mirror of
https://github.com/featurebasedb/featurebase.git
synced 2026-08-28 02:44:59 +00:00
Remove view from API, handler, docs
This commit is contained in:
Yuce Tekol
parent
9456a2076d
commit
738dead374
10 changed files with 36 additions and 169 deletions
20
api.go
20
api.go
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@ -283,9 +283,9 @@ func (api *API) DeleteFrame(ctx context.Context, indexName string, frameName str
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return nil
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}
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// ExportCSV encodes the fragment designated by the index,frame,view,slice as
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// ExportCSV encodes the fragment designated by the index,frame,slice as
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// CSV of the form <row>,<col>
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func (api *API) ExportCSV(ctx context.Context, indexName string, frameName string, viewName string, slice uint64, w io.Writer) error {
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func (api *API) ExportCSV(ctx context.Context, indexName string, frameName string, slice uint64, w io.Writer) error {
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if err := api.validate(apiExportCSV); err != nil {
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return errors.Wrap(err, "validating api method")
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}
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@ -297,7 +297,7 @@ func (api *API) ExportCSV(ctx context.Context, indexName string, frameName strin
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}
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// Find the fragment.
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f := api.Holder.Fragment(indexName, frameName, viewName, slice)
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f := api.Holder.Fragment(indexName, frameName, ViewStandard, slice)
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if f == nil {
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return ErrFragmentNotFound
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}
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@ -333,13 +333,13 @@ func (api *API) SliceNodes(ctx context.Context, indexName string, slice uint64)
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// MarshalFragment returns an object which can write the specified fragment's data
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// to an io.Writer. The serialized data can be read back into a fragment with
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// the UnmarshalFragment API call.
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func (api *API) MarshalFragment(ctx context.Context, indexName string, frameName string, viewName string, slice uint64) (io.WriterTo, error) {
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func (api *API) MarshalFragment(ctx context.Context, indexName string, frameName string, slice uint64) (io.WriterTo, error) {
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if err := api.validate(apiMarshalFragment); err != nil {
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return nil, errors.Wrap(err, "validating api method")
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}
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// Retrieve fragment from holder.
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f := api.Holder.Fragment(indexName, frameName, viewName, slice)
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f := api.Holder.Fragment(indexName, frameName, ViewStandard, slice)
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if f == nil {
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return nil, ErrFragmentNotFound
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}
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@ -349,7 +349,7 @@ func (api *API) MarshalFragment(ctx context.Context, indexName string, frameName
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// UnmarshalFragment creates a new fragment (if necessary) and reads data from a
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// Reader which was previously written by MarshalFragment to populate the
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// fragment's data.
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func (api *API) UnmarshalFragment(ctx context.Context, indexName string, frameName string, viewName string, slice uint64, reader io.ReadCloser) error {
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func (api *API) UnmarshalFragment(ctx context.Context, indexName string, frameName string, slice uint64, reader io.ReadCloser) error {
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if err := api.validate(apiUnmarshalFragment); err != nil {
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return errors.Wrap(err, "validating api method")
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}
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@ -361,7 +361,7 @@ func (api *API) UnmarshalFragment(ctx context.Context, indexName string, frameNa
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}
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// Retrieve view.
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view, err := f.CreateViewIfNotExists(viewName)
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view, err := f.CreateViewIfNotExists(ViewStandard)
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if err != nil {
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return errors.Wrap(err, "creating view")
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}
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@ -397,7 +397,7 @@ func (api *API) FragmentBlockData(ctx context.Context, body io.Reader) ([]byte,
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}
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// Retrieve fragment from holder.
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f := api.Holder.Fragment(req.Index, req.Frame, req.View, req.Slice)
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f := api.Holder.Fragment(req.Index, req.Frame, ViewStandard, req.Slice)
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if f == nil {
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return nil, ErrFragmentNotFound
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}
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@ -415,13 +415,13 @@ func (api *API) FragmentBlockData(ctx context.Context, body io.Reader) ([]byte,
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}
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// FragmentBlocks returns the checksums and block ids for all blocks in the specified fragment.
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func (api *API) FragmentBlocks(ctx context.Context, indexName string, frameName string, viewName string, slice uint64) ([]FragmentBlock, error) {
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func (api *API) FragmentBlocks(ctx context.Context, indexName string, frameName string, slice uint64) ([]FragmentBlock, error) {
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if err := api.validate(apiFragmentBlocks); err != nil {
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return nil, errors.Wrap(err, "validating api method")
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}
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// Retrieve fragment from holder.
