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a=i.state.selectValue;i.onChange(vo(i.props.isMulti,[],null),{action:"clear",removedValues:a})},i.popValue=function(){var a=i.props.isMulti,s=i.state.selectValue,c=s[s.length-1],d=s.slice(0,s.length-1),h=vo(a,d,d[0]||null);i.onChange(h,{action:"pop-value",removedValue:c})},i.getFocusedOptionId=function(a){return Va(i.state.focusableOptionsWithIds,a)},i.getFocusableOptionsWithIds=function(){return dd(_o(i.props,i.state.selectValue),i.getElementId("option"))},i.getValue=function(){return i.state.selectValue},i.cx=function(){for(var a=arguments.length,s=new Array(a),c=0;cw||h>w}},i.onTouchEnd=function(a){i.userIsDragging||(i.controlRef&&!i.controlRef.contains(a.target)&&i.menuListRef&&!i.menuListRef.contains(a.target)&&i.blurInput(),i.initialTouchX=0,i.initialTouchY=0)},i.onControlTouchEnd=function(a){i.userIsDragging||i.onControlMouseDown(a)},i.onClearIndicatorTouchEnd=function(a){i.userIsDragging||i.onClearIndicatorMouseDown(a)},i.onDropdownIndicatorTouchEnd=function(a){i.userIsDragging||i.onDropdownIndicatorMouseDown(a)},i.handleInputChange=function(a){var s=i.props.inputValue,c=a.currentTarget.value;i.setState({inputIsHiddenAfterUpdate:!1}),i.onInputChange(c,{action:"input-change",prevInputValue:s}),i.props.menuIsOpen||i.onMenuOpen()},i.onInputFocus=function(a){i.props.onFocus&&i.props.onFocus(a),i.setState({inputIsHiddenAfterUpdate:!1,isFocused:!0}),(i.openAfterFocus||i.props.openMenuOnFocus)&&i.openMenu("first"),i.openAfterFocus=!1},i.onInputBlur=function(a){var s=i.props.inputValue;if(i.menuListRef&&i.menuListRef.contains(document.activeElement)){i.inputRef.focus();return}i.props.onBlur&&i.props.onBlur(a),i.onInputChange("",{action:"input-blur",prevInputValue:s}),i.onMenuClose(),i.setState({focusedValue:null,isFocused:!1})},i.onOptionHover=function(a){if(!(i.blockOptionHover||i.state.focusedOption===a)){var s=i.getFocusableOptions(),c=s.indexOf(a);i.setState({focusedOption:a,focusedOptionId:c>-1?i.getFocusedOptionId(a):null})}},i.shouldHideSelectedOptions=function(){return Vm(i.props)},i.onValueInputFocus=function(a){a.preventDefault(),a.stopPropagation(),i.focus()},i.onKeyDown=function(a){var s=i.props,c=s.isMulti,d=s.backspaceRemovesValue,h=s.escapeClearsValue,w=s.inputValue,S=s.isClearable,v=s.isDisabled,y=s.menuIsOpen,f=s.onKeyDown,p=s.tabSelectsValue,m=s.openMenuOnFocus,P=i.state,R=P.focusedOption,g=P.focusedValue,E=P.selectValue;if(!v&&!(typeof f=="function"&&(f(a),a.defaultPrevented))){switch(i.blockOptionHover=!0,a.key){case"ArrowLeft":if(!c||w)return;i.focusValue("previous");break;case"ArrowRight":if(!c||w)return;i.focusValue("next");break;case"Delete":case"Backspace":if(w)return;if(g)i.removeValue(g);else{if(!d)return;c?i.popValue():S&&i.clearValue()}break;case"Tab":if(i.isComposing||a.shiftKey||!y||!p||!R||m&&i.isOptionSelected(R,E))return;i.selectOption(R);break;case"Enter":if(a.keyCode===229)break;if(y){if(!R||i.isComposing)return;i.selectOption(R);break}return;case"Escape":y?(i.setState({inputIsHiddenAfterUpdate:!1}),i.onInputChange("",{action:"menu-close",prevInputValue:w}),i.onMenuClose()):S&&h&&i.clearValue();break;case" ":if(w)return;if(!y){i.openMenu("first");break}if(!R)return;i.selectOption(R);break;case"ArrowUp":y?i.focusOption("up"):i.openMenu("last");break;case"ArrowDown":y?i.focusOption("down"):i.openMenu("first");break;case"PageUp":if(!y)return;i.focusOption("pageup");break;case"PageDown":if(!y)return;i.focusOption("pagedown");break;case"Home":if(!y)return;i.focusOption("first");break;case"End":if(!y)return;i.focusOption("last");break;default:return}a.preventDefault()}},i.state.instancePrefix="react-select-"+(i.props.instanceId||++DC),i.state.selectValue=Zf(r.value),r.menuIsOpen&&i.state.selectValue.length){var o=i.getFocusableOptionsWithIds(),l=i.buildFocusableOptions(),u=l.indexOf(i.state.selectValue[0]);i.state.focusableOptionsWithIds=o,i.state.focusedOption=l[u],i.state.focusedOptionId=Va(o,l[u])}return i}return Xy(n,[{key:"componentDidMount",value:function(){this.startListeningComposition(),this.startListeningToTouch(),this.props.closeMenuOnScroll&&document&&document.addEventListener&&document.addEventListener("scroll",this.onScroll,!0),this.props.autoFocus&&this.focusInput(),this.props.menuIsOpen&&this.state.focusedOption&&this.menuListRef&&this.focusedOptionRef&&Jf(this.menuListRef,this.focusedOptionRef)}},{key:"componentDidUpdate",value:function(i){var o=this.props,l=o.isDisabled,u=o.menuIsOpen,a=this.state.isFocused;(a&&!l&&i.isDisabled||a&&u&&!i.menuIsOpen)&&this.focusInput(),a&&l&&!i.isDisabled?this.setState({isFocused:!1},this.onMenuClose):!a&&!l&&i.isDisabled&&this.inputRef===document.activeElement&&this.setState({isFocused:!0}),this.menuListRef&&this.focusedOptionRef&&this.scrollToFocusedOptionOnUpdate&&(Jf(this.menuListRef,this.focusedOptionRef),this.scrollToFocusedOptionOnUpdate=!1)}},{key:"componentWillUnmount",value:function(){this.stopListeningComposition(),this.stopListeningToTouch(),document.removeEventListener("scroll",this.onScroll,!0)}},{key:"onMenuOpen",value:function(){this.props.onMenuOpen()}},{key:"onMenuClose",value:function(){this.onInputChange("",{action:"menu-close",prevInputValue:this.props.inputValue}),this.props.onMenuClose()}},{key:"onInputChange",value:function(i,o){this.props.onInputChange(i,o)}},{key:"focusInput",value:function(){this.inputRef&&this.inputRef.focus()}},{key:"blurInput",value:function(){this.inputRef&&this.inputRef.blur()}},{key:"openMenu",value:function(i){var o=this,l=this.state,u=l.selectValue,a=l.isFocused,s=this.buildFocusableOptions(),c=i==="first"?0:s.length-1;if(!this.props.isMulti){var d=s.indexOf(u[0]);d>-1&&(c=d)}this.scrollToFocusedOptionOnUpdate=!(a&&this.menuListRef),this.setState({inputIsHiddenAfterUpdate:!1,focusedValue:null,focusedOption:s[c],focusedOptionId:this.getFocusedOptionId(s[c])},function(){return o.onMenuOpen()})}},{key:"focusValue",value:function(i){var o=this.state,l=o.selectValue,u=o.focusedValue;if(this.props.isMulti){this.setState({focusedOption:null});var a=l.indexOf(u);u||(a=-1);var s=l.length-1,c=-1;if(l.length){switch(i){case"previous":a===0?c=0:a===-1?c=s:c=a-1;break;case"next":a>-1&&a0&&arguments[0]!==void 0?arguments[0]:"first",o=this.props.pageSize,l=this.state.focusedOption,u=this.getFocusableOptions();if(u.length){var a=0,s=u.indexOf(l);l||(s=-1),i==="up"?a=s>0?s-1:u.length-1:i==="down"?a=(s+1)%u.length:i==="pageup"?(a=s-o,a<0&&(a=0)):i==="pagedown"?(a=s+o,a>u.length-1&&(a=u.length-1)):i==="last"&&(a=u.length-1),this.scrollToFocusedOptionOnUpdate=!0,this.setState({focusedOption:u[a],focusedValue:null,focusedOptionId:this.getFocusedOptionId(u[a])})}}},{key:"getTheme",value:function(){return this.props.theme?typeof this.props.theme=="function"?this.props.theme(Na):$($({},Na),this.props.theme):Na}},{key:"getCommonProps",value:function(){var i=this.clearValue,o=this.cx,l=this.getStyles,u=this.getClassNames,a=this.getValue,s=this.selectOption,c=this.setValue,d=this.props,h=d.isMulti,w=d.isRtl,S=d.options,v=this.hasValue();return{clearValue:i,cx:o,getStyles:l,getClassNames:u,getValue:a,hasValue:v,isMulti:h,isRtl:w,options:S,selectOption:s,selectProps:d,setValue:c,theme:this.getTheme()}}},{key:"hasValue",value:function(){var i=this.state.selectValue;return i.length>0}},{key:"hasOptions",value:function(){return!!this.getFocusableOptions().length}},{key:"isClearable",value:function(){var i=this.props,o=i.isClearable,l=i.isMulti;return o===void 0?l:o}},{key:"isOptionDisabled",value:function(i,o){return bm(this.props,i,o)}},{key:"isOptionSelected",value:function(i,o){return