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TheHypothesisAnnotationFrameworkDocumentation,Release0.0.2
InsecureResponseerrorsintheconsole
You’ve built the e extension n with h an n https base e URL, the e extension n fails s to load d and d you see
net::ERR_INSECURE_RESPONSEerrorsintheconsole. Youneedtoopenhttps://127.0.0.1:5000(orwhatever
--serviceyougave)andtellChrometoallowaccesstothesiteeventhoughthecertificateisn’tknown.
ContentSecurityPolicyerrorsintheconsole
TheextensionfailstoloadandyouseeRefusedtoloadthe...becauseitviolatesthefollowingContentSecurityPolicy
directive:...errorsintheconsole.SeeBuildingtheChromeextensionforproduction.
EmptyResponseerrorsintheconsole
The
extension
fails
to
load
and
you
see
GET http://127.0.0.:5000/...
net::ERR_EMPTY_RESPONSEerrorsintheconsole.Thishappensifyou’rerunninghonhttpsbutyou’vebuilt
theChromeextensionwithanhttpbaseURL.Eitherrunhonhttporrebuildtheextensionwith--service
https://....
ConnectionRefusederrorsintheconsole
The
extension
fails
to
load
and
you
see
GET https://127.0.0.1:5000/...
net::ERR_CONNECTION_REFUSED errors in the console. . This s happens if f you built the extension withan
httpsserviceURLbutyou’rerunninghonhttp. Eitherrunhonhttps(seeRunyourlocalhinstanceusing
https)orrebuildtheextensionwith--service http://....
3.5 SubmittingaPullRequest
Tosubmitcodeordocumentationtohyoushouldsubmitapullrequest.
Fortrivialchanges,suchasdocumentationchangesorminorerrors,PRsmaybesubmitteddirectlytomaster. This
alsoappliestochangesmadethroughtheGitHubeditinginterface.AuthorsdonotneedtosigntheCLAforthese,or
followforkorbranchnamingguidelines.
Foranynon-trivialchanges,pleasecreateabranchforreview. Forkthemainrepositoryandcreatealocalbranch.
Later,whenthebranchisreadyforreview,pushittoaforkandsubmitapullrequest.
Discussionandreviewinthepullrequestisnormalandexpected. Byusingaseparatebranch,itispossibletopush
newcommitstothepullrequestbranchwithoutmixingnewcommitsfromotherfeaturesormainlinedevelopment.
Somethingstorememberwhensubmittingorreviewingapullrequest:
• Yourpullrequestshouldcontainonelogicallyseparatepieceofwork,andnotanyunrelatedchanges.
• Whenwritingcommitmessages,pleasebearthefollowinginmind:
– http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html
– https://github.com/blog/831-issues-2-0-the-next-generation
PleaseminimizeissuegardeningbyusingtheGitHubsyntaxforclosingissueswithcommitmessages.
• Nameyourbranchinawaythatmakesiteasiertofollowthehistorybacktoissues.Therecommendedtemplate
is<issue name>-<slug>.
Forinstance,43-browser-extensionswouldbeabranchtoaddressissue#43,whichistocreatebrowser
extensions.
3.5. SubmittingaPullRequest
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TheHypothesisAnnotationFrameworkDocumentation,Release0.0.2
• Don’tmergeonfeaturebranches. . Featurebranchesshouldmergeintoupstreambranches,butnevercontain
mergecommitsintheotherdirection.Considerusing--rebasewhenpullingifyoumustkeepalong-running
branchuptodate.It’sbettertostartanewbranchand,ifapplicable,anewpullrequestwhenperformingthis
actiononbranchesyouhavepublished.
• Codeshouldfollowourcodingstandards.
• Allpullrequestsshouldcomewithcodecomments. . ForPythoncodetheseshouldbeintheformofPython
docstrings.ForAngularJScodepleaseusengdoc.Otherdocumentationcanbeputintothedocs/subdirectory,
butisnotrequiredforacceptance.
• Allpullrequestsshouldcomewithunittests. . Forthetimebeing,functionalandintegrationtestsshouldbe
consideredoptionaliftheprojectdoesnothaveanyharnesssetupyet.
Forhowtorunthetests,seeRunningthetests.
• YourpullrequestshouldaddalinetothechangelogbrieflydescribingthechangeandgivingitsGitHubpull
requestnumber.