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f := api.Holder.Fragment(indexName, frameName, viewName, slice)
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f := api.Holder.Fragment(indexName, frameName, ViewStandard, slice)
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if f == nil {
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return nil, ErrFragmentNotFound
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}
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65
client.go
65
client.go
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@ -508,13 +508,11 @@ func (c *InternalHTTPClient) importValueNode(ctx context.Context, node *Node, bu
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}
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// ExportCSV bulk exports data for a single slice from a host to CSV format.
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func (c *InternalHTTPClient) ExportCSV(ctx context.Context, index, frame, view string, slice uint64, w io.Writer) error {
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func (c *InternalHTTPClient) ExportCSV(ctx context.Context, index, frame string, slice uint64, w io.Writer) error {
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if index == "" {
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return ErrIndexRequired
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} else if frame == "" {
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return ErrFrameRequired
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} else if view != ViewStandard {
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return ErrInvalidView
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}
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// Retrieve a list of nodes that own the slice.
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@ -528,7 +526,7 @@ func (c *InternalHTTPClient) ExportCSV(ctx context.Context, index, frame, view s
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for _, i := range rand.Perm(len(nodes)) {
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node := nodes[i]
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if err := c.exportNodeCSV(ctx, node, index, frame, view, slice, w); err != nil {
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if err := c.exportNodeCSV(ctx, node, index, frame, slice, w); err != nil {
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e = fmt.Errorf("export node: host=%s, err=%s", node.URI, err)
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continue
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} else {
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@ -540,13 +538,12 @@ func (c *InternalHTTPClient) ExportCSV(ctx context.Context, index, frame, view s
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}
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// exportNode copies a CSV export from a node to w.
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func (c *InternalHTTPClient) exportNodeCSV(ctx context.Context, node *Node, index, frame, view string, slice uint64, w io.Writer) error {
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func (c *InternalHTTPClient) exportNodeCSV(ctx context.Context, node *Node, index, frame string, slice uint64, w io.Writer) error {
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// Create URL.
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u := nodePathToURL(node, "/export")
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u.RawQuery = url.Values{
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"index": {index},
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"frame": {frame},
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"view": {view},
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"slice": {strconv.FormatUint(slice, 10)},
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}.Encode()
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@ -578,19 +575,18 @@ func (c *InternalHTTPClient) exportNodeCSV(ctx context.Context, node *Node, inde
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return nil
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}
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func (c *InternalHTTPClient) RetrieveSliceFromURI(ctx context.Context, index, frame, view string, slice uint64, uri URI) (io.ReadCloser, error) {
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func (c *InternalHTTPClient) RetrieveSliceFromURI(ctx context.Context, index, frame string, slice uint64, uri URI) (io.ReadCloser, error) {
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node := &Node{
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URI: uri,
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}
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return c.backupSliceNode(ctx, index, frame, view, slice, node)
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return c.backupSliceNode(ctx, index, frame, slice, node)
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}
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func (c *InternalHTTPClient) backupSliceNode(ctx context.Context, index, frame, view string, slice uint64, node *Node) (io.ReadCloser, error) {
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func (c *InternalHTTPClient) backupSliceNode(ctx context.Context, index, frame string, slice uint64, node *Node) (io.ReadCloser, error) {
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u := nodePathToURL(node, "/fragment/data")
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u.RawQuery = url.Values{
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"index": {index},
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"frame": {frame},
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"view": {view},
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"slice": {strconv.FormatUint(slice, 10)},
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}.Encode()
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@ -669,50 +665,13 @@ func (c *InternalHTTPClient) CreateFrame(ctx context.Context, index, frame strin
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}
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}
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// FrameViews returns a list of view names for a frame.
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func (c *InternalHTTPClient) FrameViews(ctx context.Context, index, frame string) ([]string, error) {
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// Create URL & HTTP request.
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u := uriPathToURL(c.defaultURI, fmt.Sprintf("/index/%s/frame/%s/views", index, frame))
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req, err := http.NewRequest("GET", u.String(), nil)
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if err != nil {
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return nil, errors.Wrap(err, "creating request")
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}
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req.Header.Set("Accept", "application/json")
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req.Header.Set("User-Agent", "pilosa/"+Version)
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// Execute request against the host.
