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| author | Alexander Kabui | 2021-10-13 08:28:16 +0300 |
|---|---|---|
| committer | Alexander Kabui | 2021-10-13 08:28:16 +0300 |
| commit | 5f855ab3c605201175482591073a10692516fd5c (patch) | |
| tree | 4ae1dc86a467ea3b7e3b23519b8875fa0da0548f | |
| parent | db9225caf0a78b13af1892d47c69463e00262d03 (diff) | |
| parent | a212ad123f902b6a9c74bcac1d98bc274cebbdda (diff) | |
| download | genenetwork2-5f855ab3c605201175482591073a10692516fd5c.tar.gz | |
resolve merge conflict
52 files changed, 1056 insertions, 483 deletions
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index f279a7e5..8e2c7966 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -55,11 +55,11 @@ jobs: GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \ etc/default_settings.py -c -m unittest discover -v - - name: Test for Broken Links - run: | - env GN2_PROFILE=/gn2-profile \ - TMPDIR=/tmp\ - WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \ - GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \ - etc/default_settings.py -c \ - $PWD/test/requests/links_scraper/genelinks.py + # - name: Test for Broken Links + # run: | + # env GN2_PROFILE=/gn2-profile \ + # TMPDIR=/tmp\ + # WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \ + # GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \ + # etc/default_settings.py -c \ + # $PWD/test/requests/links_scraper/genelinks.py @@ -1,12 +1,13 @@ [](https://zenodo.org/badge/latestdoi/5591/genenetwork/genenetwork2) [](http://joss.theoj.org/papers/10.21105/joss.00025) [](https://github.com/genenetwork/genenetwork2/actions) + # GeneNetwork This repository contains the current source code for GeneNetwork (GN) (https://www.genenetwork.org/ (version 2). GN2 is a Web -2.0-style framework that includes data and computational tools for online genetics and genomic analysis of -many different populations and many types of molecular, cellular, and physiological data. +2.0-style framework that includes data and computational tools for online genetics and genomic analysis of +many different populations and many types of molecular, cellular, and physiological data. The system is used by scientists and clinians in the field of precision health care and systems genetics. GN and its predecessors have been in operation since Jan 1994, making it one of the longest-lived web services in biomedical research (https://en.wikipedia.org/wiki/GeneNetwork, and see a partial list of publications using GN and its predecessor, WebQTL (https://genenetwork.org/references/). @@ -26,7 +27,7 @@ interface genenetwork2 ``` -(default is http://localhost:5003/). A quick example is +A quick example is ```sh env GN2_PROFILE=~/opt/gn-latest SERVER_PORT=5300 GENENETWORK_FILES=~/data/gn2_data/ ./bin/genenetwork2 ./etc/default_settings.py -gunicorn-dev diff --git a/doc/README.org b/doc/README.org index 43c92e3c..1236016e 100644 --- a/doc/README.org +++ b/doc/README.org @@ -2,7 +2,9 @@ * Table of Contents :TOC: - [[#introduction][Introduction]] - - [[#install][Install]] + - [[#check-list][Check list]] + - [[#installing-guix-packages][Installing Guix packages]] + - [[#creating-a-gnu-guix-profile][Creating a GNU Guix profile]] - [[#running-gn2][Running GN2]] - [[#run-gn-proxy][Run gn-proxy]] - [[#run-redis][Run Redis]] @@ -37,32 +39,106 @@ tree. Current supported versions can be found as the SHA values of For a full view of runtime dependencies as defined by GNU Guix, see an example of the [[#gn2-dependency-graph][GN2 Dependency Graph]]. -* Install +* Check list + +To run GeneNetwork the following services need to function: + +1. [ ] GNU Guix with a guix profile for genenetwork2 +1. [ ] A path to the (static) genotype files +1. [ ] Gn-proxy for authentication +1. [ ] The genenetwork3 service +1. [ ] Redis +1. [ ] Mariadb + +* Installing Guix packages Make sure to install GNU Guix using the binary download instructions on the main website. Follow the instructions on [[GUIX-Reproducible-from-source.org]] to download pre-built binaries. Note -the download amounts to several GBs of data. +the download amounts to several GBs of data. Debian-derived distros +may support + +: apt-get install guix + +* Creating a GNU Guix profile + +We run a GNU Guix channel with packages at [[https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics][guix-bioinformatics]]. The +README has instructions for hosting a channel, but typically we use +the GUIX_PACKAGE_PATH instead. First upgrade to a recent guix with + +: mkdir ~/opt +: guix pull -p ~/opt/guix-pull + +It should upgrade (ignore the locales warnings). You can optionally +specify the specific git checkout of guix with + +: guix pull -p ~/opt/guix-pull --commit=f04883d + +which is useful when you ned to roll back to an earlier version +(sometimes our channel goes out of sync). Next, we install +GeneNetwork2 with + +: source ~/opt/guix-pull/etc/profile +: git clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics +: cd ~/guix-bioinformatics +: git pull +: env GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2 + +you probably also need guix-past (the upstream channel for older packages): + +: git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past +: cd ~/guix-past +: git pull +: env GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2 + +ignore the warnings. Guix should install the software without trying +to build everything. If you system insists on building all packages, +try the `--dry-run` switch and fix the [[https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html][substitutes]]. You may add the +`--substitute-urls="http://guix.genenetwork.org https://ci.guix.gnu.org https://mirror.hydra.gnu.org"` switch. + +The guix.genenetwork.org has most of our packages pre-built(!). To use +it on your own machine the public key is + +#+begin_src scheme +(public-key + (ecc + (curve Ed25519) + (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#))) +#+end_src + +Once we have a GNU Guix profile, a running database (see below) and the file storage, +we should be ready to fire up GeneNetwork: * Running GN2 -Default settings for GN2 are listed in a file called -[[../etc/default_settings.py][default_settings.py]]. You can copy this file and pass it as a new -parameter to the genenetwork2 command, e.g. +Check out the source with git: -: genenetwork2 mysettings.py +: git clone git@github.com:genenetwork/genenetwork2.git +: cd genenetwork2 -or you can set environment variables to override individual parameters, e.g. +Run GN2 with above Guix profile -: env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2 +: export GN2_PROFILE=$HOME/opt/genenetwork2 +: env TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev the debug and logging switches can be particularly useful when -developing GN2. +developing GN2. Location and files are the current ones for Penguin2. + +It may be useful to tunnel the web server to your local browser with +an ssh tunnel: + +If you want to test a service running on the server on a certain +port (say 8202) use + + ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org + +And browse on your local machine to http://localhost:8202/ * Run gn-proxy GeneNetwork requires a separate gn-proxy server which handles -authorisation and access control. For instructions see the [[https://github.com/genenetwork/gn-proxy][README]]. +authorisation and access control. For instructions see the +[[https://github.com/genenetwork/gn-proxy][README]]. Note it may already be running on our servers! * Run Redis diff --git a/doc/docker-container.org b/doc/docker-container.org index ef0d71fc..79b8272f 100644 --- a/doc/docker-container.org +++ b/doc/docker-container.org @@ -28,13 +28,6 @@ which will be added to a base mariaDB image. First create the gn2 tar archive by running: #+begin_src sh -# For the Python 2 version: -env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules" \ - ./pre-inst-env guix pack --no-grafts\ - -S /gn2-profile=/ \ - screen python2-genenetwork2 - -# For the Python 3 version: env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules" \ ./pre-inst-env guix pack --no-grafts\ -S /gn2-profile=/ \ diff --git a/scripts/add_missing_columns.sh b/scripts/add_missing_columns.sh index 70d5fdeb..611e2dd6 100644 --- a/scripts/add_missing_columns.sh +++ b/scripts/add_missing_columns.sh @@ -13,6 +13,9 @@ ALTER TABLE PublishXRef ADD mean double AFTER DataId; + ALTER TABLE CaseAttribute + ADD Description varchar(255) AFTER Name; + -- This takes some time ALTER TABLE ProbeSet ADD UniProtID varchar(20) AFTER ProteinName; diff --git a/scripts/authentication/group.py b/scripts/authentication/group.py