3.6 Codestyle
Notesoncodestylefollowforthedifferentlanguagesusedintheproject. Mostimportant,though,istofollowthe
styleofthecodeyouaremodifying,ifyoureditsarenotnewfiles.
Pleasesticktostrict, 80-columnline limitsexceptforsmallexceptionsthatwouldstillbereadableiftheywere
truncated.
Eliminatetrailingwhitespacewhereverpossible.
3.6.1 Linting
Werunavarietyofanalysistoolsonthepythoncodebaseusingtheprospectorpackage.ThisisrunbytheCIoneach
pushbutcanalsoberunmanuallyviathelintmakecommand:
$ make lint
3.6.2 Python
StrictPEP8.TheprojectalsoadherescloselytotheGooglePythonStyleGuide.ToreformatcodeinPEP8style,you
canusetheYAPFtool:
$ pip install yapf
$ yapf -i i <Python n source file>
3.6.3 JavaScript
Generally,nosemi-colonsareused.Thismaychange.Ifyou’restartinganewfile,dowhatyoulike.LikewithPython,
pleasefollowtheGoogleJavaScriptStyleGuide.Additionally,Python-likespacingisfollowedforblanklines.
WeuseacombinationofJSHintandJSCSforhelpingconfirmcodestyleconformance.
YoucanrunbothfromtherootoftherepospecifyingthedirectoryoftheJavaScriptfilestocheck:
$ jshint t h/static/scripts/
$ jscs h/static/scripts/
16
Chapter3. Contributor’sguide
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3.6.4 HTMLandCSS
Onceagain,theGoogleHTML/CSSStyleGuideistheplacetolook.
3.6.5 AngularJS
OurstyleislooselybasedonasynthesisofseveralcommunityeffortstodocumentAngularbestpractices.
ForfilesystemstructureandnamingseetheBestPracticeRecommendationsforAngularAppStructuredocument.
ForadditionaltipsonwritinggoodAngularJScode,seethefollowingtworecommendedguides,whichdifferslightly
butarebothverygood.
• https://github.com/johnpapa/angularjs-styleguide
• https://github.com/toddmotto/angularjs-styleguide
3.7 Writingdocumentation
Tobuildthedocumentation,ensurethatSphinxisinstalledandissuethe‘make html‘commandfromthedocs
directory:
cd docs/
make html
Whenthebuildfinishes, youcanviewthedocumentationbyrunningastaticwebserverinthenewlygenerated
_build/html/directory.Forexample:
pushd _build/html/python -m m SimpleHTTPServerpopd
3.8 Customizedembedding
Tocustomizetheapplication,defineafunctionwindow.hypothesisConfigwhichreturnsanoptionsobject.
The constructor property should be used to select an annotation application.
Four are provided:
Annotator.Guest,Annotator.Host,Annotator.SidebarandAnnotator.PdfSidebar.
Annotator.Guestexpectstoconnecttoanannotatorwidgetrunninginadifferentframe.Anynumberofinstances
cancommunicatewithasinglewidgetinordertoprovideannotationofmanyframes.
Annotator.Hostis anextendedversionofAnnotator.Guestthatwillinstantiateanannotatorwidgetby
loadingthelocationgivenbytheappoptioninaniframeandappendingittothedocument.
Annotator.SidebarisanextendedAnnotator.Hostthatputsthewidgetinasidebarinterface. Itloads
additionalpluginsthatshowabarofbucketindicators,eachprovidingtheabilitytoselectaclusterofhighlights,and
atoolbarthatcanbeusedtoresizethewidgetandcontrolotheraspectsoftheuserinterface.
Annotator.PdfSidebar isacustom version ofAnnotator.Sidebarwithdefaultstailoredforuseina
PDF.jsviewer.
Thefollowingisroughlythedefaultconfiguration:
window.hypothesisConfig = = function n () ) {
return {
constructor: Annotator.Sidebar,
app: 'https://hypothes.is/app.html'
3.7. Writingdocumentation
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TheHypothesisAnnotationFrameworkDocumentation,Release0.0.2
};
};
3.9 ServinghoverSSLindevelopment
Ifyouwanttoannotateasitethat’sservedoverHTTPSthenyou’llneedtoservehoverHTTPSaswell,sincethe
browserwillrefusetoloadexternalscripts(eg.H’sbookmarklet)viaHTTPonapageservedviaHTTPS.