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resp, err := c.HTTPClient.Do(req.WithContext(ctx))
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if err != nil {
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return nil, errors.Wrap(err, "executing request")
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}
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defer resp.Body.Close()
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// Handle response based on status code.
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switch resp.StatusCode {
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case http.StatusOK:
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case http.StatusNotFound:
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return nil, ErrFrameNotFound
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default:
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body, _ := ioutil.ReadAll(resp.Body)
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return nil, errors.New(string(body))
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}
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// Decode response.
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var rsp getFrameViewsResponse
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if err := json.NewDecoder(resp.Body).Decode(&rsp); err != nil {
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return nil, errors.Wrap(err, "decoding")
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}
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return rsp.Views, nil
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}
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// FragmentBlocks returns a list of block checksums for a fragment on a host.
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// Only returns blocks which contain data.
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func (c *InternalHTTPClient) FragmentBlocks(ctx context.Context, index, frame, view string, slice uint64) ([]FragmentBlock, error) {
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func (c *InternalHTTPClient) FragmentBlocks(ctx context.Context, index, frame string, slice uint64) ([]FragmentBlock, error) {
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u := uriPathToURL(c.defaultURI, "/fragment/blocks")
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u.RawQuery = url.Values{
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"index": {index},
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"frame": {frame},
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"view": {view},
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"slice": {strconv.FormatUint(slice, 10)},
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}.Encode()
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@ -749,11 +708,10 @@ func (c *InternalHTTPClient) FragmentBlocks(ctx context.Context, index, frame, v
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}
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// BlockData returns row/column id pairs for a block.
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func (c *InternalHTTPClient) BlockData(ctx context.Context, index, frame, view string, slice uint64, block int) ([]uint64, []uint64, error) {
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func (c *InternalHTTPClient) BlockData(ctx context.Context, index, frame string, slice uint64, block int) ([]uint64, []uint64, error) {
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buf, err := proto.Marshal(&internal.BlockDataRequest{
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Index: index,
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Frame: frame,
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View: view,
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Slice: slice,
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Block: uint64(block),
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})
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@ -1101,11 +1059,10 @@ type InternalClient interface {
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EnsureIndex(ctx context.Context, name string, options IndexOptions) error
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EnsureFrame(ctx context.Context, indexName string, frameName string, options FrameOptions) error
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ImportValue(ctx context.Context, index, frame, field string, slice uint64, vals []FieldValue) error
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ExportCSV(ctx context.Context, index, frame, view string, slice uint64, w io.Writer) error
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ExportCSV(ctx context.Context, index, frame string, slice uint64, w io.Writer) error
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CreateFrame(ctx context.Context, index, frame string, opt FrameOptions) error
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FrameViews(ctx context.Context, index, frame string) ([]string, error)
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FragmentBlocks(ctx context.Context, index, frame, view string, slice uint64) ([]FragmentBlock, error)
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BlockData(ctx context.Context, index, frame, view string, slice uint64, block int) ([]uint64, []uint64, error)
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FragmentBlocks(ctx context.Context, index, frame string, slice uint64) ([]FragmentBlock, error)
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BlockData(ctx context.Context, index, frame string, slice uint64, block int) ([]uint64, []uint64, error)
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ColumnAttrDiff(ctx context.Context, index string, blks []AttrBlock) (map[uint64]map[string]interface{}, error)
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RowAttrDiff(ctx context.Context, index, frame string, blks []AttrBlock) (map[uint64]map[string]interface{}, error)
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SendMessage(ctx context.Context, uri *URI, pb proto.Message) error
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@ -335,7 +335,7 @@ func TestClient_FragmentBlocks(t *testing.T) {
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// Retrieve blocks.
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c := test.MustNewClient(s.Host(), defaultClient)
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blocks, err := c.FragmentBlocks(context.Background(), "i", "f", pilosa.ViewStandard, 0)
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blocks, err := c.FragmentBlocks(context.Background(), "i", "f", 0)
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if err != nil {
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t.Fatal(err)
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} else if len(blocks) != 2 {
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@ -1259,7 +1259,7 @@ func (c *Cluster) FollowResizeInstruction(instr *internal.ResizeInstruction) err
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// Stream slice from remote node.