new file mode 100644 index 00000000..c8c2caad --- /dev/null +++ b/scripts/authentication/group.py @@ -0,0 +1,153 @@ +"""A script for adding users to a specific group. + +Example: + +Assuming there are no groups and 'test@bonfacemunyoki.com' does not +exist in Redis: + +.. code-block:: bash + python group.py -g "editors" -m "test@bonfacemunyoki.com" + +results in:: + + Successfully created the group: 'editors' + Data: '{"admins": [], "members": []}' + +If 'me@bonfacemunyoki.com' exists in 'users' in Redis and we run: + +.. code-block:: bash + python group.py -g "editors" -m "me@bonfacemunyoki.com" + +now results in:: + + No new group was created. + Updated Data: {'admins': [], 'members': ['me@bonfacemunyoki.com']} + +""" + +import argparse +import datetime +import redis +import json +import uuid + +from typing import Dict, Optional, Set + + +def create_group_data(users: Dict, target_group: str, + members: Optional[str] = None, + admins: Optional[str] = None) -> Dict: + """Return a dictionary that contains the following keys: "key", + "field", and "value" that can be used in a redis hash as follows: + HSET key field value + + The "field" return value is a unique-id that is used to + distinguish the groups. + + Parameters: + + - `users`: a list of users for example: + + {'8ad942fe-490d-453e-bd37-56f252e41603': + '{"email_address": "me@test.com", + "full_name": "John Doe", + "organization": "Genenetwork", + "password": {"algorithm": "pbkdf2", + "hashfunc": "sha256", + "salt": "gJrd1HnPSSCmzB5veMPaVk2ozzDlS1Z7Ggcyl1+pciA=", + "iterations": 100000, "keylength": 32, + "created_timestamp": "2021-09-22T11:32:44.971912", + "password": "edcdaa60e84526c6"}, + "user_id": "8ad942fe", "confirmed": 1, + "registration_info": { + "timestamp": "2021-09-22T11:32:45.028833", + "ip_address": "127.0.0.1", + "user_agent": "Mozilla/5.0"}}'} + + - `target_group`: the group name that will be stored inside the + "groups" hash in Redis. + + - `members`: a comma-separated list of values that contain members + of the `target_group` e.g. "me@test1.com, me@test2.com, + me@test3.com" + + - `admins`: a comma-separated list of values that contain + administrators of the `target_group` e.g. "me@test1.com, + me@test2.com, me@test3.com" + + """ + # Emails + _members: Set = set("".join(members.split()).split(",") + if members else []) + _admins: Set = set("".join(admins.split()).split(",") + if admins else []) + + # Unique IDs + member_ids: Set = set() + admin_ids: Set = set() + + for user_id, user_details in users.items(): + _details = json.loads(user_details) + if _details.get("email_address") in _members: + member_ids.add(user_id) + if _details.get("email_address") in _admins: + admin_ids.add(user_id) + + timestamp: str = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') + return {"key": "groups", + "field": str(uuid.uuid4()), + "value": json.dumps({ + "name": target_group, + "admins": list(admin_ids), + "members": list(member_ids), + "changed_timestamp": timestamp, + })} + + +if __name__ == "__main__": + # Initialising the parser CLI arguments + parser = argparse.ArgumentParser() + parser.add_argument("-g", "--group-name", + help="This is the name of the GROUP mask") + parser.add_argument("-m", "--members", + help="Members of the GROUP mask") + parser.add_argument("-a", "--admins", + help="Admins of the GROUP mask") + args = parser.parse_args() + + if not args.group_name: + exit("\nExiting. Please specify a group name to use!\n") + + members = args.members if args.members else None + admins = args.admins if args.admins else None + + REDIS_CONN = redis.Redis(decode_responses=True) + USERS = REDIS_CONN.hgetall("users") + + if not any([members, admins]): + exit("\nExiting. Please provide a value for " + "MEMBERS(-m) or ADMINS(-a)!\n") + + data = create_group_data( + users=USERS, + target_group=args.group_name, + members=members, + admins=admins) + + if not REDIS_CONN.hget("groups", data.get("field")): + updated_data = json.loads(data["value"]) + timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') + updated_data["created_timestamp"] = timestamp + data["value"] = json.dumps(updated_data) + + created_p = REDIS_CONN.hset(data.get("key", ""), + data.get("field", ""), + data.get("value", "")) + + groups = json.loads(REDIS_CONN.hget("groups", + data.get("field"))) # type: ignore + if created_p: + exit(f"\nSuccessfully created the group: '{args.group_name}'\n" + f"`HGETALL groups {args.group_name}`: {groups}\n") + exit("\nNo new group was created.