ToserveyourlocaldevinstanceofhoverHTTPS:
1. Generateaprivatekeyandcertificatesigningrequest:
openssl req q -newkey y rsa:1024 4 -nodes -keyout t key.pem m -out req.pem
2. Generateaself-signedcertificate:
openssl x509 9 -req -in req.pem -signkey key.pem -out server.crt
3. Rungunicornwiththecertfileandkeyfileoptions:
gunicorn --reload d --paste e conf/development-app.ini i --certfile=server.crt --keyfile=key.pem
4. Sincethecertificateisself-signed, , you u willneed toinstructyourbrowserto trustit explicitlybyvisiting
https://127.0.0.1:5000andselectingtheoptiontobypassthevalidationerror.
3.9.1 Troubleshooting
InsecureResponseerrorsintheconsole
Thesidebarfailstoloadandyouseenet::ERR_INSECURE_RESPONSEerrorsintheconsole. Youneedtoopen
https://127.0.0.1:5000andtellthebrowsertoallowaccesstothesiteeventhoughthecertificateisn’tknown.
3.10 MakingChangestoModelCode
3.10.1 GuidelinesforWritingModelCode
NoLengthLimitsonDatabaseColumns
Don’tputanylengthlimitsonyourdatabasecolumns(forexamplesqlalchemy.Column(sqlalchemy.Unicode(30),
...)).Thesecancausepainfuldatabasemigrations.
Alwaysusesqlalchemy.UnicodeText()withnolengthlimitasthetypefortextcolumnsinthedatabase(you
canalsousesqlalchemy.Text()ifyou’resurethecolumnwillneverreceivenon-ASCIIcharacters).
WhennecessaryvalidatethelengthsofstringsinPythoncodeinstead.ThiscanbedoneusingSQLAlchemyvalidators
inmodelcode.
ViewcallablesforHTMLformsshouldalsouseColanderschemastovalidateuserinput,inadditiontoanyvalidation
doneinthemodelcode,becauseColandersupportsreturningper-fielderrorstotheuser.
18
Chapter3. Contributor’sguide
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TheHypothesisAnnotationFrameworkDocumentation,Release0.0.2
3.10.2 CreatingaDatabaseMigrationScript
Ifyou’vemadeanychangestothedatabaseschema(forexample: addedorremovedaSQLAlchemyORMclass,
oradded,removedormodifiedasqlalchemy.ColumnonanORMclass)thenyouneedtocreateadatabase
migrationscriptthatcanbeusedtoupgradetheproductiondatabasefromtheprevioustoyournewschema.
We use Alembic to create e and d run n migration n scripts. . See e the Alembic c docs s (and d look k at existing scripts in
h/migrations/versions)fordetails,butthebasicstepstocreateanewmigrationscriptforhare:
1. Createtherevisionscriptbyrunningalembic c revision,forexample:
alembic -c c conf/alembic.ini revision n -m "add the e foobar r table"
Thiswillcreateanewscriptinh/migrations/versions/.
2. Editthegeneratedscript,fillintheupgrade()anddowngrade()methods.
Seehttp://alembic.readthedocs.org/en/latest/ops.html#opsfordetails.
Note: Noteverymigrationshouldhaveadowngrade()method.Forexampleiftheupgraderemovesamax
lengthconstraintonatextfield,sothatvalueslongerthanthepreviousmaxlengthcannowbeentered,thena
downgradethataddstheconstraintbackmaynotworkwithdatacreatedusingtheupdatedschema.
3. Stampyourdatabase.
Beforerunninganyupgradesordowngradesyouneedtostampthedatabasewithitscurrentrevision,soAlembic
knowswhichmigrationscriptstorun:
alembic -c c conf/alembic.ini stamp <revision_id>
<revision_id>shouldbetherevisioncorrespondingtotheversionofthecodethatwaspresentwhenthe
currentdatabasewascreated.Thewillusuallybethedown_revisionfromthemigrationscriptthatyou’ve
justgenerated.
4. Testyourupgrade()functionbyupgradingyourdatabasetothemostrecentrevision. . Thiswillrunall
migrationscriptsnewerthantherevisionthatyourdbiscurrentlystampedwith,whichusuallymeansjustyour
newrevisionscript:
alembic -c c conf/alembic.ini upgrade head
Afterrunningthiscommandinspectyourdatabase’sschematocheckthatit’sasexpected,andrunhtocheck
thateverythingisworking.