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c.Logger.Printf("retrieve slice %d for index %s from host %s", src.Slice, src.Index, src.Node.URI)
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rd, err := client.RetrieveSliceFromURI(context.Background(), src.Index, src.Frame, src.View, src.Slice, srcURI)
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rd, err := client.RetrieveSliceFromURI(context.Background(), src.Index, src.Frame, src.Slice, srcURI)
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if err != nil {
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// For now it is an acceptable error if the fragment is not found
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// on the remote node. This occurs when a slice has been skipped and
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@ -89,7 +89,7 @@ func (cmd *ExportCommand) Run(ctx context.Context) error {
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// Export each slice.
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for slice := uint64(0); slice <= maxSlices[cmd.Index]; slice++ {
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logger.Printf("exporting slice: %d", slice)
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if err := client.ExportCSV(ctx, cmd.Index, cmd.Frame, pilosa.ViewStandard, slice, w); err != nil {
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if err := client.ExportCSV(ctx, cmd.Index, cmd.Frame, slice, w); err != nil {
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return errors.Wrap(err, "exporting")
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}
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}
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@ -70,9 +70,9 @@ pilosa import -i project -f stargazer --field star_count project-stargazer-count
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#### Exporting
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Exporting data to csv can be performed on a live instance of Pilosa. You need to specify the index, frame, and view (default is standard). The API also expects the slice number, but the `pilosa export` sub command will export all slices within a Frame. The data will be in csv format `Row,Column` and sorted by column.
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Exporting data to csv can be performed on a live instance of Pilosa. You need to specify the index and the frame. The API also expects the slice number, but the `pilosa export` sub command will export all slices within a Frame. The data will be in csv format `Row,Column` and sorted by column.
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```request
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curl "http://localhost:10101/export?index=repository&frame=stargazer&slice=0&view=standard" \
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curl "http://localhost:10101/export?index=repository&frame=stargazer&slice=0" \
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--header "Accept: text/csv"
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```
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```response
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@ -244,29 +244,6 @@ threshold = 90
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return the set of molecules that have at least a 90% similarity with the given molecule.
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The Inverse view swaps the rows and columns automatically to enable queries over either the chembl_id or fingerprint.
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Standard View is used to calculate similarity
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```
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Index: mole
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View: Standard
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Col: chembl_id
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Frame: fingerprint
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Row: position_id ("on" bit positions of a fingerprint)
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```
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Inverse View is used for finding chembl_id based on given SMILES.
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From a given SMILES, we use RDKit to convert it to fingerprints with "on" bit position. From "on" bit positions, we can search a list of chembl_ids that match the bit positions. To choose the right chembl_id, we need another query to Standard View then choose the right chembl_id which has the length that matches the given fingerprint's length after using RDKit to convert SMILES to fingerprint.
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```
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Index: mole
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View: Inverse
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Col: position_id ("on" bit positions of a fingerprint)
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Frame: fingerprint
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Row: chembl_id
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```
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After retrieving chembl_id from the Inverse View, we can use the Tanimoto coefficient to compare chembl_id with the entire data set of molecules. The result of this comparison is the list of `chembl_id`s that have a Tanimoto coefficient greater than the given threshold.
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#### Import process
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To import data into Pilosa, we need to get chembl_id and SMILES from SD files, convert SMILES to Morgan fingerprints, and then write chembl_id and fingerprint to Pilosa. The fastest way is to extracted chembl_id and SMILES from SD file to csv file, then use the `pilosa import` command to import the csv file into Pilosa. Since chembl_id in the SD file is always paired with CHEMBL, e.g CHEMBL6329, and because Pilosa doesn't support string keys, we will ignore CHEMBL and instead use chembl_id as an integer key.
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@ -312,15 +289,6 @@ Return chembl_id = 6223. This script uses Pilosa’s Intersection query to get a
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fp = list(AllChem.GetMorganFingerprintAsBitVect(mol, 2, nBits=4096).GetOnBits())
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```
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* Query all chembl_id that have all "on" positions from the inverse view, return list of chembl_id
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```python
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bit_maps = ["Bitmap(col=%s, frame=%s, inversed=%s)" % (f, frame, True) for f in fp]
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bitmap_string = ', '.join(bit_maps)
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intersection = "Intersect(%s)" % bitmap_string
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mole_ids = requests.post("http://%s/index/%s/query" % (host, db), data=intersection).json()["results"][0]["bits"]
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```
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* From list of chembl_id, query all "on" position from mol index, if the length of array of "on" position is matched to len(fp) then return that chembl_id, otherwise the given SMILES does not exist.
