Error: user-error ("Org export aborted. Unable to resolve link: \"introduction\"
See `org-export-with-broken-links'")
signal(user-error ("Org export aborted. Unable to resolve link: \"introduction\"\nSee `org-export-with-broken-links'"))
user-error("Org export aborted. Unable to resolve link: %S\nSee `org-export-with-broken-links'" "introduction")
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This means that at any point in the future the exact same data\ncan be retrieved using a known non-changeable identifier (see also\n" 0 398 (:parent #43)) (link (:standard-properties [1540 nil nil nil 1611 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "https" :type-explicit-p t :path "//github.com/pjotrp/genenetwork2/blob/staging/doc/submit-data.org" :format plain :raw-link "https://github.com/pjotrp/genenetwork2/blob/staging/doc/submit-data.org" :application nil :search-option nil)) #(").\n" 0 3 (:parent #43))) (paragraph (:standard-properties [1615 1615 1615 1949 1950 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Synchronisation, integrity checking and backups become trivial using\nthese HASH values, even for very large datasets. Since everything is\nmanaged at the file system level we can also use Unix authorisation\nsystems. HIPAA compliancy is achieved by using HASH references and\nbringing the software into the controlled HIPAA environment.\n" 0 334 (:parent #44))) (paragraph (:standard-properties [1950 1950 1950 2419 2420 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("In the context of GeneNetwork we are using git for version control of\nsoftware source code (" 0 92 (:parent #45)) (link (:standard-properties [2042 nil nil nil 2073 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "https" :type-explicit-p t :path "//github.com/genenetwork/" :format plain :raw-link "https://github.com/genenetwork/" :application nil :search-option nil)) #("). Software can\nbe treated just like data, i.e., git uses HASH identifiers to retrieve\nspecific versions of source. I.e., versions of source code are\nidentifiable and retrievable and can be matched with data into an\nanalysis pipeline. The combination of software and data, again, makes\na unique HASH value which identifies the analysis pipeline.\n" 0 346 (:parent #45))) (paragraph (:standard-properties [2420 2420 2420 3231 3232 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("For combining runnable software and data into an analysis pipeline we\nuse GNU Guix which, yet again, turns everything into a unique HASH\nvalue which allows for exact retrieval and reproducibility. Not only\nthat, GNU Guix gives control of the software and all its dependencies,\nuse GNU Guix which, yet again, turns everything into a unique HASH\nvalue which allows for exact retrieval and reproducibility. Not only\nthat, GNU Guix gives control of the software and all its dependencies,\ncalculating a HASH value for all dependencies, all the way down to\nversions of R, BLAS and glibc. This way of packaging software\nascertains that identical software pipelines are easily setup on\ndifferent system or in the Cloud. Meaning that everyone ends up using\nthe exact same combination of software versions in a pipeline.\n" 0 811 (:parent #46))) (paragraph (:standard-properties [3232 3232 3232 3924 3925 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("For software development we use GNU Guix for integration testing and\ndeployment (described in JOSS paper). We also use automated test tools\n(Ruby mechanize) for integration testing of the web services and we\nuse unit testing of all backend services. All our software source code\nis published as `free and open source software' (FOSS) which means\nthat anyone can view code on github, comment on, or even contribute\nto. 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The routing\ntables are defined in " 0 60 (:parent #43)) (link (:standard-properties [4249 nil 4333 4341 4343 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "https" :type-explicit-p t :path "//github.com/genenetwork/genenetwork2/blob/master/wqflask/wqflask/views.py" :format bracket :raw-link "https://github.com/genenetwork/genenetwork2/blob/master/wqflask/wqflask/views.py" :application nil :search-option nil) #("views.py" 0 8 (:parent #53))) #(". For example the main page is loaded\nfrom a template named " 0 60 (:parent #43)) (link (:standard-properties [4403 nil 4503 4518 4521 1 nil nil nil nil nil nil nil nil # nil nil #43] :type "https" :type-explicit-p t :path "//github.com/genenetwork/genenetwork2/blob/master/wqflask/wqflask/templates/index_page.htm" :format bracket :raw-link "https://github.com/genenetwork/genenetwork2/blob/master/wqflask/wqflask/templates/index_page.htm" :application nil :search-option nil) #("index" 0 5 (:parent #55)) (subscript (:standard-properties [4508 nil 4509 4518 4518 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("page.html" 0 9 (:parent #59)))) #("in the " 0 7 (:parent #43)) (link (:standard-properties [4528 nil 4613 4622 4625 1 nil nil nil nil nil nil nil nil # nil nil #43] :type "https" :type-explicit-p t :path "//github.com/genenetwork/genenetwork2/tree/master/wqflask/wqflask/templates" :format bracket :raw-link "https://github.com/genenetwork/genenetwork2/tree/master/wqflask/wqflask/templates" :application nil :search-option nil) #("templates" 0 9 (:parent #57))) #("directory. In\nthe template you can find get the form gets filled by a Javascript\nroutine defined in " 0 100 (:parent #43)) (link (:standard-properties [4725 nil 4845 4864 4867 1 nil nil nil nil nil nil nil nil # nil nil #43] :type "https" :type-explicit-p t :path "//github.com/genenetwork/genenetwork2/blob/master/wqflask/wqflask/static/new/javascript/dataset_select_menu.js" :format bracket :raw-link "https://github.com/genenetwork/genenetwork2/blob/master/wqflask/wqflask/static/new/javascript/dataset_select_menu.js" :application nil :search-option nil) #("data" 0 4 (:parent #59)) (subscript (:standard-properties [4849 nil 4850 4856 4856 0 nil nil nil nil nil nil nil nil # nil nil #59] :use-brackets-p nil) #("select" 0 6 (:parent #63))) (subscript (:standard-properties [4856 nil 4857 4864 4864 0 nil nil nil nil nil nil nil nil # nil nil #59] :use-brackets-p nil) #("menu.js" 0 7 (:parent #64)))) #("which picks up a static JSON\nfile for the menu. This static file is generated with\n" 0 83 (:parent #43)) (link (:standard-properties [4950 nil 5051 5072 5074 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "https" :type-explicit-p t :path "//github.com/genenetwork/genenetwork2/blob/master/wqflask/maintenance/gen_select_dataset.py" :format bracket :raw-link "https://github.com/genenetwork/genenetwork2/blob/master/wqflask/maintenance/gen_select_dataset.py" :application nil :search-option nil) #("gen" 0 3 (:parent #61)) (subscript (:standard-properties [5054 nil 5055 5061 5061 0 nil nil nil nil nil nil nil nil # nil nil #61] :use-brackets-p nil) #("select" 0 6 (:parent #65))) (subscript (:standard-properties [5061 nil 5062 5072 5072 0 nil nil nil nil nil nil nil nil # nil nil #61] :use-brackets-p nil) #("dataset.py" 0 10 (:parent #66)))) #(". Note that this JSON data is served by\ngn" 0 43 (:parent #43)) (subscript (:standard-properties [5117 nil 5118 5124 5125 1 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("server" 0 6 (:parent #63))) #("in the latest version, see " 0 27 (:parent #43)) (link (:standard-properties [5152 nil 5170 5185 5187 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "custom-id" :type-explicit-p nil :path "gnserver-rest" :format bracket :raw-link "#gnserver-rest" :application nil :search-option nil) #("GnServer (REST)" 0 15 (:parent #65))) #(".\n" 0 2 (:parent #43))) (paragraph (:standard-properties [5190 5190 5190 5895 5896 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("When you hit a search with, for example,\n'http://localhost:5003/search?species=mouse&group=BXD&type=Hippocampus+mRNA&dataset=HC" 0 127 (:parent #44)) (subscript (:standard-properties [5317 nil 5318 5320 5320 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("M2" 0 2 (:parent #48))) (subscript (:standard-properties [5320 nil 5321 5325 5325 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("0606" 0 4 (:parent #49))) (subscript (:standard-properties [5325 nil 5326 5327 5327 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("P" 0 1 (:parent #50))) #("&search" 0 7 (:parent #44)) (subscript (:standard-properties [5334 nil 5335 5340 5340 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("terms" 0 5 (:parent #52))) (subscript (:standard-properties [5340 nil 5341 5343 5343 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("or" 0 2 (:parent #53))) #("=&search" 0 8 (:parent #44)) (subscript (:standard-properties [5351 nil 5352 5357 5357 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("terms" 0 5 (:parent #55))) (subscript (:standard-properties [5357 nil 5358 5361 5361 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("and" 0 3 (:parent #56))) #("=MEAN%3D%2815+16%29+LRS%3D%2823+46%29+&FormID=searchResult'\nit has the menu items as parameters. According to the routing table,\nthe search is executed and Redis caching is used (we'll probably\nchange that to the level of the gn" 0 228 (:parent #44)) (subscript (:standard-properties [5589 nil 5590 5596 5596 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("server" 0 6 (:parent #58))) #("). The logic is in\nsearch" 0 25 (:parent #44)) (subscript (:standard-properties [5621 nil 5622 5631 5632 1 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("result.py" 0 9 (:parent #60))) #("which invokes database functions in\nwqflask/dbFunction/webqtlDatabaseFunction.py, for example. The\nreceiving template lives at " 0 127 (:parent #44)) (link (:standard-properties [5759 nil 5868 5891 5893 0 nil nil nil nil nil nil nil nil # nil nil #44] :type "https" :type-explicit-p t :path "//github.com/genenetwork/genenetwork2/blob/master/wqflask/wqflask/templates/search_result_page.html" :format bracket :raw-link "https://github.com/genenetwork/genenetwork2/blob/master/wqflask/wqflask/templates/search_result_page.html" :application nil :search-option nil) #("search" 0 6 (:parent #62)) (subscript (:standard-properties [5874 nil 5875 5881 5881 0 nil nil nil nil nil nil nil nil # nil nil #62] :use-brackets-p nil) #("result" 0 6 (:parent #66))) (subscript (:standard-properties [5881 nil 5882 5891 5891 0 nil nil nil nil nil nil nil nil # nil nil #62] :use-brackets-p nil) #("page.html" 0 9 (:parent #67)))) #(".