Fm(this.props,i,o)}},{key:"filterOption",value:function(i,o){return Nm(this.props,i,o)}},{key:"formatOptionLabel",value:function(i,o){if(typeof this.props.formatOptionLabel=="function"){var l=this.props.inputValue,u=this.state.selectValue;return this.props.formatOptionLabel(i,{context:o,inputValue:l,selectValue:u})}else return this.getOptionLabel(i)}},{key:"formatGroupLabel",value:function(i){return this.props.formatGroupLabel(i)}},{key:"startListeningComposition",value:function(){document&&document.addEventListener&&(document.addEventListener("compositionstart",this.onCompositionStart,!1),document.addEventListener("compositionend",this.onCompositionEnd,!1))}},{key:"stopListeningComposition",value:function(){document&&document.removeEventListener&&(document.removeEventListener("compositionstart",this.onCompositionStart),document.removeEventListener("compositionend",this.onCompositionEnd))}},{key:"startListeningToTouch",value:function(){document&&document.addEventListener&&(document.addEventListener("touchstart",this.onTouchStart,!1),document.addEventListener("touchmove",this.onTouchMove,!1),document.addEventListener("touchend",this.onTouchEnd,!1))}},{key:"stopListeningToTouch",value:function(){document&&document.removeEventListener&&(document.removeEventListener("touchstart",this.onTouchStart),document.removeEventListener("touchmove",this.onTouchMove),document.removeEventListener("touchend",this.onTouchEnd))}},{key:"renderInput",value:function(){var i=this.props,o=i.isDisabled,l=i.isSearchable,u=i.inputId,a=i.inputValue,s=i.tabIndex,c=i.form,d=i.menuIsOpen,h=i.required,w=this.getComponents(),S=w.Input,v=this.state,y=v.inputIsHidden,f=v.ariaSelection,p=this.commonProps,m=u||this.getElementId("input"),P=$($($({"aria-autocomplete":"list","aria-expanded":d,"aria-haspopup":!0,"aria-errormessage":this.props["aria-errormessage"],"aria-invalid":this.props["aria-invalid"],"aria-label":this.props["aria-label"],"aria-labelledby":this.props["aria-labelledby"],"aria-required":h,role:"combobox","aria-activedescendant":this.isAppleDevice?void 0:this.state.focusedOptionId||""},d&&{"aria-controls":this.getElementId("listbox")}),!l&&{"aria-readonly":!0}),this.hasValue()?(f==null?void 0:f.action)==="initial-input-focus"&&{"aria-describedby":this.getElementId("live-region")}:{"aria-describedby":this.getElementId("placeholder")});return l?C.createElement(S,U({},p,{autoCapitalize:"none",autoComplete:"off",autoCorrect:"off",id:m,innerRef:this.getInputRef,isDisabled:o,isHidden:y,onBlur:this.onInputBlur,onChange:this.handleInputChange,onFocus:this.onInputFocus,spellCheck:"false",tabIndex:s,form:c,type:"text",value:a},P)):C.createElement(oC,U({id:m,innerRef:this.getInputRef,onBlur:this.onInputBlur,onChange:cl,onFocus:this.onInputFocus,disabled:o,tabIndex:s,inputMode:"none",form:c,value:""},P))}},{key:"renderPlaceholderOrValue",value:function(){var i=this,o=this.getComponents(),l=o.MultiValue,u=o.MultiValueContainer,a=o.MultiValueLabel,s=o.MultiValueRemove,c=o.SingleValue,d=o.Placeholder,h=this.commonProps,w=this.props,S=w.controlShouldRenderValue,v=w.isDisabled,y=w.isMulti,f=w.inputValue,p=w.placeholder,m=this.state,P=m.selectValue,R=m.focusedValue,g=m.isFocused;if(!this.hasValue()||!S)return f?null:C.createElement(d,U({},h,{key:"placeholder",isDisabled:v,isFocused:g,innerProps:{id:this.getElementId("placeholder")}}),p);if(y)return P.map(function(O,I){var D=O===R,B="".concat(i.getOptionLabel(O),"-").concat(i.getOptionValue(O));return C.createElement(l,U({},h,{components:{Container:u,Label:a,Remove:s},isFocused:D,isDisabled:v,key:B,index:I,removeProps:{onClick:function(){return i.removeValue(O)},onTouchEnd:function(){return i.removeValue(O)},onMouseDown:function(ie){ie.preventDefault()}},data:O}),i.formatOptionLabel(O,"value"))});if(f)return null;var E=P[0];return C.createElement(c,U({},h,{data:E,isDisabled:v}),this.formatOptionLabel(E,"value"))}},{key:"renderClearIndicator",value:function(){var i=this.getComponents(),o=i.ClearIndicator,l=this.commonProps,u=this.props,a=u.isDisabled,s=u.isLoading,c=this.state.isFocused;if(!this.isClearable()||!o||a||!this.hasValue()||s)return null;var d={onMouseDown:this.onClearIndicatorMouseDown,onTouchEnd:this.onClearIndicatorTouchEnd,"aria-hidden":"true"};return C.createElement(o,U({},l,{innerProps:d,isFocused:c}))}},{key:"renderLoadingIndicator",value:function(){var i=this.getComponents(),o=i.LoadingIndicator,l=this.commonProps,u=this.props,a=u.isDisabled,s=u.isLoading,c=this.state.isFocused;if(!o||!s)return null;var d={"aria-hidden":"true"};return C.createElement(o,U({},l,{innerProps:d,isDisabled:a,isFocused:c}))}},{key:"renderIndicatorSeparator",value:function(){var i=this.getComponents(),o=i.DropdownIndicator,l=i.IndicatorSeparator;if(!o||!l)return null;var u=this.commonProps,a=this.props.isDisabled,s=this.state.isFocused;return C.createElement(l,U({},u,{isDisabled:a,isFocused:s}))}},{key:"renderDropdownIndicator",value:function(){var i=this.getComponents(),o=i.DropdownIndicator;if(!o)return null;var l=this.commonProps,u=this.props.isDisabled,a=this.state.isFocused,s={onMouseDown:this.onDropdownIndicatorMouseDown,onTouchEnd:this.onDropdownIndicatorTouchEnd,"aria-hidden":"true"};return C.createElement(o,U({},l,{innerProps:s,isDisabled:u,isFocused:a}))}},{key:"renderMenu",value:function(){var i=this,o=this.getComponents(),l=o.Group,u=o.GroupHeading,a=o.Menu,s=o.MenuList,c=o.MenuPortal,d=o.LoadingMessage,h=o.NoOptionsMessage,w=o.Option,S=this.commonProps,v=this.state.focusedOption,y=this.props,f=y.captureMenuScroll,p=y.inputValue,m=y.isLoading,P=y.loadingMessage,R=y.minMenuHeight,g=y.maxMenuHeight,E=y.menuIsOpen,O=y.menuPlacement,I=y.menuPosition,D=y.menuPortalTarget,B=y.menuShouldBlockScroll,X=y.menuShouldScrollIntoView,ie=y.noOptionsMessage,xe=y.onMenuScrollToTop,pe=y.onMenuScrollToBottom;if(!E)return null;var ae=function(ve,ue){var Le=ve.type,se=ve.data,je=ve.isDisabled,Et=ve.isSelected,Yn=ve.label,Yl=ve.value,We=v===se,nn=je?void 0:function(){return i.onOptionHover(se)},Ui=je?void 0:function(){return i.selectOption(se)},Hi="".concat(i.getElementId("option"),"-").concat(ue),Ut={id:Hi,onClick:Ui,onMouseMove:nn,onMouseOver:nn,tabIndex:-1,role:"option","aria-selected":i.isAppleDevice?void 0:Et};return C.createElement(w,U({},S,{innerProps:Ut,data:se,isDisabled:je,isSelected:Et,key:Hi,label:Yn,type:Le,value:Yl,isFocused:We,innerRef:We?i.getFocusedOptionRef:void 0}),i.formatOptionLabel(ve.data,"menu"))},q;if(this.hasOptions())q=this.getCategorizedOptions().map(function(Q){if(Q.type==="group"){var ve=Q.data,ue=Q.options,Le=Q.index,se="".concat(i.getElementId("group"),"-").concat(Le),je="".concat(se,"-heading");return C.createElement(l,U({},S,{key:se,data:ve,options:ue,Heading:u,headingProps:{id:je,data:Q.data},label:i.formatGroupLabel(Q.data)}),Q.options.map(function(Et){return ae(Et,"".concat(Le,"-").concat(Et.index))}))}else if(Q.type==="option")return ae(Q,"".concat(Q.index))});else if(m){var T=P({inputValue:p});if(T===null)return null;q=C.createElement(d,S,T)}else{var V=ie({inputValue:p});if(V===null)return null;q=C.createElement(h,S,V)}var z={minMenuHeight:R,maxMenuHeight:g,menuPlacement:O,menuPosition:I,menuShouldScrollIntoView:X},Z=C.createElement(VS,U({},S,z),function(Q){var ve=Q.ref,ue=Q.placerProps,Le=ue.placement,se=ue.maxHeight;return C.createElement(a,U({},S,z,{innerRef:ve,innerProps:{onMouseDown:i.onMenuMouseDown,onMouseMove:i.onMenuMouseMove},isLoading:m,placement:Le}),C.createElement(fC,{captureEnabled:f,onTopArrive:xe,onBottomArrive:pe,lockEnabled:B},function(je){return C.createElement(s,U({},S,{innerRef:function(Yn){i.getMenuListRef(Yn),je(Yn)},innerProps:{role:"listbox","aria-multiselectable":S.isMulti,id:i.getElementId("listbox")},isLoading:m,maxHeight:se,focusedOption:v}),q)}))});return D||I==="fixed"?C.createElement(c,U({},S,{appendTo:D,controlElement:this.controlRef,menuPlacement:O,menuPosition:I}),Z):Z}},{key:"renderFormField",value:function(){var i=this,o=this.props,l=o.delimiter,u=o.isDisabled,a=o.isMulti,s=o.name,c=o.required,d=this.state.selectValue;if(c&&!this.hasValue()&&!u)return C.createElement(hC,{name:s,onFocus:this.onValueInputFocus});if(!