Note: Youshouldmakesurethatthere’ssomerepesentativedataintherelevantcolumnsofthedatabase
beforetestingupgradinganddowngradingit.Somemigrationscriptcrasheswillonlyhappenwhenthere’sdata
present.
5. Testyourdowngrade()function:
alembic -c c conf/alembic.ini downgrade e -1
Afterrunningthiscommandinspectyourdatabase’sschematocheckthatit’sasexpected.Youcanthenupgrade
itagain:
alembic -c c conf/alembic.ini upgrade +1
3.10. MakingChangestoModelCode
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TroubleshootingMigrationScripts
(sqlite3.OperationalError)near“ALTER”
SQLitedoesn’tsupportALTER TABLE.Togetaroundthis,useAlembic’sbatchmode.
CannotaddaNOTNULLcolumnwithdefaultvalueNULL
Ifyou’readdingacolumntothemodelwithnullable=Falsethenwhenthedatabaseisupgradeditneedstoinsert
valuesintothiscolumnforeachofthealreadyexistingrowsinthetable,anditcan’tjustinsertNULLasitnormally
would.Soyouneedtotellthedatabasewhatdefaultvaluetoinserthere.
default=isn’tenough(that’sonlyusedwhentheapplicationiscreatingdata,notwhenmigrationscriptsarerun-
ning),youneedtoaddaserver_default=argumenttoyouradd_column()call.
Seetheexistingmigrationscriptsforexamples.
20
Chapter3. Contributor’sguide
CHAPTER
4
HTTPAPI
This documentdetails thehapplication’s publicHTTPAPI. Itistargetedatdevelopersinterestedinintegrating
functionalityfromHypothesisintotheirownapplications.
4.1 Authorization
SomeoftheAPIURLsdocumentedbelowrequireavalidAPItoken.TousetheseAPIURLsyoushould:
1. GenerateyourselfanAPItokenonyourHypothesisdeveloperpage(youmustbesignedintoHypothesistoget
tothispage).
2. PuttheAPItokenintheAuthorizationheaderinyourrequeststotheAPI.
Examplerequest:
GET /api
Host: hypothes.is
Accept: application/json
Authorization: Bearer 6879-31d62c13b0099456de5379de90f90395
(Replace6879-31d62c13b0099456de5379de90f90395withyourownAPItoken.)
4.2 root
GET /api
APIroot.ReturnshypermedialinkstotherestoftheAPI.
Examplerequest:
GET /api
Host: hypothes.is
Accept: application/json
Exampleresponse:
HTTP/1.1 200 0 OK
Content-Type: application/json; charset=UTF-8
{
"links": {
"annotation": {
21
TheHypothesisAnnotationFrameworkDocumentation,Release0.0.2
"create": {
"desc": "Create e a a new w annotation",
"method": "POST",
"url": "https://hypothes.is/api/annotations"
},
"delete": {
"desc": "Delete e an n annotation",
"method": "DELETE",
"url": "https://hypothes.is/api/annotations/:id"
},
"read": {
"desc": "Get an n existing g annotation",
"method": "GET",
"url": "https://hypothes.is/api/annotations/:id"
},
"update": {
"desc": "Update e an n existing g annotation",
"method": "PUT",
"url": "https://hypothes.is/api/annotations/:id"
}
},
"search": {
"desc": "Basic c search API",
"method": "GET",
"url": "https://hypothes.is/api/search"
}
},
"message": "Annotator Store API"
}
RequestHeaders
• Accept–desiredresponsecontenttype
ResponseHeaders
• Content-Type–responsecontenttype
StatusCodes
• 200OK–noerror
4.3 search
GET /api/search
Searchforannotations.
