxx") +;; (sql-database . "db_webqtl") +;; (sql-host . "localhost") +;; (sql-port . 3306) +;; (output-dir . "/tmp/data") +;; (log-file . "/tmp/export.log")) + +(use-modules (dbi dbi) + (rnrs bytevectors) + (system foreign) + (ice-9 match) + (srfi srfi-1) + (srfi srfi-26) + (srfi srfi-43) + (rnrs io ports) + (hashing md5) + ((lmdb lmdb) #:prefix mdb:) + (ice-9 format) + (ice-9 exceptions) + (json) + (logging logger) + (logging rotating-log) + (logging port-log) + (oop goops)) + + +;; Set up logging +(define* (setup-logging #:key (log-file "lmdb-dump-log")) + "Initialize the logging system with rotating file logs and error port output. + Creates a new logger, adds rotating and error port handlers, + sets it as the default logger, and opens the log for writing." + (let ((lgr (make <logger>)) + (rotating (make <rotating-log> + #:num-files 3 + #:size-limit 1024 + #:file-name log-file)) + (err (make <port-log> #:port (current-error-port)))) + ;; add the handlers to our logger + (add-handler! lgr rotating) + (add-handler! lgr err) + ;; make this the application's default logger + (set-default-logger! lgr) + (open-log! lgr))) + +(define (shutdown-logging) + "Properly shutdown the logging system. + Flushes any pending log messages, closes the log handlers, + and removes the default logger reference." + (flush-log) ;; since no args, it uses the default + (close-log!) ;; since no args, it uses the default + (set-default-logger! #f)) + +(define (call-with-database backend connection-string proc) + "Execute PROC with an open database connection. BACKEND is the +database type (e.g. \"mysql\"). CONNECTION-STRING is the database +connection string." + (let ((db #f)) + (dynamic-wind + (lambda () + (set! db (dbi-open backend connection-string))) + (cut proc db) + (lambda () + (when db + (dbi-close db)))))) + +(define (call-with-target-database connection-settings proc) + "Connect to the target database using CONNECTION-SETTINGS and execute +PROC." + (call-with-database "mysql" (string-join + (list (assq-ref connection-settings 'sql-username) + (assq-ref connection-settings 'sql-password) + (assq-ref connection-settings 'sql-database) + "tcp" + (assq-ref connection-settings 'sql-host) + (number->string + (assq-ref connection-settings 'sql-port))) + ":") + proc)) + +(define* (lmdb-save path key value) + "Save a NUM with KEY to PATH." + (mdb:with-env-and-txn + (path) (env txn) + (let ((dbi (mdb:dbi-open txn #f 0))) + (mdb:put txn dbi key + (if (number? value) + (number->string value) + value))))) + +(define (sql-exec db statement) + "Execute an SQL STATEMENT on database connection DB. Throws an error +if the statement execution fails." + (dbi-query db statement) + (database-check-status db)) + +(define (sql-fold proc init db statement) + "Fold over SQL query results." + (sql-exec db statement) + (let loop ((result init)) + (let ((row (dbi-get_row db))) + (if row + (loop (proc row result)) + result)))) + +(define (sql-for-each proc db statement) + "Apply PROC to each row returned by STATEMENT." + (sql-fold (lambda (row _) + (proc row)) + #f db statement)) + +(define (sql-map proc db statement) + "Map PROC over rows returned by STATEMENT." + (sql-fold (lambda (row result) + (cons (proc row) result)) + (list) db statement)) + +(define (sql-find db statement) + (sql-exec db statement) + (dbi-get_row db)) + +(define (database-check-status db) + "Check the status of the last database operation on DB. Throws an +error if the status code is non-zero." + (match (dbi-get_status db) + ((code . str) + (unless (zero? code) + (error str))))) + +(define* (save-dataset-values settings) + "Main function to extract and save dataset values. Queries the +database for datasets and their values, computes MD5 hashes for +dataset-trait combinations, and saves strain values to LMDB files in +/export5/lmdb-data-hashes/." + (dynamic-wind + (lambda () + (setup-logging #:log-file (assq-ref settings 'log-file)) + (log-msg 'INFO "Starting dataset value extraction")) + (lambda () + (call-with-target-database + settings + (lambda (db) + (sql-for-each + (lambda (row) + (match row + ((("Name" . dataset-name) + ("Id" . trait-id)) + (let* ((data-query (format #f "SELECT +JSON_ARRAYAGG(JSON_ARRAY(Strain.Name, PublishData.Value)) AS data, + MD5(JSON_ARRAY(Strain.Name, PublishData.Value)) as md5hash +FROM + PublishData + INNER JOIN Strain ON PublishData.StrainId = Strain.Id + INNER JOIN PublishXRef ON PublishData.Id = PublishXRef.DataId + INNER JOIN PublishFreeze ON PublishXRef.InbredSetId = PublishFreeze.InbredSetId +LEFT JOIN PublishSE ON + PublishSE.DataId = PublishData.Id AND + PublishSE.StrainId = PublishData.StrainId +LEFT JOIN NStrain ON + NStrain.DataId = PublishData.Id AND + NStrain.StrainId = PublishData.StrainId +WHERE + PublishFreeze.Name = \"~a\" AND + PublishXRef.Id = ~a AND + PublishFreeze.public > 0 AND + PublishData.value IS NOT NULL AND + PublishFreeze.confidentiality < 1 +ORDER BY + LENGTH(Strain.Name), Strain.Name" dataset-name trait-id))) + (match (call-with-target-database + settings + (lambda (db2) (sql-find db2 data-query))) + ((("data" . data) + ("md5hash" . md5-hash)) + (let* ((trait-name (format #f "~a~a" dataset-name trait-id)) + (base-dir (assq-ref settings 'output-dir)) + (out (format #f "~a-~a" trait-name + (substring md5-hash 0 12))) + (out-dir (format #f "~a/~a" base-dir out))) + (log-msg + 'INFO (format #f "Writing ~a to: ~a" trait-name out-dir)) + (unless (file-exists? out-dir) + (mkdir out-dir)) + (lmdb-save (format #f "~a/index" base-dir) trait-name out) + (vector-for-each + (lambda (_ x) + (match x + (#(strain value) + (lmdb-save out-dir strain value)))) + (json-string->scm data))))))))) + db + "SELECT DISTINCT PublishFreeze.Name, PublishXRef.Id FROM +PublishData INNER JOIN Strain ON PublishData.StrainId = Strain.Id +INNER JOIN PublishXRef ON PublishData.Id = PublishXRef.DataId +INNER JOIN PublishFreeze ON PublishXRef.InbredSetId = PublishFreeze.InbredSetId +LEFT JOIN PublishSE ON + PublishSE.DataId = PublishData.Id AND + PublishSE.StrainId = PublishData.StrainId +LEFT JOIN NStrain ON + NStrain.DataId = PublishData.Id AND + NStrain.StrainId = PublishData.StrainId +WHERE + PublishFreeze.public > 0 AND + PublishFreeze.confidentiality < 1 +ORDER BY + PublishFreeze.Id, PublishXRef.Id")))) + (lambda () + (shutdown-logging)))) + +(define main + (match-lambda* + ((_ connection-settings-file) + (save-dataset-values (call-with-input-file connection-settings-file + read))) + ((arg0 _ ...) + (display (format "Usage: ~a CONNECTION-SETTINGS-FILE~%" arg0) + (current-error-port)) + (exit #f)))) + +(apply main (command-line)) diff --git a/web/.guix-shell b/web/.guix-shell deleted file mode 100644 index b4aee2a..0000000 --- a/web/.guix-shell +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash -# -# run with options '-- ./webserver.scm 8091' e.g. -# . .guix-shell -- guile -L .. --fresh-auto-compile --listen=1970 -e main ./webserver.scm 8091 - -echo "Note run: running web-server" - -guix shell guile guile-commonmark guile-fibers guile-json guile-gnutls guile-readline guile-redis openssl nss-certs $* diff --git a/web/css/gn-template-style.css b/web/css/gn-template-style.css new file mode 100644 index 0000000..38893c6 --- /dev/null +++ b/web/css/gn-template-style.css @@ -0,0 +1,39 @@ +* { + box-sizing: border-box; +} + +body { + margin: 0.7em; + display: grid; + grid-template-columns: 9fr 1fr; + grid-gap: 20px; + + font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; + font-style: normal; + font-size: 20px; +} + +#header { + grid-column-start: 1; + grid-column-end: 3; + + background-color: #336699; + color: #FFFFFF; + border-radius: 3px; + min-height: 30px; +} + +#header #header-text { + padding-left: 0.2em; +} + +#main { + grid-column-start: 1; + grid-column-end: 2; + + max-width: 650px; +} + +#main img { + max-width: 650px; +} diff --git a/web/templates/genenetwork.scm b/web/templates/genenetwork.scm new file mode 100644 index 0000000..64e9852 --- /dev/null +++ b/web/templates/genenetwork.scm @@ -0,0 +1,18 @@ +(define-module (web templates genenetwork) + #:use-module (web view markdown) + + #:export (default-gn-template)) + +(define* (default-gn-template path #:optional (title "Default Page Template")) + "Render `PATH' with a default template and styling that fits in with + GeneNetwork's look and feel." + `(html + (head + (meta (@ (charset "UTF-8"))) + (meta (@ (name "viewport") (content "width=device-width, initial-scale=1.0"))) + (title ,title) + (link (@ (rel "stylesheet") (type "text/css") + (href "/css/gn-template-style.css")))) + (body + (header (@ (id "header")) (span (@ (id "header-text")) "GeneNetwork")) + (main (@ (id "main")) ,(markdown-github->sxml path))))) diff --git a/web/view/view.scm b/web/view/view.scm index 4584cf8..4300863 100644 --- a/web/view/view.scm +++ b/web/view/view.scm @@ -10,6 +10,7 @@ #:use-module (web view markdown) #:use-module (web view brand msk) #:use-module (web view brand aging) + #:use-module (web templates genenetwork) #:export (view-brand)) @@ -45,6 +46,9 @@ data to benefit from the power of integrated datasets, please contact:") (define* (view-brand path) (match path ("aging" (view-aging)) + ("gnqa" (default-gn-template + "genenetwork/gn-docs/general/brand/gnqa/gnqa.md" + "GeneNetwork Question and Answer System")) ( _ (msk-html #:info `( ,(markdown-github->sxml "genenetwork/gn-docs/general/brand/msk/home.md") diff --git a/web/webserver.scm b/web/webserver.scm index c0fb9a1..d2a8c8d 100644 --- a/web/webserver.scm +++ b/web/webserver.scm @@ -34,14 +34,14 @@ (getenv "CGIT_REPO_PATH")) (define +info+ - `(("name" . "GeneNetwork REST API") ("version" ,get-version) + `(("name" . "GeneNetwork REST API") ("version" . ,get-version) ("comment" . "This is the official REST API for the GeneNetwork service hosted at https://genenetwork.org/") ("license" ("source code (unless otherwise specified)" . "Affero GNU Public License 3.0 (AGPL3)") ("data (unless otherwise specified)" . "Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)")) ("note" . "This is work in progress (WIP). Note that the final base URL will change! The temporary prefix is:") - ("prefix" ,(prefix)) - ("links" ("species" ,(mk-meta "species"))))) + ("prefix" . ,(prefix)) + ("links" ("species" . ,(mk-meta "species"))))) (define +info-meta+ `(("doc" ,(mk-html "info")) @@ -87,9 +87,9 @@ otherwise search for set/group data" (modified (and stat (make-time time-utc 0 (stat:mtime stat))))) - (list `((content-type ,(assoc-ref file-mime-types - (file-extension file-name))) - (last-modified ,(time-utc->date modified))) + (list `((content-type . ,(assoc-ref file-mime-types + (file-extension file-name))) + (last-modified . ,(time-utc->date modified))) (call-with-input-file file-name get-bytevector-all)))) @@ -100,9 +100,9 @@ otherwise search for set/group data" (modified (and stat (make-time time-utc 0 (stat:mtime stat))))) - (list `((content-type ,(assoc-ref file-mime-types - (file-extension path))) - (last-modified ,(time-utc->date modified))) + (list `((content-type . ,(assoc-ref file-mime-types + (file-extension path))) + (last-modified . ,(time-utc->date modified))) (call-with-input-file path get-bytevector-all)))) @@ -172,8 +172,8 @@ otherwise search for set/group data" (lambda (key . args) (let ((msg (car args))) (build-json-response 400 - `(("error" ,key) - ("msg" ,msg))))))) + `(("error" . ,key) + ("msg" . ,msg))))))) (define (invalid-data? data target) (if (string? (assoc-ref data target)) @@ -214,8 +214,8 @@ otherwise search for set/group data" (lambda (key . args) (let ((msg (car args))) (build-json-response 400 - `(("error" ,key) - ("msg" ,msg))))))) + `(("error" . ,key) + ("msg" . ,msg))))))) (define (controller request body) (match-lambda @@ -224,13 +224,13 @@ otherwise search for set/group data" (('GET "version") (render-json get-version)) (('GET "css" fn) - (render-static-file (string-append "css/" fn))) + (render-static-file (string-append (dirname (current-filename)) "/css/" fn))) (('GET "map" fn) - (render-static-file (string-append "css/" fn))) + (render-static-file (string-append (dirname (current-filename)) "/css/" fn))) (('GET "static" "images" fn) - (render-static-image (string-append "static/images/" fn))) + (render-static-image (string-append (dirname (current-filename)) "/static/images/" fn))) (('GET "home" path) - (render-brand path)) + (render-brand path)) ; branding route for /home/aging, /home/msk etc (('GET "doc" "species.html") (render-doc "doc" "species.html" (get-species-meta))) |