(!s||u))if(a)if(l){var h=d.map(function(v){return i.getOptionValue(v)}).join(l);return C.createElement("input",{name:s,type:"hidden",value:h})}else{var w=d.length>0?d.map(function(v,y){return C.createElement("input",{key:"i-".concat(y),name:s,type:"hidden",value:i.getOptionValue(v)})}):C.createElement("input",{name:s,type:"hidden",value:""});return C.createElement("div",null,w)}else{var S=d[0]?this.getOptionValue(d[0]):"";return C.createElement("input",{name:s,type:"hidden",value:S})}}},{key:"renderLiveRegion",value:function(){var i=this.commonProps,o=this.state,l=o.ariaSelection,u=o.focusedOption,a=o.focusedValue,s=o.isFocused,c=o.selectValue,d=this.getFocusableOptions();return C.createElement(qw,U({},i,{id:this.getElementId("live-region"),ariaSelection:l,focusedOption:u,focusedValue:a,isFocused:s,selectValue:c,focusableOptions:d,isAppleDevice:this.isAppleDevice}))}},{key:"render",value:function(){var i=this.getComponents(),o=i.Control,l=i.IndicatorsContainer,u=i.SelectContainer,a=i.ValueContainer,s=this.props,c=s.className,d=s.id,h=s.isDisabled,w=s.menuIsOpen,S=this.state.isFocused,v=this.commonProps=this.getCommonProps();return C.createElement(u,U({},v,{className:c,innerProps:{id:d,onKeyDown:this.onKeyDown},isDisabled:h,isFocused:S}),this.renderLiveRegion(),C.createElement(o,U({},v,{innerRef:this.getControlRef,innerProps:{onMouseDown:this.onControlMouseDown,onTouchEnd:this.onControlTouchEnd},isDisabled:h,isFocused:S,menuIsOpen:w}),C.createElement(a,U({},v,{isDisabled:h}),this.renderPlaceholderOrValue(),this.renderInput()),C.createElement(l,U({},v,{isDisabled:h}),this.renderClearIndicator(),this.renderLoadingIndicator(),this.renderIndicatorSeparator(),this.renderDropdownIndicator())),this.renderMenu(),this.renderFormField())}}],[{key:"getDerivedStateFromProps",value:function(i,o){var l=o.prevProps,u=o.clearFocusValueOnUpdate,a=o.inputIsHiddenAfterUpdate,s=o.ariaSelection,c=o.isFocused,d=o.prevWasFocused,h=o.instancePrefix,w=i.options,S=i.value,v=i.menuIsOpen,y=i.inputValue,f=i.isMulti,p=Zf(S),m={};if(l&&(S!==l.value||w!==l.options||v!==l.menuIsOpen||y!==l.inputValue)){var P=v?TC(i,p):[],R=v?dd(_o(i,p),"".concat(h,"-option")):[],g=u?IC(o,p):null,E=_C(o,P),O=Va(R,E);m={selectValue:p,focusedOption:E,focusedOptionId:O,focusableOptionsWithIds:R,focusedValue:g,clearFocusValueOnUpdate:!1}}var I=a!=null&&i!==l?{inputIsHidden:a,inputIsHiddenAfterUpdate:void 0}:{},D=s,B=c&&d;return c&&!B&&(D={value:vo(f,p,p[0]||null),options:p,action:"initial-input-focus"},B=!d),(s==null?void 0:s.action)==="initial-input-focus"&&(D=null),$($($({},m),I),{},{prevProps:i,ariaSelection:D,prevWasFocused:B})}}]),n}(C.Component);zm.defaultProps=LC;var bC=C.forwardRef(function(e,t){var n=Yy(e);return C.createElement(zm,U({ref:t},n))}),FC=bC;const NC=()=>{const[e,t]=$y(),[n,r]=C.useState(),[i,o]=C.useState();return C.useEffect(()=>{r(e.get("schema")),o(e.get("namespace"))}),F.jsxs("div",{children:[F.jsx("a",{href:"/",children:"Home"})," ",i?F.jsxs(F.Fragment,{children:[" » ",F.jsx("a",{href:`/?namespace=${i}`,children:i})," "]}):""," » ",n?F.jsx(F.Fragment,{children:n}):"...",F.jsx(VC,{schema:n,namespace:i,setNamespace:o,setSchema:r,setSearchParams:t})]})},VC=e=>e.namespace?e.schema?F.jsx(zC,{namespace:e.namespace,schema:e.schema}):F.jsx(jC,{namespace:e.namespace,setSchema:e.setSchema,setSearchParams:e.setSearchParams}):F.jsx($C,{setNamespace:e.setNamespace,setSearchParams:e.setSearchParams}),zC=e=>{const[t,n]=C.useState([]);C.useEffect(()=>{fetch(`/${e.namespace}/${e.schema}.yaml`).then(i=>i.text()).then(i=>{n(i),console.log("schema:",i)})},[]);const r={backgroundColor:"#eee",padding:"10px",fontSize:"0.7em"};return F.jsxs("div",{children:[F.jsx("h3",{children:"Schema"}),F.jsx("b",{children:"Description:"})," ",t.description,F.jsx("br",{}),F.jsx("b",{children:"Relative path:"})," ",`${e.namespace}/${e.schema}.yaml`," ",F.jsx("br",{}),F.jsx("b",{children:"Endpoint:"})," https://schema.databio.org/",`${e.namespace}/${e.schema}.yaml`,F.jsx("br",{}),F.jsx("b",{children:"Preview (this page):"})," https://schema.databio.org/?namespace=",`${e.namespace}`,"&schema=",`${e.schema}`,F.jsx("br",{}),F.jsx("a",{href:`/${e.namespace}/${e.schema}.yaml`,children:F.jsx("button",{className:"btn btn-primary my-4",children:"Download schema"})}),F.jsx("h4",{children:"Preview"}),F.jsx("pre",{style:r,children:F.jsx("code",{children:t})})]})},jC=e=>{const[t,n]=C.useState([]);C.useEffect(()=>{fetch(`/${e.namespace}/schemas.json`).then(i=>i.json()).then(i=>{n(i),console.log("schemaList:",Object.values(i))})},[]);const r=i=>{e.setSearchParams(o=>(o.append("schema",i),o)),e.setSchema(i)};return F.jsxs("div",{children:[F.jsxs("h2",{children:["Namespace: ",e.namespace]}),F.jsx("h4",{children:"Schemas"}),t?F.jsx(AC,{schemas:t,selectSchema:r}):F.jsx("div",{className:"spinner-border",role:"status",children:F.jsx("span",{className:"visually-hidden",children:"Loading..."})})]})},AC=e=>{const t=Object.values(e.schemas).map(n=>F.jsxs("li",{children:[F.jsx("a",{href:`/?namespace=${n.namespace}&schema=${n.schema}`,className:"a",onClick:r=>{r.preventDefault(),e.selectSchema(n.schema)},children:n.schema})," -- ",n.description," ",F.jsx("a",{href:n.url,children:"Download"})]},n.schema));return console.log(e.schemas),F.jsx("div",{children:F.jsx("ul",{children:t})})},$C=e=>{const[t,n]=C.useState([]);C.useEffect(()=>{fetch("/namespaces.json").then(i=>i.json()).then(i=>{console.log("Namespaces:",i);const o=i.map(l=>({value:l,label:l}));console.log("options:",o),n(o)})},[]);const r=i=>{e.setSearchParams({namespace:i.value}),e.setNamespace(i.value)};return F.jsxs(F.Fragment,{children:[F.jsx("h2",{children:"Select namespace"}),F.jsx(FC,{options:t,onChange:r}),F.jsx("hr",{}),F.jsx("h2",{children:"Guide"}),"This is a schema registry and API. It is hosted on GitHub Pages. Schemas are identified by a ",F.jsx("i",{children:"namespace"})," and ",F.jsx("i",{children:"schema name"}),", put together to form a *registry path*, of this form:",F.jsx("br",{}),F.jsx("br",{}),F.jsx("pre",{children:F.jsx("code",{children:"{namespace}/{schema}"})}),F.jsx("h3",{children:"Browsing"}),"To browse existing schemas, select a namespace from the dropdown above. This will show you a list of all schemas in that namespace",F.jsx("h3",{children:"API"}),"To access a schema via the API, use the following URL format:",F.jsx("br",{}),F.jsx("br",{}),F.jsx("pre",{children:F.jsx("code",{children:"https://schema.databio.org/{namespace}/{schema}.yaml"})}),"You can also get a list of schemas in a namespace via the API:",F.jsx("br",{}),F.jsx("br",{}),F.jsx("pre",{children:F.jsx("code",{children:"https://schema.databio.org/{namespace}/schemas.json"})}),F.jsx("h3",{children:"Contributing"}),"You can contribute your own schema via PR to the GitHub repository."]