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```python
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@ -584,10 +584,7 @@ func (e *Executor) executeTopNSlice(ctx context.Context, index string, c *pql.Ca
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frame = DefaultFrame
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}
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// Determine view.
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view := ViewStandard
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f := e.Holder.Fragment(index, frame, view, slice)
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f := e.Holder.Fragment(index, frame, ViewStandard, slice)
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if f == nil {
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return nil, nil
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}
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@ -1783,7 +1783,7 @@ func (s *FragmentSyncer) SyncFragment() error {
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// Retrieve remote blocks.
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client := NewInternalHTTPClientFromURI(&node.URI, s.RemoteClient)
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blocks, err := client.FragmentBlocks(context.Background(), s.Fragment.Index(), s.Fragment.Frame(), s.Fragment.View(), s.Fragment.Slice())
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blocks, err := client.FragmentBlocks(context.Background(), s.Fragment.Index(), s.Fragment.Frame(), s.Fragment.Slice())
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if err != nil && err != ErrFragmentNotFound {
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return errors.Wrap(err, "getting blocks")
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}
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@ -1862,7 +1862,7 @@ func (s *FragmentSyncer) syncBlock(id int) error {
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clients = append(clients, client)
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// Only sync the standard block.
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rowIDs, columnIDs, err := client.BlockData(context.Background(), f.Index(), f.Frame(), ViewStandard, f.Slice(), id)
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rowIDs, columnIDs, err := client.BlockData(context.Background(), f.Index(), f.Frame(), f.Slice(), id)
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if err != nil {
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return errors.Wrap(err, "getting block")
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}
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69
handler.go
69
handler.go
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@ -108,10 +108,10 @@ func (h *Handler) populateValidators() {
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h.validators["GetFragmentNodes"] = queryValidationSpecRequired("slice", "index")
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h.validators["GetSliceMax"] = queryValidationSpecRequired()
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h.validators["PostQuery"] = queryValidationSpecRequired().Optional("slices", "columnAttrs", "excludeRowAttrs", "excludeColumns")
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h.validators["GetExport"] = queryValidationSpecRequired("index", "frame", "view", "slice")
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h.validators["GetFragmentData"] = queryValidationSpecRequired("index", "frame", "view", "slice")
|
||||
h.validators["PostFragmentData"] = queryValidationSpecRequired("index", "frame", "view", "slice")
|
||||
h.validators["GetFragmentBlocks"] = queryValidationSpecRequired("index", "frame", "view", "slice")
|
||||
h.validators["GetExport"] = queryValidationSpecRequired("index", "frame", "slice")
|
||||
h.validators["GetFragmentData"] = queryValidationSpecRequired("index", "frame", "slice")
|
||||
h.validators["PostFragmentData"] = queryValidationSpecRequired("index", "frame", "slice")
|
||||
h.validators["GetFragmentBlocks"] = queryValidationSpecRequired("index", "frame", "slice")
|
||||
}
|
||||
|
||||
func (h *Handler) queryArgValidator(next http.Handler) http.Handler {
|
||||
|
|
@ -172,8 +172,6 @@ func NewRouter(handler *Handler) *mux.Router {
|
|||
router.HandleFunc("/index/{index}/frame/{frame}/field/{field}", handler.handlePostFrameField).Methods("POST")
|
||||
router.HandleFunc("/index/{index}/frame/{frame}/fields", handler.handleGetFrameFields).Methods("GET")
|
||||
router.HandleFunc("/index/{index}/frame/{frame}/field/{field}", handler.handleDeleteFrameField).Methods("DELETE")
|
||||
router.HandleFunc("/index/{index}/frame/{frame}/views", handler.handleGetFrameViews).Methods("GET")
|
||||
router.HandleFunc("/index/{index}/frame/{frame}/view/{view}", handler.handleDeleteView).Methods("DELETE")
|
||||
router.HandleFunc("/index/{index}/query", handler.handlePostQuery).Methods("POST").Name("PostQuery")
|
||||
router.HandleFunc("/recalculate-caches", handler.handleRecalculateCaches).Methods("POST")
|
||||
|
||||
|
|
@ -703,59 +701,6 @@ type getFrameFieldsResponse struct {
|
|||
|
||||
type deleteFrameFieldResponse struct{}
|
||||
|
||||
// handleGetFrameViews handles GET /frame/views request.