\n" + f"`HGETALL groups {args.group_name}`: {groups}\n") diff --git a/scripts/authentication/resource.py b/scripts/authentication/resource.py new file mode 100644 index 00000000..4996f34c --- /dev/null +++ b/scripts/authentication/resource.py @@ -0,0 +1,104 @@ +"""A script that: + +- Optionally restores data from a json file. + +- By default, without any args provided, adds the group: 'editors' to +every resource. 'editors' should have the right to edit both metadata +and data. + +- Optionally creates a back-up every time you edit a resource. + + +To restore a back-up: + +.. code-block:: python + python resource.py --restore <PATH/TO/RESOURCE/BACK-UP/FILE> + +To add editors to every resource without creating a back-up: + +.. code-block:: python + python resource.py + +To add editors to every resource while creating a back-up before any +destructive edits: + +.. code-block:: python + python resource.py --enable-backup + +""" +import argparse +import json +import redis +import os + +from datetime import datetime + + +def recover_hash(name: str, file_path: str, set_function) -> bool: + """Recover back-ups using the `set_function` + + Parameters: + + - `name`: Redis hash where `file_path` will be restored + + - `file_path`: File path where redis hash is sourced from + + - `set_function`: Function used to do the Redis backup for + example: HSET + + """ + try: + with open(file_path, "r") as f: + resources = json.load(f) + for resource_id, resource in resources.items(): + set_function(name=name, + key=resource_id, + value=resource) + return True + except Exception as e: + print(e) + return False + + +if __name__ == "__main__": + # Initialising the parser CLI arguments + parser = argparse.ArgumentParser() + parser.add_argument("--group-id", + help="Add the group id to all resources") + parser.add_argument("--restore", + help="Restore from a given backup") + parser.add_argument("--enable-backup", action="store_true", + help="Create a back up before edits") + args = parser.parse_args() + + if not args.group_id: + exit("Please specify the group-id!\n") + if args.restore: + if recover_hash(name="resources", + file_path=args.back_up, + set_function=redis.Redis(decode_responses=True).hset): + exit(f"\n Done restoring {args.back_up}!\n") + else: + exit(f"\n There was an error restoring {args.back_up}!\n") + + REDIS_CONN = redis.Redis(decode_responses=True) + RESOURCES = REDIS_CONN.hgetall("resources") + BACKUP_DIR = os.path.join(os.getenv("HOME"), "redis") + if args.enable_backup: + FILENAME = ("resources-" + f"{datetime.now().strftime('%Y-%m-%d-%I:%M:%S-%p')}" + ".json") + if not os.path.exists(BACKUP_DIR): + os.mkdir(BACKUP_DIR) + with open(os.path.join(BACKUP_DIR, FILENAME), "w") as f: + json.dump(RESOURCES, f, indent=4) + print(f"\nDone backing upto {FILENAME}") + + for resource_id, resource in RESOURCES.items(): + _resource = json.loads(resource) # str -> dict conversion + _resource["group_masks"] = {args.group_id: {"metadata": "edit", + "data": "edit"}} + REDIS_CONN.hset("resources", + resource_id, + json.dumps(_resource)) + exit("Done updating `resources`\n") diff --git a/scripts/convert_dol_genotypes.py b/scripts/convert_dol_genotypes.py new file mode 100644 index 00000000..81b3bd6d --- /dev/null +++ b/scripts/convert_dol_genotypes.py @@ -0,0 +1,74 @@ +# This is just to convert the Rqtl2 format genotype files for DOL into a .geno file +# Everything is hard-coded since I doubt this will be re-used and I just wanted to generate the file quickly + +import os + +geno_dir = "/home/zas1024/gn2-zach/DO_genotypes/" +markers_file = "/home/zas1024/gn2-zach/DO_genotypes/SNP_Map.txt" +gn_geno_path = "/home/zas1024/gn2-zach/DO_genotypes/DOL.geno" + +# Iterate through the SNP_Map.txt file to get marker positions +marker_data = {} +with open(markers_file, "r") as markers_fh: + for i, line in enumerate(markers_fh): + if i == 0: + continue + else: + line_items = line.split("\t") + this_marker = {} + this_marker['chr'] = line_items[2] if line_items[2] != "0" else "M" + this_marker['pos'] = f'{float(line_items[3])/1000000:.6f}' + marker_data[line_items[1]] = this_marker + +# Iterate through R/qtl2 format genotype files and pull out the samplelist and genotypes for each marker +sample_names = [] +for filename in os.listdir(geno_dir): + if "gm4qtl2_geno" in filename: + with open(geno_dir + "/" + filename, "r") as rqtl_geno_fh: + for i, line in enumerate(rqtl_geno_fh): + line_items = line.split(",") + if i < 3: + continue + elif not len(sample_names) and i == 3: + sample_names = [item.replace("TLB", "TB") for item in line_items[1:]] + elif i > 3: + marker_data[line_items[0]]['genotypes'] = ["X" if item.strip() == "-" else item.strip() for item in line_items[1:]] + +# Generate list of marker obs to iterate through when writing to .geno file +marker_list = [] +for key, value in marker_data.items(): + if 'genotypes' in value: + this_marker = { + 'chr': value['chr'], + 'locus': key, + 'pos': value['pos'], + 'genotypes': value['genotypes'] + } + marker_list.append(this_marker) + +def sort_func(e): + """For ensuring that X/Y chromosomes/mitochondria are sorted to the end correctly""" + try: + return float((e['chr']))*1000 + float(e['pos']) + except: + if e['chr'] == "X": + return 20000 + float(e['pos']) + elif e['chr'] == "Y": + return 21000 + float(e['pos']) + elif e['chr'] == "M": + return 22000 + float(e['pos']) + +# Sort markers by chromosome +marker_list.sort(key=sort_func) + +# Write lines to .geno file +with open(gn_geno_path, "w") as gn_geno_fh: + gn_geno_fh.write("\t".join((["Chr", "Locus", "cM", "Mb"] + sample_names))) + for marker in marker_list: + row_contents = [ + marker['chr'], + marker['locus'], + marker['pos'], + marker['pos'] + ] + marker['genotypes'] + gn_geno_fh.write("\t".join(row_contents) + "\n") diff --git a/wqflask/.DS_Store b/wqflask/.DS_Store Binary files differdeleted file mode 100644 index d992942f..00000000 --- a/wqflask/.DS_Store +++ /dev/null diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 4cb82665..8906ab69 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -277,7 +277,6 @@ class Markers: filtered_markers = [] for marker in self.markers: if marker['name'] in p_values: - # logger.debug("marker {} IS in p_values".format(i)) marker['p_value'] = p_values[marker['name']] if math.isnan(marker['p_value']) or (marker['p_value'] <= 0): marker['lod_score'] = 0 @@ -298,7 +297,6 @@ class HumanMarkers(Markers): self.markers = [] for line in marker_data_fh: splat = line.strip().split() - # logger.debug("splat:", splat) if len(specified_markers) > 0: if splat[1] in specified_markers: marker = {} @@ -398,6 +396,15 @@ class DatasetGroup: if maternal and paternal: self.parlist = [maternal, paternal] + def get_study_samplelists(self): + study_sample_file = locate_ignore_error(self.name + ".json", 'study_sample_lists') + try: + f = open(study_sample_file) + except: + return [] + study_samples = json.load(f) + return study_samples + def get_genofiles(self): jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, self.name) try: @@ -737,7 +744,6 @@ class DataSet: and Strain.SpeciesId=Species.Id and Species.name = '{}' """.format(create_in_clause(self.samplelist), *mescape(self.group.species)) - logger.sql(query) results = dict(g.db.execute(query).fetchall()) sample_ids = [results[item] for item in self.samplelist] @@ -908,7 +914,6 @@ class PhenotypeDataSet(DataSet): Geno.Name = '%s' and Geno.SpeciesId = Species.Id """ % (species, this_trait.locus) - logger.sql(query) result = g.db.execute(query).fetchone() if result: @@ -938,7 +943,6 @@ class PhenotypeDataSet(DataSet): Order BY Strain.Name """ - logger.sql(query) results = g.db.execute(query, (trait, self.id)).fetchall() return results @@ -1005,7 +1009,6 @@ class GenotypeDataSet(DataSet): Order BY Strain.Name """ - logger.sql(query) results = g.db.execute(query, (webqtlDatabaseFunction.retrieve_species_id(self.group.name), trait, self.name)).fetchall() @@ -1126,8 +1129,6 @@ class MrnaAssayDataSet(DataSet): ProbeSet.Name = '%s' """ % (escape(str(this_trait.dataset.id)), escape(this_trait.name))) - - logger.sql(query) result = g.db.execute(query).fetchone() mean = result[0] if result else 0 @@ -1147,7 +1148,6 @@ class MrnaAssayDataSet(DataSet): Geno.Name = '{}' and Geno.SpeciesId = Species.Id """.format(species, this_trait.locus) - logger.sql(query) result = g.db.execute(query).fetchone() if result: @@ -1179,7 +1179,6 @@ class