})},UC=Ty(Nu(F.jsx(Kh,{path:"/",element:F.jsx(NC,{})})));ja.createRoot(document.getElementById("root")).render(F.jsx(kd.StrictMode,{children:F.jsx(jy,{router:UC})})); diff --git a/docs/bulker/cdid.yaml b/docs/bulker/cdid.yaml deleted file mode 100644 index dd0b4cb..0000000 --- a/docs/bulker/cdid.yaml +++ /dev/null @@ -1,12 +0,0 @@ -description: "Two druids that describe the manifest" -type: object -properties: - imports: - type: string - commands: - type: string -recursive: - - imports - - commands -required: - - commands \ No newline at end of file diff --git a/docs/bulker/cmdlist.yaml b/docs/bulker/cmdlist.yaml deleted file mode 100644 index 5fcb200..0000000 --- a/docs/bulker/cmdlist.yaml +++ /dev/null @@ -1,16 +0,0 @@ -description: "A list of commands and the containers that run them." -type: array -items: - type: object - properties: - command: - type: string - docker_args: - type: string - docker_image: - type: string - docker_command: - type: string - required: - - command - - docker_image \ No newline at end of file diff --git a/docs/bulker/importlist.yaml b/docs/bulker/importlist.yaml deleted file mode 100644 index 630f2c1..0000000 --- a/docs/bulker/importlist.yaml +++ /dev/null @@ -1,4 +0,0 @@ -description: "A priority list of bulker manifests that are imported." -type: array -items: - type: string diff --git a/docs/bulker/manifest.yaml b/docs/bulker/manifest.yaml deleted file mode 100644 index 93122b2..0000000 --- a/docs/bulker/manifest.yaml +++ /dev/null @@ -1,31 +0,0 @@ -description: "Schema for bulker manifest" -properties: - manifest: - type: object - properties: - name: - type: string - version: - type: string - imports: - type: array - items: - type: string - commands: - type: array - items: - type: object - properties: - command: - type: string - docker_args: - type: string - docker_image: - type: string - docker_command: - type: string - required: - - command - - docker_image - required: - - commands diff --git a/docs/bulker/schemas.json b/docs/bulker/schemas.json deleted file mode 100644 index ff7dcd1..0000000 --- a/docs/bulker/schemas.json +++ /dev/null @@ -1,26 +0,0 @@ -{ - "cdid": { - "namespace": "bulker", - "schema": "cdid", - "url": "bulker/cdid.yaml", - "description": "Two druids that describe the manifest" - }, - "cmdlist": { - "namespace": "bulker", - "schema": "cmdlist", - "url": "bulker/cmdlist.yaml", - "description": "A list of commands and the containers that run them." - }, - "manifest": { - "namespace": "bulker", - "schema": "manifest", - "url": "bulker/manifest.yaml", - "description": "Schema for bulker manifest" - }, - "importlist": { - "namespace": "bulker", - "schema": "importlist", - "url": "bulker/importlist.yaml", - "description": "A priority list of bulker manifests that are imported." - } -} \ No newline at end of file diff --git a/docs/index.html b/docs/index.html deleted file mode 100644 index dc9b5cc..0000000 --- a/docs/index.html +++ /dev/null @@ -1,37 +0,0 @@ - - - - - - - - - - - - Lab schemas - - - - -
-
-
- - diff --git a/docs/list.json b/docs/list.json deleted file mode 100644 index 5266998..0000000 --- a/docs/list.json +++ /dev/null @@ -1,147 +0,0 @@ -{ - "schemas/bulker/cdid": { - "project": "bulker", - "url": "bulker/cdid.yaml", - "description": "Two druids that describe the manifest" - }, - "schemas/bulker/cmdlist": { - "project": "bulker", - "url": "bulker/cmdlist.yaml", - "description": "A list of commands and the containers that run them." - }, - "schemas/bulker/manifest": { - "project": "bulker", - "url": "bulker/manifest.yaml", - "description": "Schema for bulker manifest" - }, - "schemas/bulker/importlist": { - "project": "bulker", - "url": "bulker/importlist.yaml", - "description": "A priority list of bulker manifests that are imported." - }, - "schemas/refget/SeqColArraySetInherent": { - "project": "refget", - "url": "refget/SeqColArraySetInherent.yaml", - "description": "SeqColArraySet" - }, - "schemas/refget/sequence": { - "project": "refget", - "url": "refget/sequence.yaml", - "description": "Schema for a single raw sequence" - }, - "schemas/refget/annotated_collection_digest": { - "project": "refget", - "url": "refget/annotated_collection_digest.yaml", - "description": "Schema for an Annotated Collection Digest; this is analogous to a single fasta file with metadata." - }, - "schemas/refget/ArrayedNestedSequenceCollection": { - "project": "refget", - "url": "refget/ArrayedNestedSequenceCollection.yaml", - "description": "A collection of sequences" - }, - "schemas/refget/ASDList": { - "project": "refget", - "url": "refget/ASDList.yaml", - "description": "Schema for List of ASDs" - }, - "schemas/refget/annotated_sequence_digest": { - "project": "refget", - "url": "refget/annotated_sequence_digest.yaml", - "description": "Schema for an Annotated Sequence Digest; a digested Sequence plus metadata" - }, - "schemas/refget/ACDList": { - "project": "refget", - "url": "refget/ACDList.yaml", - "description": "Schema for a list of ACDs; analogous to a collection of fasta files" - }, - "schemas/refget/ArrayedSequenceCollection": { - "project": "refget", - "url": "refget/ArrayedSequenceCollection.yaml", - "description": "A collection of sequences" - }, - "schemas/refget/RawSeqCol": { - "project": "refget", - "url": "refget/RawSeqCol.yaml", - "description": "Schema for List of ASDs" - }, - "schemas/refget/TASeqCol": { - "project": "refget", - "url": "refget/TASeqCol.yaml", - "description": "TAseqcol" - }, - "schemas/refget/CustomAnnotatedArrayedSequenceCollection": { - "project": "refget", - "url": "refget/CustomAnnotatedArrayedSequenceCollection.yaml", - "description": "A collection of sequences" - }, - "schemas/refget/SeqColArraySet": { - "project": "refget", - "url": "refget/SeqColArraySet.yaml", - "description": "SeqColArraySet" - }, - "schemas/refget/AnnotatedArrayedSequenceCollection": { - "project": "refget", - "url": "refget/AnnotatedArrayedSequenceCollection.yaml", - "description": "A collection of sequences" - }, - "schemas/refget/AnnotatedSequenceList": { - "project": "refget", - "url": "refget/AnnotatedSequenceList.yaml", - "description": "Schema for List of ASDs" - }, - "schemas/refgenie/refgenie_build": { - "project": "refgenie", - "url": "refgenie/refgenie_build.yaml", - "description": "databio_genomes PEP schema" - }, - "schemas/pep/2.1.0": { - "project": "pep", - "url": "pep/2.1.0.yaml", - "description": "Schema for a minimal PEP" - }, - "schemas/pep/2.0.0": { - "project": "pep", - "url": "pep/2.0.0.yaml", - "description": "Schema for a minimal PEP" - }, - "schemas/pipelines/pipeline_interface": { - "project": "pipelines", - "url": "pipelines/pipeline_interface.yaml", - "description": "pipeline interface schema" - }, - "schemas/pipelines/geofetch_sra_convert": { - "project": "pipelines", - "url": "pipelines/geofetch_sra_convert.yaml", - "description": "A PEP for converting SRA files into fastq or bam format." - }, - "schemas/pipelines/bedmaker": { - "project": "pipelines", - "url": "pipelines/bedmaker.yaml", - "description": "bedmaker PEP schema" - }, - "schemas/pipelines/bedbuncher": { - "project": "pipelines", - "url": "pipelines/bedbuncher.yaml", - "description": "bedbuncher PEP schema" - }, - "schemas/pipelines/pepatac": { - "project": "pipelines", - "url": "pipelines/pepatac.yaml", - "description": "A PEP for ATAC-seq samples for the PEPATAC pipeline." - }, - "schemas/pipelines/ProseqPEP": { - "project": "pipelines", - "url": "pipelines/ProseqPEP.yaml", - "description": "A PEP for nascent RNA samples for the PEPPRO pipeline." - }, - "schemas/pipelines/bedstat": { - "project": "pipelines", - "url": "pipelines/bedstat.yaml", - "description": "bedstat PEP schema" - }, - "schemas/pipelines/bedboss": { - "project": "pipelines", - "url": "pipelines/bedboss.yaml", - "description": "bedboss run-all pep schema" - } -} \ No newline at end of file diff --git a/docs/namespaces.json b/docs/namespaces.json deleted