|
||||
func (h *Handler) handleGetFrameViews(w http.ResponseWriter, r *http.Request) {
|
||||
indexName := mux.Vars(r)["index"]
|
||||
frameName := mux.Vars(r)["frame"]
|
||||
|
||||
views, err := h.API.Views(r.Context(), indexName, frameName)
|
||||
if err != nil {
|
||||
if errors.Cause(err) == ErrFrameNotFound {
|
||||
http.Error(w, err.Error(), http.StatusNotFound)
|
||||
} else {
|
||||
http.Error(w, err.Error(), http.StatusInternalServerError)
|
||||
}
|
||||
return
|
||||
}
|
||||
|
||||
names := make([]string, len(views))
|
||||
for i := range views {
|
||||
names[i] = views[i].Name()
|
||||
}
|
||||
|
||||
// Encode response.
|
||||
if err := json.NewEncoder(w).Encode(getFrameViewsResponse{Views: names}); err != nil {
|
||||
h.Logger.Printf("response encoding error: %s", err)
|
||||
}
|
||||
}
|
||||
|
||||
// handleDeleteView handles Delete /frame/view request.
|
||||
func (h *Handler) handleDeleteView(w http.ResponseWriter, r *http.Request) {
|
||||
indexName := mux.Vars(r)["index"]
|
||||
frameName := mux.Vars(r)["frame"]
|
||||
viewName := mux.Vars(r)["view"]
|
||||
|
||||
if err := h.API.DeleteView(r.Context(), indexName, frameName, viewName); err != nil {
|
||||
if errors.Cause(err) == ErrFrameNotFound {
|
||||
http.Error(w, err.Error(), http.StatusNotFound)
|
||||
} else {
|
||||
http.Error(w, err.Error(), http.StatusBadRequest)
|
||||
}
|
||||
return
|
||||
}
|
||||
|
||||
// Encode response.
|
||||
if err := json.NewEncoder(w).Encode(deleteViewResponse{}); err != nil {
|
||||
h.Logger.Printf("response encoding error: %s", err)
|
||||
}
|
||||
}
|
||||
|
||||
type deleteViewResponse struct{}
|
||||
|
||||
type getFrameViewsResponse struct {
|
||||
Views []string `json:"views,omitempty"`
|
||||
}
|
||||
|
||||
// handlePostFrameAttrDiff handles POST /frame/attr/diff requests.
|
||||
func (h *Handler) handlePostFrameAttrDiff(w http.ResponseWriter, r *http.Request) {
|
||||
indexName := mux.Vars(r)["index"]
|
||||
|
|
@ -990,7 +935,7 @@ func (h *Handler) handleGetExport(w http.ResponseWriter, r *http.Request) {
|
|||
func (h *Handler) handleGetExportCSV(w http.ResponseWriter, r *http.Request) {
|
||||
// Parse query parameters.
|
||||
q := r.URL.Query()
|
||||
index, frame, view := q.Get("index"), q.Get("frame"), q.Get("view")
|
||||
index, frame := q.Get("index"), q.Get("frame")
|
||||
|
||||
slice, err := strconv.ParseUint(q.Get("slice"), 10, 64)
|
||||
if err != nil {
|
||||
|
|
@ -998,7 +943,7 @@ func (h *Handler) handleGetExportCSV(w http.ResponseWriter, r *http.Request) {
|
|||
return
|
||||
}
|
||||
|
||||
if err = h.API.ExportCSV(r.Context(), index, frame, view, slice, w); err != nil {
|
||||
if err = h.API.ExportCSV(r.Context(), index, frame, slice, w); err != nil {
|
||||
switch errors.Cause(err) {
|
||||
case ErrFragmentNotFound:
|
||||
break
|
||||
|
|
@ -1066,7 +1011,7 @@ func (h *Handler) handleGetFragmentBlocks(w http.ResponseWriter, r *http.Request
|
|||
return
|
||||
}
|
||||
|
||||
blocks, err := h.API.FragmentBlocks(r.Context(), q.Get("index"), q.Get("frame"), q.Get("view"), slice)
|
||||
blocks, err := h.API.FragmentBlocks(r.Context(), q.Get("index"), q.Get("frame"), slice)
|
||||
if err != nil {
|
||||
if errors.Cause(err) == ErrFragmentNotFound {
|
||||
http.Error(w, err.Error(), http.StatusNotFound)
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue