Make backend dev server script serve the image files

Previously, image files in backend/data/img were moved to, or
symlinked from, public/. This needed to be changed before each
build, otherwise vite would end up copying gigabytes of images.

1 files changed, 0 insertions, 152 deletions

diff --git a/backend/data/README.md b/backend/data/README.md
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-This directory holds files used to generate data.db, which contains tree-of-life data.
-
-# Tables
-## Tree Structure data
--   `nodes` <br>
-    Format : `name TEXT PRIMARY KEY, id TEXT UNIQUE, tips INT` <br>
-    Represents a tree-of-life node. `tips` represents the number of no-child descendants.
--   `edges` <br>
-    Format: `parent TEXT, child TEXT, p_support INT, PRIMARY KEY (parent, child)` <br>
-    `p_support` is 1 if the edge has 'phylogenetic support', and 0 otherwise
-## Node name data
--   `eol_ids` <br>
-    Format: `id INT PRIMARY KEY, name TEXT` <br>
-    Associates an EOL ID with a node's name.
--   `names` <br>
-    Format: `name TEXT, alt_name TEXT, pref_alt INT, src TEXT, PRIMARY KEY(name, alt_name)` <br>
-    Associates a node with alternative names.
-    `pref_alt` is 1 if the alt-name is the most 'preferred' one.
-    `src` indicates the dataset the alt-name was obtained from (can be 'eol', 'enwiki', or 'picked').
-## Node description data
--   `wiki_ids` <br>
-    Format: `name TEXT PRIMARY KEY, id INT, redirected INT` <br>
-    Associates a node with a wikipedia page ID.
-    `redirected` is 1 if the node was associated with a different page that redirected to this one.
--   `descs` <br>
-    Format: `wiki_id INT PRIMARY KEY, desc TEXT, from_dbp INT` <br>
-    Associates a wikipedia page ID with a short-description.
-    `from_dbp` is 1 if the description was obtained from DBpedia, and 0 otherwise.
-## Node image data
--   `node_imgs` <br>
-    Format: `name TEXT PRIMARY KEY, img_id INT, src TEXT` <br>
-    Associates a node with an image.
--   `images` <br>
-    Format: `id INT, src TEXT, url TEXT, license TEXT, artist TEXT, credit TEXT, PRIMARY KEY (id, src)` <br>
-    Represents an image, identified by a source ('eol', 'enwiki', or 'picked'), and a source-specific ID.
--   `linked_imgs` <br>
-    Format: `name TEXT PRIMARY KEY, otol_ids TEXT` <br>
-    Associates a node with an image from another node.
-    `otol_ids` can be an otol ID, or two comma-separated otol IDs or empty strings.
-        The latter is used for compound nodes.
-## Reduced tree data
--   `nodes_t`, `nodes_i`, `nodes_p` <br>
-    These are like `nodes`, but describe the nodes for various reduced trees.
--   `edges_t`, `edges_i`, `edges_p` <br>
-    Like `edges` but for reduced trees.
-
-# Generating the Database
-
-For the most part, these steps should be done in order.
-
-As a warning, the whole process takes a lot of time and file space. The tree will probably
-have about 2.5 billion nodes. Downloading the images takes several days, and occupies over
-200 GB. And if you want good data, you'll need to do some manual review, which can take weeks.
-
-## Environment
-The scripts are written in python and bash.
-Some of the python scripts require third-party packages:
--   jsonpickle: For encoding class objects as JSON.
--   requests: For downloading data.
--   PIL: For image processing.
--   tkinter: For providing a basic GUI to review images.
--   mwxml, mwparserfromhell: For parsing Wikipedia dumps.
-
-## Generate tree structure data
-1.  Obtain files in otol/, as specified in it's README.
-2.  Run genOtolData.py, which creates data.db, and adds the `nodes` and `edges` tables,
-    using data in otol/. It also uses these files, if they exist:
-    -   pickedOtolNames.txt: Has lines of the form `name1|otolId1`. Some nodes in the
-        tree may have the same name (eg: Pholidota can refer to pangolins or orchids).
-        Normally, such nodes will get the names 'name1', 'name1 [2]', 'name1 [3], etc.
-        This file can be used to manually specify which node should be named 'name1'.
-
-## Generate node name data
-1.  Obtain 'name data files' in eol/, as specified in it's README.
-2.  Run genEolNameData.py, which adds the `names` and `eol_ids` tables, using data in
-    eol/ and the `nodes` table. It also uses these files, if they exist:
-    -   pickedEolIds.txt: Has lines of the form `nodeName1|eolId1` or `nodeName1|`.
-        Specifies node names that should have a particular EOL ID, or no ID.
-        Quite a few taxons have ambiguous names, and may need manual correction.
-        For example, Viola may resolve to a taxon of butterflies or of plants.
-    -   pickedEolAltsToSkip.txt: Has lines of the form `nodeName1|altName1`.
-        Specifies that a node's alt-name set should exclude altName1.
-
-## Generate node description data
-### Get data from DBpedia
-1.  Obtain files in dbpedia/, as specified in it's README.
-2.  Run genDbpData.py, which adds the `wiki_ids` and `descs` tables, using data in
-    dbpedia/ and the `nodes` table. It also uses these files, if they exist:
-    -   pickedEnwikiNamesToSkip.txt: Each line holds the name of a node for which
-        no description should be obtained. Many node names have a same-name
-        wikipedia page that describes something different (eg: Osiris).
-    -   pickedDbpLabels.txt: Has lines of the form `nodeName1|label1`.
-        Specifies node names that should have a particular associated page label.
-### Get data from Wikipedia
-1.  Obtain 'description database files' in enwiki/, as specified in it's README.
-2.  Run genEnwikiDescData.py, which adds to the `wiki_ids` and `descs` tables,
-    using data in enwiki/ and the `nodes` table.
-    It also uses these files, if they exist:
-    -   pickedEnwikiNamesToSkip.txt: Same as with genDbpData.py.
-    -   pickedEnwikiLabels.txt: Similar to pickedDbpLabels.txt.
-
-## Generate node image data
-### Get images from EOL
-1.  Obtain 'image metadata files' in eol/, as specified in it's README.
-2.  In eol/, run downloadImgs.py, which downloads images (possibly multiple per node),
-    into eol/imgsForReview, using data in eol/, as well as the `eol_ids` table.
-3.  In eol/, run reviewImgs.py, which interactively displays the downloaded images for
-    each node, providing the choice of which to use, moving them to eol/imgs/.
-    Uses `names` and `eol_ids` to display extra info.
-### Get images from Wikipedia
-1.  In enwiki/, run genImgData.py, which looks for wikipedia image names for each node,
-    using the `wiki_ids` table, and stores them in a database.
-2.  In enwiki/, run downloadImgLicenseInfo.py, which downloads licensing information for
-    those images, using wikipedia's online API.
-3.  In enwiki/, run downloadImgs.py, which downloads 'permissively-licensed'
-    images into enwiki/imgs/.
-### Merge the image sets
-1.  Run reviewImgsToGen.py, which displays images from eol/imgs/ and enwiki/imgs/,
-    and enables choosing, for each node, which image should be used, if any,
-    and outputs choice information into imgList.txt. Uses the `nodes`,
-    `eol_ids`, and `wiki_ids` tables (as well as `names` to display extra info).
-2.  Run genImgs.py, which creates cropped/resized images in img/, from files listed in
-    imgList.txt and located in eol/ and enwiki/, and creates the `node_imgs` and
-    `images` tables. If pickedImgs/ is present, images within it are also used. <br>
-    The outputs might need to be manually created/adjusted:
-    -   An input image might have no output produced, possibly due to
-        data incompatibilities, memory limits, etc. A few input image files
-        might actually be html files, containing a 'file not found' page.
-    -   An input x.gif might produce x-1.jpg, x-2.jpg, etc, instead of x.jpg.
-    -   An input image might produce output with unexpected dimensions.
-        This seems to happen when the image is very large, and triggers a
-        decompression bomb warning.
-    The result might have as many as 150k images, with about 2/3 of them
-    being from wikipedia.
-### Add more image associations
-1.  Run genLinkedImgs.py, which tries to associate nodes without images to
-    images of it's children. Adds the `linked_imgs` table, and uses the
-    `nodes`, `edges`, and `node_imgs` tables.
-
-## Do some post-processing
-1.  Run genEnwikiNameData.py, which adds more entries to the `names` table,
-    using data in enwiki/, and the `names` and `wiki_ids` tables.
-2.  Optionally run addPickedNames.py, which allows adding manually-selected name data to
-    the `names` table, as specified in pickedNames.txt.
-    -   pickedNames.txt: Has lines of the form `nodeName1|altName1|prefAlt1`.
-        These correspond to entries in the `names` table. `prefAlt` should be 1 or 0.
-        A line like `name1|name1|1` causes a node to have no preferred alt-name.
-3.  Run genReducedTrees.py, which generates multiple reduced versions of the tree,
-    adding the `nodes_*` and `edges_*` tables, using `nodes` and `names`. Reads from
-    pickedNodes.txt, which lists names of nodes that must be included (1 per line).
-    The original tree isn't used for web-queries, as some nodes would have over 
-    10k children, which can take a while to render (took over a minute in testing).