file mode 100644 index e29f22f..0000000 --- a/docs/namespaces.json +++ /dev/null @@ -1,7 +0,0 @@ -[ - "bulker", - "refget", - "refgenie", - "pep", - "pipelines" -] \ No newline at end of file diff --git a/docs/pep/2.0.0.yaml b/docs/pep/2.0.0.yaml deleted file mode 100644 index 56f2034..0000000 --- a/docs/pep/2.0.0.yaml +++ /dev/null @@ -1,69 +0,0 @@ -description: "Schema for a minimal PEP" -version: "2.0.0" -properties: - config: - properties: - name: - type: string - pattern: "^\\S*$" - description: "Project name with no whitespace" - pep_version: - description: "Version of the PEP Schema this PEP follows" - type: string - sample_table: - type: string - description: "Path to the sample annotation table with one row per sample" - subsample_table: - type: string - description: "Path to the subsample annotation table with one row per subsample and sample_name attribute matching an entry in the sample table" - sample_modifiers: - type: object - properties: - append: - type: object - duplicate: - type: object - imply: - type: array - items: - type: object - properties: - if: - type: object - then: - type: object - derive: - type: object - properties: - attributes: - type: array - items: - type: string - sources: - type: object - project_modifiers: - type: object - properties: - amend: - description: "Object overwriting original project attributes" - type: object - import: - description: "List of external PEP project config files to import" - type: array - items: - type: string - required: - - pep_version - samples: - type: array - items: - type: object - properties: - sample_name: - type: string - pattern: "^\\S*$" - description: "Unique name of the sample with no whitespace" - required: - - sample_name -required: - - samples diff --git a/docs/pep/2.1.0.yaml b/docs/pep/2.1.0.yaml deleted file mode 100644 index e3982aa..0000000 --- a/docs/pep/2.1.0.yaml +++ /dev/null @@ -1,77 +0,0 @@ -description: "Schema for a minimal PEP" -version: "2.1.0" -properties: - config: - properties: - name: - type: string - pattern: "^\\S*$" - description: "Project name with no whitespace" - pep_version: - description: "Version of the PEP Schema this PEP follows" - type: string - sample_table: - type: string - description: "Path to the sample annotation table" - subsample_table: - type: string - description: "Path to the subsample annotation table with one row per subsample and sample_name attribute matching an entry in the sample table" - sample_table_index: - type: string - pattern: "^\\S*$" - description: "Name of the column in sample table to use as an index. It's 'sample_name' by default" - subsample_table_index: - type: array - items: - type: string - pattern: "^\\S*$" - description: "Names of the columns in subsample table to use as an index. It's ['sample_name', 'subsample_name'] by default" - sample_modifiers: - type: object - properties: - append: - type: object - duplicate: - type: object - imply: - type: array - items: - type: object - properties: - if: - type: object - then: - type: object - derive: - type: object - properties: - attributes: - type: array - items: - type: string - sources: - type: object - project_modifiers: - type: object - properties: - amend: - description: "Object overwriting original project attributes" - type: object - import: - description: "List of external PEP project config files to import" - type: array - items: - type: string - required: - - pep_version - samples: - type: array - items: - type: object - properties: - sample_name: - type: string - pattern: "^\\S*$" - description: "Unique name of the sample with no whitespace" -required: - - samples diff --git a/docs/pep/schemas.json b/docs/pep/schemas.json deleted file mode 100644 index eef3d24..0000000 --- a/docs/pep/schemas.json +++ /dev/null @@ -1,14 +0,0 @@ -{ - "2.1.0": { - "namespace": "pep", - "schema": "2.1.0", - "url": "pep/2.1.0.yaml", - "description": "Schema for a minimal PEP" - }, - "2.0.0": { - "namespace": "pep", - "schema": "2.0.0", - "url": "pep/2.0.0.yaml", - "description": "Schema for a minimal PEP" - } -} \ No newline at end of file diff --git a/docs/pipelines/ProseqPEP.yaml b/docs/pipelines/ProseqPEP.yaml deleted file mode 100644 index ab1f130..0000000 --- a/docs/pipelines/ProseqPEP.yaml +++ /dev/null @@ -1,50 +0,0 @@ -description: A PEP for nascent RNA samples for the PEPPRO pipeline. -imports: - - http://schema.databio.org/pep/2.0.0.yaml -properties: - samples: - type: array - items: - type: object - properties: - sample_name: - type: string - description: "Name of the sample" - organism: - type: string - description: "Organism" - protocol: - type: string - description: "Specifies whether the sample is pro-seq or gro-seq" - enum: ["PRO", "pro", "PRO-SEQ", "PRO-seq", "proseq", "PROSEQ", "GRO", "gro", "groseq", "GROSEQ", "GRO-SEQ", "GRO-seq"] - genome: - type: string - description: "Refgenie genome registry identifier" - read_type: - type: string - description: "Is this single or paired-end data?" - enum: ["SINGLE", "PAIRED"] - read1: - anyOf: - - type: string - description: "Fastq file for read 1" - - type: array - items: - type: string - read2: - anyOf: - - type: string - description: "Fastq file for read 2 (for paired-end experiments)" - - type: array - items: - type: string - umi_len: - type: string - description: "Length of the Unique Molecular Identifier, if any" - required: - - sample_name - - protocol - - read1 - - genome -required: - - samples diff --git a/docs/pipelines/bedboss.yaml b/docs/pipelines/bedboss.yaml deleted file mode 100644 index e6ffa0c..0000000 --- a/docs/pipelines/bedboss.yaml +++ /dev/null @@ -1,47 +0,0 @@ -description: bedboss run-all pep schema - -properties: - samples: - type: array - items: - type: object - properties: - sample_name: - type: string - description: "Name of the sample" - input_file: - type: string - description: "Absolute path to the input file" - input_type: - type: string - description: "file format" - enum: [ "bigWig", "bigBed", "bed", "wig", "bedGraph" ] - genome: - type: string - description: "organism genome code" - format_type: - type: string - description: "whether the regions are narrow (transcription factor implies narrow, histone mark implies broad peaks)" - enum: [ "narrowPeak", "broadPeak" ] - description: - type: string - description: "freeform description of the sample" - open_signal_matrix: - type: string - description: "A full path to the openSignalMatrix required for the tissue" - chrom_sizes: - type: string - description: "A full path to the chrom.sizes required for the bedtobigbed conversion" - treatment: - type: string - description: "freeform description of the sample treatment" - cell_type: - type: string - description: "cell type code" - required: - - sample_name - - input_file - - input_type - - genome -required: - - samples diff --git a/docs/pipelines/bedbuncher.yaml b/docs/pipelines/bedbuncher.yaml deleted file mode 100644 index cd42998..0000000 --- a/docs/pipelines/bedbuncher.yaml +++ /dev/null @@ -1,25 +0,0 @@ -description: bedbuncher PEP schema -imports: - - http://schema.databio.org/pep/2.0.0.yaml - -properties: - samples: - type: array - items: - type: object - properties: - JSONquery_path: - type: string - description: "path to the JSON file with the Elasticsearch query" - bedset_name: - type: string - pattern: "^\\S*$" - description: "name of the bedset that will be created" - bbconfig_path: - type: string - description: "path to bedbase config file" - required: - - JSONquery_path - - bedset_name -required: - - samples \ No newline at end of file diff --git a/docs/pipelines/bedmaker.yaml b/docs/pipelines/bedmaker.yaml deleted file mode 100644 index 93806d0..0000000 --- a/docs/pipelines/bedmaker.yaml +++ /dev/null @@ -1,59 +0,0 @@ -description: bedmaker PEP schema - -properties: - samples: - type: array - items: - type: object - properties: - sample_name: - type: string - description: "name of the sample, which is the name of the output BED file" - input_file_path: - type: string - description: "absolute path the file to convert" - output_bed_path: - type: string - description: "absolute path the file to the output BED file (derived attribute)" - output_bigbed_path: - type: string - description: "absolute path the file to the output bigBed file (derived attribute)" - genome: - type: string - description: "organism genome code" - narrowpeak: - type: boolean - description: "whether the regions are narrow (transcription factor implies narrow, histone mark implies broad peaks)" - format: - type: string - description: "file format" - enum: ["bigWig", "bigBed", "bed", "wig", "bedGraph"] - cell_type: - type: string - description: "cell type code" - antibody: - type: string - description: "antibody used if ChIP-seq experiment" - description: - type: string - description: "freeform description of the sample" - exp_protocol: - type: string - description: "type of the experiment the file was generated in" - data_source: - type: string - description: "source of the sample, preferably a GSE* code" - treatment: - type: string - description: "freeform description of the sample treatment" - required_files: - - input_file_path - required: - - input_file_path - - output_bed_path - - output_bigbed_path - - genome - - narrowpeak - - sample_name -required: - - samples diff --git a/docs/pipelines/bedstat.yaml b/docs/pipelines/bedstat.yaml deleted file mode 100644 index 8810191..0000000 --- a/docs/pipelines/bedstat.yaml +++ /dev/null @@ -1,41 +0,0 @@ -description: bedstat PEP schema -imports: - - http://schema.databio.org/pep/2.0.0.yaml - -properties: - samples: - type: array - items: - type: object - properties: - output_file_path: - type: string - description: "absolute path to the output BED files (.bed or .bed.gz)" - genome: - type: string - description: "organism reference genome" - cell_type: - type: string - description: "cell type used to perform the experimental protocol" - antibody: - type: string - description: "TF or Histone mark antibody used if ChIP-seq experiment" - description: - type: string - description: "freeform description of the sample" - exp_protocol: - type: string - description: "experimental protocol used to generate the genomic regions" - data_source: - type: string - description: "source of the sample, preferably a GSE* code" - treatment: - type: string - description: "freeform description of the sample treatment" - required_files: - - output_file_path - required: - - output_file_path - - genome -required: - - samples diff --git a/docs/pipelines/geofetch_sra_convert.yaml b/docs/pipelines/geofetch_sra_convert.yaml deleted file mode 100644 index dd057d7..0000000 --- a/docs/pipelines/geofetch_sra_convert.yaml +++ /dev/null @@ -1,27 +0,0 @@ -description: A PEP for converting SRA files into fastq or bam format. -imports: - - http://schema.databio.org/pep/2.0.0.yaml -properties: - samples: - type: array - items: - type: object - properties: - sample_name: - type: string - description: "Name of the sample" - protocol: - type: string - description: "Can be anything" - SRR_files: - type: string - description: "SRR files" - required_files: - - SRR_files - files: - - SRR_files - required: - - sample_name - - SRR_files -required: - - samples diff --git a/docs/pipelines/pepatac.yaml b/docs/pipelines/pepatac.yaml deleted file mode 100644 index 5b204c5..0000000 --- a/docs/pipelines/pepatac.yaml +++ /dev/null @@ -1,51 +0,0 @@ -description: A PEP for ATAC-seq samples for the PEPATAC pipeline. -imports: - - http://schema.databio.org/pep/2.0.0.yaml -properties: - samples: - type: array - items: - type: object - properties: - sample_name: - type: string - description: "Name of the sample" - organism: - type: string - description: "Organism" - protocol: - type: string - description: "Must be an ATAC-seq or DNAse-seq sample" - genome: - type: string - description: "Refgenie genome registry identifier" - read_type: - type: string - description: "Is this single or paired-end data?" - enum: ["SINGLE", "PAIRED"] - read1: - anyOf: - - type: string - description: "Fastq file for read 1" - - type: array - items: - type: string - read2: - anyOf: - - type: string - description: "Fastq file for read 2 (for paired-end experiments)" - - type: array - items: - type: string - required_files: - - read1 - files: - - read1 - - read2 - required: - - sample_name - - protocol - - read1 - - genome -required: - - samples diff --git a/docs/pipelines/pipeline_interface.yaml b/docs/pipelines/pipeline_interface.yaml deleted file mode 100644 index d428e3d..0000000 --- a/docs/pipelines/pipeline_interface.yaml +++ /dev/null @@ -1,47 +0,0 @@ -description: pipeline interface schema - -properties: - pipeline_name: - type: string - pattern: "^\\S*$" - description: "name of the pipeline with no whitespaces" - pipeline_type: - type: string - enum: ["project", "sample"] - description: "type of the pipeline, either 'project' or 'sample'" - command_template: - type: string - description: "Jinja2-like template to construct the command to run" - path: - type: string - description: "path to the pipeline program. Relative to pipeline interface file or absolute." - compute: - type: object - description: "Section that defines compute environment settings" - properties: - dynamic_variables_command_template: - type: string - description: "Jinja2-like template to construct the command that returns a JSON object used to populate compute environment settings" - size_dependent_variables: - type: string - description: "Path to the TSV-formatted file with compute environment settings" - bulker_crate: - type: string - description: "Bulker registry path idendifying the crate to use" - docker_image: - type: string - description: "Docker image identifier" - singularity_image: - type: string - description: "Singularity image identifier" -if: - properties: - pipeline_type: - const: "project" -then: - properties: - linked_pipeline_interfaces: - type: array - items: - type: string -required: [pipeline_name, pipeline_type, command_template] \ No newline at end of file diff --git a/docs/pipelines/schemas.json b/docs/pipelines/schemas.json deleted file mode 100644 index 895c315..0000000 --- a/docs/pipelines/schemas.json +++ /dev/null @@ -1,50 +0,0 @@ -{ - "pipeline_interface": { - "namespace": "pipelines", - "schema": "pipeline_interface", - "url": "pipelines/pipeline_interface.yaml", - "description": "pipeline interface schema" - }, - "geofetch_sra_convert": { - "namespace": "pipelines", - "schema": "geofetch_sra_convert", - "url": "pipelines/geofetch_sra_convert.yaml", - "description": "A PEP for converting SRA files into fastq or bam format." - }, - "bedmaker": { - "namespace": "pipelines", - "schema": "bedmaker", - "url": "pipelines/bedmaker.yaml", - "description": "bedmaker PEP schema" - }, - "bedbuncher": { - "namespace": "pipelines", - "schema": "bedbuncher", - "url": "pipelines/bedbuncher.yaml", - "description": "bedbuncher PEP schema" - }, - "pepatac": { - "namespace": "pipelines", - "schema": "pepatac", - "url": "pipelines/pepatac.yaml", - "description": "A PEP for ATAC-seq samples for the PEPATAC pipeline." - }, - "ProseqPEP": { - "namespace": "pipelines", - "schema": "ProseqPEP", - "url": "pipelines/ProseqPEP.yaml", - "description": "A PEP for nascent RNA samples for the PEPPRO pipeline." - }, - "bedstat": { - "namespace": "pipelines", - "schema": "bedstat", - "url": "pipelines/bedstat.yaml", - "description": "bedstat PEP schema" - }, - "bedboss": { - "namespace": "pipelines", - "schema": "bedboss", - "url": "pipelines/bedboss.yaml", - "description": "bedboss run-all pep schema" - } -} \ No newline at end of file diff --git a/docs/refgenie/refgenie_build.yaml b/docs/refgenie/refgenie_build.yaml deleted file mode 100644 index bbd293c..0000000 --- a/docs/refgenie/refgenie_build.yaml +++ /dev/null @@ -1,42 +0,0 @@ -description: databio_genomes PEP schema - -properties: - samples: - type: array - items: - type: object - properties: - sample_name: - type: string - description: "name of the sample, which is the name of the output BED file" - genome: - type: string - description: "namespace for the assets to be build" - pattern: ^[^/:]*$ - asset: - type: string - description: "name of the asset to be build" - pattern: ^[^/:]*$ - tag: - type: string - description: "tag of the asset to be build" - pattern: ^[^/:]*$ - input_value: - type: string - description: "value of refgenie build function input" - local_input: - type: string - description: "absolute path for the input file" - input_type: - type: string - pattern: "^assets*|^params*|^files*" - description: "type of the refgenie build function input" - files: - - local_input - required: - - sample_name - - asset - - genome - - local_input -required: - - samples \ No newline at end of file diff --git a/docs/refgenie/schemas.json b/docs/refgenie/schemas.json deleted file mode 100644 index bb36f76..0000000 --- a/docs/refgenie/schemas.json +++ /dev/null @@ -1,8 +0,0 @@ -{ - "refgenie_build": { - "namespace": "refgenie", - "schema": "refgenie_build", - "url": "refgenie/refgenie_build.yaml", - "description": "databio_genomes PEP schema" - } -} \ No newline at end of file diff --git a/docs/refget/ACDList.yaml b/docs/refget/ACDList.yaml deleted file mode 100644 index 6ba1309..0000000 --- a/docs/refget/ACDList.yaml +++ /dev/null @@ -1,13 +0,0 @@ -description: "Schema for a list of ACDs; analogous to a collection of fasta files" -type: array -items: - type: object - properties: - name: - type: string - collection_digest: - type: string - required: - - collection_digest - recursive: - - collection_digest diff --git a/docs/refget/ASDList.yaml b/docs/refget/ASDList.yaml deleted file mode 100644 index 8f2f299..0000000 --- a/docs/refget/ASDList.yaml +++ /dev/null @@ -1,25 +0,0 @@ -description: "Schema for List of ASDs" -type: array -items: - type: object - properties: - name: - type: string - length: - type: "integer" - topology: - type: string - enum: ["circular", "linear"] - default: "linear" - sequence_digest: - type: string - description: "The sequence digest" - required: - - length - - name - - topology - recursive: - - sequence_digest - not: - required: - - sequence diff --git a/docs/refget/AnnotatedArrayedSequenceCollection.yaml b/docs/refget/AnnotatedArrayedSequenceCollection.yaml deleted file mode 100644 index a64dcd5..0000000 --- a/docs/refget/AnnotatedArrayedSequenceCollection.yaml +++ /dev/null @@ -1,48 +0,0 @@ -description: "A collection of sequences" -type: object -henge_class: "ArrayedNestedSequenceCollection" -properties: - seqcol: - type: object - henge_class: "SeqCol" - properties: - names: - type: array - henge_class: "Names" - items: - type: string - lengths: - type: array - henge_class: "Lengths" - items: - type: integer - sequences: - type: array - henge_class: "Sequences" - items: - type: string - henge_class: "Sequence" - description: "Actual sequence content" - annotation: - type: object - henge_class: "SeqColAnno" - properties: - topologies: - type: array - henge_class: "Topologies" - items: - type: string - enum: ["circular", "linear"] - default: "linear" - masks: - type: array - henge_class: "Masks" - items: - type: string - importances: - type: array - henge_class: "Importances" - items: - type: boolean -required: - - lengths diff --git a/docs/refget/AnnotatedSequenceList.yaml b/docs/refget/AnnotatedSequenceList.yaml deleted file mode 100644 index 320fdf9..0000000 --- a/docs/refget/AnnotatedSequenceList.yaml +++ /dev/null @@ -1,33 +0,0 @@ -description: "Schema for List of ASDs" -henge_class: "AnnotatedSequenceList" -recursive: true -type: array -items: - description: "Schema for an Annotated Sequence Digest; a digested Sequence plus metadata" - type: object - henge_class: ASD - properties: - name: - type: string - length: - type: "integer" - topology: - type: string - enum: ["circular", "linear"] - default: "linear" - sequence: - description: "Schema for a single raw sequence" - henge_class: sequence - type: object - properties: - sequence: - type: string - description: "Actual sequence content" - required: - - sequence - required: - - length - - name - - topology - recursive: - - sequence diff --git a/docs/refget/ArrayedNestedSequenceCollection.yaml b/docs/refget/ArrayedNestedSequenceCollection.yaml deleted file mode 100644 index ad0b060..0000000 --- a/docs/refget/ArrayedNestedSequenceCollection.yaml +++ /dev/null @@ -1,44 +0,0 @@ -description: "A collection of sequences" -type: object -henge_class: "ArrayedNestedSequenceCollection" -properties: - seqcol: - type: object - henge_class: "SeqCol" - properties: - names: - type: array - henge_class: "Names" - items: - type: string - lengths: - type: array - henge_class: "Lengths" - items: - type: integer - sequences: - type: array - henge_class: "Sequences" - items: - type: string - henge_class: "Sequence" - description: "Actual sequence content" - topologies: - type: array - henge_class: "Topologies" - items: - type: string - enum: ["circular", "linear"] - default: "linear" - masks: - type: array - henge_class: "Masks" - items: - type: string - importances: - type: array - henge_class: "Importances" - items: - type: boolean -required: - - lengths diff --git a/docs/refget/ArrayedSequenceCollection.yaml b/docs/refget/ArrayedSequenceCollection.yaml deleted file mode 100644 index 196813f..0000000 --- a/docs/refget/ArrayedSequenceCollection.yaml +++ /dev/null @@ -1,40 +0,0 @@ -description: "A collection of sequences" -type: object -henge_class: "ArrayedSequenceCollection" -properties: - names: - type: array - henge_class: "Names" - items: - type: string - lengths: - type: array - henge_class: "Lengths" - items: - type: integer - sequences: - type: array - henge_class: "Sequences" - items: - type: string - henge_class: "Sequence" - description: "Actual sequence content" - topologies: - type: array - henge_class: "Topologies" - items: - type: string - enum: ["circular", "linear"] - default: "linear" - masks: - type: array - henge_class: "Masks" - items: - type: string - importances: - type: array - henge_class: "Importances" - items: - type: boolean -required: - - lengths diff --git a/docs/refget/CustomAnnotatedArrayedSequenceCollection.yaml b/docs/refget/CustomAnnotatedArrayedSequenceCollection.yaml deleted file mode 100644 index decf5d8..0000000 --- a/docs/refget/CustomAnnotatedArrayedSequenceCollection.yaml +++ /dev/null @@ -1,38 +0,0 @@ -description: "A collection of sequences" -type: object -henge_class: "AnnotatedArrayedSequenceCollection" -properties: - seqcol: - type: object - henge_class: "SeqCol" - properties: - names: - type: array - henge_class: "Names" - items: - type: string - lengths: - type: array - henge_class: "Lengths" - items: - type: integer - sequences: - type: array - henge_class: "Sequences" - items: - type: string - henge_class: "Sequence" - description: "Actual sequence content" - annotation: - type: array - henge_class: "SeqColAnnos" - items: - type: object - henge_class: "SeqColAnno" - properties: - property_name: - type: string - property_value: - type: array -required: - - lengths diff --git a/docs/refget/RawSeqCol.yaml b/docs/refget/RawSeqCol.yaml deleted file mode 100644 index 1881280..0000000 --- a/docs/refget/RawSeqCol.yaml +++ /dev/null @@ -1,19 +0,0 @@ -description: "Schema for List of ASDs" -type: array -henge_class: "RawSeqCol" -items: - description: "Schema for an Annotated Sequence Digest; a digested Sequence plus metadata" - type: object - henge_class: ASD - properties: - name: - type: string - length: - type: "integer" - sequence: - description: "Actual sequence content for a single raw sequence" - henge_class: sequence - type: string - required: - - length - - name diff --git a/docs/refget/SeqColArraySet.yaml b/docs/refget/SeqColArraySet.yaml deleted file mode 100644 index d37158f..0000000 --- a/docs/refget/SeqColArraySet.yaml +++ /dev/null @@ -1,27 +0,0 @@ -description: "SeqColArraySet" -type: object -henge_class: "SeqColArraySet" -properties: - topologies: - type: array - henge_class: "array" - items: - type: string - enum: ["circular", "linear"] - default: "linear" - names: - type: array - henge_class: "array" - items: - type: string - lengths: - type: array - henge_class: "array" - items: - type: string - sequences: - type: array - henge_class: "seqarray" - items: - type: string - henge_class: sequence diff --git a/docs/refget/SeqColArraySetInherent.yaml b/docs/refget/SeqColArraySetInherent.yaml deleted file mode 100644 index 743cc28..0000000 --- a/docs/refget/SeqColArraySetInherent.yaml +++ /dev/null @@ -1,36 +0,0 @@ -description: "SeqColArraySet" -type: object -henge_class: "SeqColArraySet" -properties: - topologies: - type: array - henge_class: "strarray" - items: - type: string - enum: ["circular", "linear"] - default: "linear" - names: - type: array - henge_class: "strarray" - items: - type: string - lengths: - type: array - henge_class: "intarray" - items: - type: integer - sequences: - type: array - henge_class: "seqarray" - items: - type: string - henge_class: sequence - sorted_name_length_pairs: - type: array - henge_class: "strarray" - items: - type: string -inherent: - - names - - lengths - - sequences diff --git a/docs/refget/TASeqCol.yaml b/docs/refget/TASeqCol.yaml deleted file mode 100644 index 19a4eb7..0000000 --- a/docs/refget/TASeqCol.yaml +++ /dev/null @@ -1,31 +0,0 @@ -description: "TAseqcol" -type: object -henge_class: "TASeqCol" -properties: - topology: - type: array - henge_class: "TopologyVec" - items: - type: string - enum: ["circular", "linear"] - default: "linear" - rawseqcol: - description: "Schema for List of ASDs" - type: array - henge_class: "RawSeqCol" - items: - description: "Schema for an Annotated Sequence Digest; a digested Sequence plus metadata" - type: object - henge_class: ASD - properties: - name: - type: string - length: - type: "integer" - sequence: - type: string - henge_class: sequence - description: "Actual sequence content" - required: - - length - - name diff --git a/docs/refget/annotated_collection_digest.yaml b/docs/refget/annotated_collection_digest.yaml deleted file mode 100644 index b351c2c..0000000 --- a/docs/refget/annotated_collection_digest.yaml +++ /dev/null @@ -1,11 +0,0 @@ -description: "Schema for an Annotated Collection Digest; this is analogous to a single fasta file with metadata." -type: object -properties: - name: - type: string - collection_digest: - type: string -required: - - collection_digest -recursive: - - collection_digest \ No newline at end of file diff --git a/docs/refget/annotated_sequence_digest.yaml b/docs/refget/annotated_sequence_digest.yaml deleted file mode 100644 index a9062a8..0000000 --- a/docs/refget/annotated_sequence_digest.yaml +++ /dev/null @@ -1,23 +0,0 @@ -description: "Schema for an Annotated Sequence Digest; a digested Sequence plus metadata" -type: object -properties: - name: - type: string - length: - type: "integer" - topology: - type: string - enum: ["circular", "linear"] - default: "linear" - sequence_digest: - type: string - description: "The sequence digest" -required: - - length - - name - - topology -recursive: - - sequence_digest -not: - required: - - sequence diff --git a/docs/refget/schemas.json b/docs/refget/schemas.json deleted file mode 100644 index d22f569..0000000 --- a/docs/refget/schemas.json +++ /dev/null @@ -1,86 +0,0 @@ -{ - "SeqColArraySetInherent": { - "namespace": "refget", - "schema": "SeqColArraySetInherent", - "url": "refget/SeqColArraySetInherent.yaml", - "description": "SeqColArraySet" - }, - "sequence": { - "namespace": "refget", - "schema": "sequence", - "url": "refget/sequence.yaml", - "description": "Schema for a single raw sequence" - }, - "annotated_collection_digest": { - "namespace": "refget", - "schema": "annotated_collection_digest", - "url": "refget/annotated_collection_digest.yaml", - "description": "Schema for an Annotated Collection Digest; this is analogous to a single fasta file with metadata." - }, - "ArrayedNestedSequenceCollection": { - "namespace": "refget", - "schema": "ArrayedNestedSequenceCollection", - "url": "refget/ArrayedNestedSequenceCollection.yaml", - "description": "A collection of sequences" - }, - "ASDList": { - "namespace": "refget", - "schema": "ASDList", - "url": "refget/ASDList.yaml", - "description": "Schema for List of ASDs" - }, - "annotated_sequence_digest": { - "namespace": "refget", - "schema": "annotated_sequence_digest", - "url": "refget/annotated_sequence_digest.yaml", - "description": "Schema for an Annotated Sequence Digest; a digested Sequence plus metadata" - }, - "ACDList": { - "namespace": "refget", - "schema": "ACDList", - "url": "refget/ACDList.yaml", - "description": "Schema for a list of ACDs; analogous to a collection of fasta files" - }, - "ArrayedSequenceCollection": { - "namespace": "refget", - "schema": "ArrayedSequenceCollection", - "url": "refget/ArrayedSequenceCollection.yaml", - "description": "A collection of sequences" - }, - "RawSeqCol": { - "namespace": "refget", - "schema": "RawSeqCol", - "url": "refget/RawSeqCol.yaml", - "description": "Schema for List of ASDs" - }, - "TASeqCol": { - "namespace": "refget", - "schema": "TASeqCol", - "url": "refget/TASeqCol.yaml", - "description": "TAseqcol" - }, - "CustomAnnotatedArrayedSequenceCollection": { - "namespace": "refget", - "schema": "CustomAnnotatedArrayedSequenceCollection", - "url": "refget/CustomAnnotatedArrayedSequenceCollection.yaml", - "description": "A collection of sequences" - }, - "SeqColArraySet": { - "namespace": "refget", - "schema": "SeqColArraySet", - "url": "refget/SeqColArraySet.yaml", - "description": "SeqColArraySet" - }, - "AnnotatedArrayedSequenceCollection": { - "namespace": "refget", - "schema": "AnnotatedArrayedSequenceCollection", - "url": "refget/AnnotatedArrayedSequenceCollection.yaml", - "description": "A collection of sequences" - }, - "AnnotatedSequenceList": { - "namespace": "refget", - "schema": "AnnotatedSequenceList", - "url": "refget/AnnotatedSequenceList.yaml", - "description": "Schema for List of ASDs" - } -} \ No newline at end of file diff --git a/docs/refget/sequence.yaml b/docs/refget/sequence.yaml deleted file mode 100644 index fe33ead..0000000 --- a/docs/refget/sequence.yaml +++ /dev/null @@ -1,8 +0,0 @@ -description: "Schema for a single raw sequence" -type: object -properties: - sequence: - type: string - description: "Actual sequence content" -required: - - sequence \ No newline at end of file