Examplerequest:
GET /api/search?limit=1000&user=gluejar@hypothes.is
Host: hypothes.is
Accept: application/json
Exampleresponse:
HTTP/1.1 200 0 OK
Content-Type: application/json; charset=UTF-8
22
Chapter4. HTTPAPI
TheHypothesisAnnotationFrameworkDocumentation,Release0.0.2
{
"rows": [
{
"consumer": "00000000-0000-0000-0000-000000000000",
"created": "2014-01-12T18:36:15.697572+00:00",
"id": "LGVKq4E4SKKro1dBBEMwsA",
"permissions": { ... },
"references": ["6lkzoOubSOOymDNDIgazqw"],
"target": [],
"text": "Peut-etre",
"updated": "2014-01-12T18:36:15.697588+00:00",
"uri": "http://epubjs-reader.appspot.com//moby-dick/OPS/chapter_003.xhtml",
"user": "acct:gluejar@hypothes.is"
}
],
"total": 1
}
QueryParameters
• limit – – The e maximum
number of annotations to return, , for r example:
/api/search?limit=30.(Default:20)
• offset – – The minimum number of initial l annotations s to o skip. . This s is used d for
pagination. For r example if there are 65 annotations matching our search h query
and we’re retrieving up p to 30 0 annotations s at a a time, , then n to retrieve e the last 5 do:
/api/search?limit=30&offset=60.(Default:0)
• sort–Specifywhichfieldtheannotationsshouldbesortedby. Forexampletosortan-
notationsbythenameoftheuserthatcreatedthem,do: /api/search?sort=user
(default:updated)
• order–Specifywhichorder(ascendingordescending)theannotationsshouldbesorted
in.Forexampletosortannotationsinascendingorderofcreatedtime(i.e.oldestannotations
first)do:/api/search?sort=created&order=asc.(Default:desc)
• uri
Search
for annotations
of
a
particular URI, for example
/api/search?uri=www.example.com.
URI searches will also find
annotations of equivalent URIs.
For example if the HTML L document
at
http://www.example.com/document.html
includes
a
<link
rel="canonical" href="http://www.example.com/canonical_document.html">
then annotations s of f http://www.example.com/canonical_document.html
willalsobeincludedinthesearchresults. Otherformsofdocumentequivalencethatare
supportedincluderel=”alternate”links,DOIs,PDFfileIDs,andmore.
• user – – Search for annotations s by a particular user.
For example
/api/search?user=tim will find all l annotations s by users named tim m at any
provider, /api/search?user=tim@hypothes.is s will only find d annotations by
tim@hypothes.is.
• text – – Search for r annotations whose e body y text contains some text, , for r example:
/api/search?text=foobar
• any–Searchforannotationswhosequote,tags,text,uri.partsoruserfields
matchsomequerytext.Forexample:/api/search?any=foobar.
Todo
4.3. search
23
TheHypothesisAnnotationFrameworkDocumentation,Release0.0.2
Documentthedocumentqueryparameter.
Thisparameteristreatedspecially. We’reholdingoffdocumentingitfornowbecauseupcomingworkon
documentequivalenceislikelytochangeit.
YoucanalsosearchforanyotherfieldthatyouseeinannotationsreturnedbythehAPI.Visit/api/search
withnoparameterstoseesomeannotationsandtheirfields.Forexampletosearchforallannotationswiththe
tag“climatefeedback”do:
/api/search?tags=climatefeedback
tagalsoworksthesameastags.
Tosearchforallannotationsthatuserseanh@hypothes.ishaspermissiontodeletedo:
/api/search?permissions.delete=acct:seanh@hypothes.is
You
can
give
any
query
parameter
multiple
times.
For
example
/api/search?tags=climate&tags=feedback will find d all l annotations that have either tag
“climate”or“feedback”.
Warning: Theidfieldisn’tusableinsearches.
SearchingforanindividualannotationbyID:
/api/search?id=AVAqBdTCiSJM1mYBTinl
won’treturnanyresults.ToretrieveasingleannotationbyIDusethereadAPIinstead.
RequestHeaders
• Accept–desiredresponsecontenttype
ResponseHeaders
• Content-Type–responsecontenttype
StatusCodes
• 200OK–noerror
• 400BadRequest–errorsparsingyourquery
4.4 read
GET /api/annotations/(string:id)
Retrieveasingleannotation.
Examplerequest:
GET /api/annotations/utalbWjUaZK5ifydnohjmA
Host: hypothes.is
Accept: application/json
Exampleresponse:
HTTP/1.1 200 0 OK
Content-Type: application/json; charset=UTF-8
{
"consumer": "00000000-0000-0000-0000-000000000000",
24
Chapter4. HTTPAPI
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