Error - file not found
ltosti opened this issue · comments
Hi there,
I tried to run the SPRING Viewer but I get the following message and nothing is displayed:
127.0.0.1 - - [08/Nov/2018 15:12:22] "GET /scripts_1_6_dev/jquery-3.1.0.min.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/newSpringPlot.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/colorBar.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/d3-queue.v3.min.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/d3.min.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/forceLayout_script.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/rotation_script.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/selection_script.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/settings_script.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/diffex_script.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/jspdf.min.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/coexpression_script.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/simg.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/canvg.min.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/FileSaver.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/pixi.min.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/spin.min.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/make_new_SPRINGplot_script.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/LineSprite.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/clone_viewer.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/stickyNote.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/smoothing_imputation.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/downloadSelectedExpr_script.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_dev_shared/jquery.autocomplete.min.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/sweetalert.min.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/doublet_detector.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/PAGA_viewer.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/cluster2_script.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/colorpicker.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] code 404, message File not found
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/text_annotations.js HTTP/1.1" 404 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/selection_logic.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/colorpicker_eye.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/colorpicker_layout.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/colorpicker_utils.js HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /scripts_1_6_dev/sound_effects/icon_mute.svg HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] code 404, message File not found
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /Users/luca_work/Desktop/spring//coordinates.txt HTTP/1.1" 404 -
127.0.0.1 - - [08/Nov/2018 15:12:23] code 404, message File not found
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /Users/luca_work/Desktop/spring//mutability.txt HTTP/1.1" 404 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /stuff/colorpicker_images/custom_background.png HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /stuff/colorpicker_images/custom_rgb_r.png HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] code 404, message File not found
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /stuff/colorpicker_images/custom_hsb_b.png HTTP/1.1" 404 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /stuff/colorpicker_images/custom_submit.png HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /stuff/colorpicker_images/colorpicker_overlay.png HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /stuff/colorpicker_images/custom_rgb_b.png HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /stuff/colorpicker_images/custom_rgb_g.png HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /stuff/colorpicker_images/custom_hex.png HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] code 404, message File not found
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /stuff/colorpicker_images/custom_hsb_h.png HTTP/1.1" 404 -
127.0.0.1 - - [08/Nov/2018 15:12:23] code 404, message File not found
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /stuff/colorpicker_images/custom_hsb_s.png HTTP/1.1" 404 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /stuff/colorpicker_images/colorpicker_select.gif HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:23] "GET /stuff/colorpicker_images/custom_indic.gif HTTP/1.1" 304 -
127.0.0.1 - - [08/Nov/2018 15:12:31] "GET /stuff/ex-mark.svg HTTP/1.1" 304 - Any idea of what is causing this?
Thank you!
Can you tell me the URL you used when trying to view the SPRING plot? I think you may not be supplying the correct path to the directory where you saved the SPRING data.
For example, if your SPRING subplot data files (e.g., categorical_coloring_data.json, color_data_gene_sets.csv, color_stats.json, coordinates.txt) are stored in SPRING_dev/datasets/hpc/allMerged, then the URL should be
http://localhost:8000/springViewer_1_6_dev.html?datasets/hpc/allMerged
(note the path after the "?")
Hi @swolock,
Thank you for your reply. I actually went to the test data (pbmc4k) to see if I was able to run that. I had very similar issues as reported in #1 so I spent a couple of hours looking at the errors in the web console. Indeed the preprocessing went smoothly, but with the visualisation I had quite a few issues:
-
categorical_coloring_data.json, color_data_gene_sets.csv, coordinates.txtfor example were in/datasets/pbmc4k/fulland I had to move them to/datasets/pbmc4k/; -
some files were not found; for example in
/stuff/colorpicker_images/it looks forcustom_hsb_b.png, custom_hsb_h.png, custom_hsb_s.pngbut they were actually calledcustom_hsb_b_.png, custom_hsb_h_.png, custom_hsb_s_.png, so I had to rename them and remove the_. -
now I keep getting this error of File not found
http://localhost:8000/scripts_1_6_dev/text_annotations.jsand it is actually missing; -
when I look for a gene, nothing happens and when I check my tmplog2 file this is the output:
import cgi -- 0.015
import numpy -- 0.096
import h5py -- 0.036
got cgi data -- 0.000
CD6
got cell filter-- 0.000
I managed to run louvain clustering and this is how my screen looks, but at the moment I'm stuck.
Ok, I think there are two separate issues here.
First, the missing files are actually not needed to view and interact with the SPRING plot. They correspond to extra functionality that is only available for certain datasets, and the pbmc4k example is fairly barebones. I admit that it would be good for us to deal with these missing file errors more elegantly.
Second, the files you moved from/datasets/pbmc4k/full/ to /datasets/pbmc4k/ were all in the correct place originally. Perhaps you entered an incomplete URL (e.g., http://localhost:8000/springViewer_1_6_dev.html?datasets/pbmc4k/ instead of http://localhost:8000/springViewer_1_6_dev.html?datasets/pbmc4k/full)? This would explain why you can now view the graph but not gene expression, which involves a CGI call to Python to read from files that are no longer in the correct location.
Regarding this second point, see the README for a description of the directory structure of a SPRING dataset. Let me know if this fails to clear things up.