\n" 0 2 (:parent #44))) (paragraph (:standard-properties [5896 5896 5896 5957 5958 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("For what happens at the database level see " 0 43 (:parent #45)) (link (:standard-properties [5939 nil nil nil 5955 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "fuzzy" :type-explicit-p nil :path "database.org" :format bracket :raw-link "database.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #45))) (paragraph (:standard-properties [5958 5958 5958 6563 6564 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("A view consists of an HTML template with JS libraries for managing\nmenus, tables etc. For example, for the search results see the\n" 0 130 (:parent #46)) (link (:standard-properties [6088 nil 6197 6220 6223 1 nil nil nil nil nil nil nil nil # nil nil #46] :type "https" :type-explicit-p t :path "//github.com/genenetwork/genenetwork2/blob/master/wqflask/wqflask/templates/search_result_page.html" :format bracket :raw-link "https://github.com/genenetwork/genenetwork2/blob/master/wqflask/wqflask/templates/search_result_page.html" :application nil :search-option nil) #("search" 0 6 (:parent #50)) (subscript (:standard-properties [6203 nil 6204 6210 6210 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("result" 0 6 (:parent #54))) (subscript (:standard-properties [6210 nil 6211 6220 6220 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("page.html" 0 9 (:parent #55)))) #("which is a Flask template. The first section\nputs the search in plain English, e.g. 'We searched Hippocampus\nConsortium M430v2 (Jun06) PDNN to find all records with MEAN between\n15 and 16 and with LRS between 23 and 46.'. Then the results are added\nto a table which is displayed using a JS " 0 290 (:parent #46)) (link (:standard-properties [6513 nil 6540 6559 6561 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "https" :type-explicit-p t :path "//datatables.net/" :format bracket :raw-link "https://datatables.net/" :application nil :search-option nil) #("DataTable container" 0 19 (:parent #52))) #(".\n" 0 2 (:parent #46))))) (headline (:standard-properties [6564 6564 6583 7139 7139 0 (:title) nil nil nil nil 6585 7137 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 17) t] :title (#("GnServer (REST)" 0 15 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6583 6583 6583 7139 7139 0 nil section nil nil nil 6583 7139 nil # nil nil #38]) (paragraph (:standard-properties [6583 6583 6583 6905 6906 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("The " 0 4 (:parent #44)) (link (:standard-properties [6587 nil 6631 6648 6651 1 nil nil nil nil nil nil nil nil # nil nil #44] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn_server" :format bracket :raw-link "https://github.com/genenetwork/gn_server" :application nil :search-option nil) #("GnServer REST API" 0 17 (:parent #48))) #("is built on high performance " 0 29 (:parent #44)) (link (:standard-properties [6680 nil 6707 6713 6716 1 nil nil nil nil nil nil nil nil # nil nil #44] :type "http" :type-explicit-p t :path "//elixir-lang.org/" :format bracket :raw-link "http://elixir-lang.org/" :application nil :search-option nil) #("Elixir" 0 6 (:parent #50))) #("with " 0 5 (:parent #44)) (link (:standard-properties [6721 nil 6755 6759 6761 0 nil nil nil nil nil nil nil nil # nil nil #44] :type "https" :type-explicit-p t :path "//github.com/falood/maru" :format bracket :raw-link "https://github.com/falood/maru" :application nil :search-option nil) #("Maru" 0 4 (:parent #52))) #(".\nMainly the GnServer serves JSON requests, for example to fetch data\nfrom the database. To get the menu data in YAML you can do something like\n" 0 144 (:parent #44))) (fixed-width (:standard-properties [6906 6906 nil nil 6972 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "curl localhost:8880/int/menu/main.json|ruby extra/json2yaml.rb")) (paragraph (:standard-properties [6972 6972 6972 7138 7139 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("(json2yaml.rb is in the gn" 0 26 (:parent #46)) (subscript (:standard-properties [6998 nil 6999 7005 7006 1 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("server" 0 6 (:parent #50))) #("repo). 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