MrnaAssayDataSet(DataSet): Order BY Strain.Name """ % (escape(trait), escape(self.name)) - logger.sql(query) results = g.db.execute(query).fetchall() return results @@ -1190,7 +1189,6 @@ class MrnaAssayDataSet(DataSet): where ProbeSetXRef.ProbeSetFreezeId = %s and ProbeSetXRef.ProbeSetId=ProbeSet.Id; """ % (column_name, escape(str(self.id))) - logger.sql(query) results = g.db.execute(query).fetchall() return dict(results) @@ -1224,7 +1222,6 @@ def geno_mrna_confidentiality(ob): query = '''SELECT Id, Name, FullName, confidentiality, AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table, ob.name) - logger.sql(query) result = g.db.execute(query) (dataset_id, diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 10851e00..96a09302 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -27,11 +27,13 @@ def create_trait(**kw): assert bool(kw.get('name')), "Needs trait name" - if kw.get('dataset_name'): + if bool(kw.get('dataset')): + dataset = kw.get('dataset') + else: if kw.get('dataset_name') != "Temp": dataset = create_dataset(kw.get('dataset_name')) - else: - dataset = kw.get('dataset') + else: + dataset = create_dataset("Temp", group_name=kw.get('group_name')) if dataset.type == 'Publish': permissions = check_resource_availability( diff --git a/wqflask/runserver.py b/wqflask/runserver.py index df957bd9..8198b921 100644 --- a/wqflask/runserver.py +++ b/wqflask/runserver.py @@ -23,6 +23,9 @@ app_config() werkzeug_logger = logging.getLogger('werkzeug') if WEBSERVER_MODE == 'DEBUG': + from flask_debugtoolbar import DebugToolbarExtension + app.debug = True + toolbar = DebugToolbarExtension(app) app.run(host='0.0.0.0', port=SERVER_PORT, debug=True, diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py index 4003d68f..58a44b2a 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py @@ -81,10 +81,12 @@ class TestGemmaMapping(unittest.TestCase): def test_gen_pheno_txt_file(self): """add tests for generating pheno txt file""" with mock.patch("builtins.open", mock.mock_open())as mock_open: - gen_pheno_txt_file(this_dataset={}, genofile_name="", vals=[ - "x", "w", "q", "we", "R"], trait_filename="fitr.re") + gen_pheno_txt_file( + this_dataset=AttributeSetter({"name": "A"}), + genofile_name="", vals=[ + "x", "w", "q", "we", "R"]) mock_open.assert_called_once_with( - '/home/user/data/gn2/fitr.re.txt', 'w') + '/home/user/data/gn2/PHENO_KiAEKlCvM6iGTM9Kh_TAlQ.txt', 'w') filehandler = mock_open() values = ["x", "w", "q", "we", "R"] write_calls = [mock.call('NA\n'), mock.call('w\n'), mock.call( @@ -112,7 +114,7 @@ class TestGemmaMapping(unittest.TestCase): create_trait.side_effect = create_trait_side_effect group = MockGroup({"name": "group_X", "samplelist": samplelist}) - this_dataset = AttributeSetter({"group": group}) + this_dataset = AttributeSetter({"group": group, "name": "A"}) flat_files.return_value = "Home/Genenetwork" with mock.patch("builtins.open", mock.mock_open())as mock_open: @@ -132,7 +134,7 @@ class TestGemmaMapping(unittest.TestCase): flat_files.assert_called_once_with('mapping') mock_open.assert_called_once_with( - 'Home/Genenetwork/group_X_covariates.txt', 'w') + 'Home/Genenetwork/COVAR_anFZ_LfZYV0Ulywo+7tRCw.txt', 'w') filehandler = mock_open() filehandler.write.assert_has_calls([mock.call( '-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('\n')]) diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py index c220a072..868b0b0b 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py @@ -43,11 +43,11 @@ class TestRunMapping(unittest.TestCase): }) } self.dataset = AttributeSetter( - {"fullname": "dataser_1", "group": self.group, "type": "ProbeSet"}) + {"fullname": "dataset_1", "group": self.group, "type": "ProbeSet"}) self.chromosomes = AttributeSetter({"chromosomes": chromosomes}) self.trait = AttributeSetter( - {"symbol": "IGFI", "chr": "X1", "mb": 123313}) + {"symbol": "IGFI", "chr": "X1", "mb": 123313, "display_name": "Test Name"}) def tearDown(self): self.dataset = AttributeSetter( @@ -180,34 +180,36 @@ class TestRunMapping(unittest.TestCase): with mock.patch("wqflask.marker_regression.run_mapping.datetime.datetime", new=datetime_mock): export_mapping_results(dataset=self.dataset, trait=self.trait, markers=markers, - results_path="~/results", mapping_scale="physic", score_type="-log(p)", - transform="qnorm", covariates="Dataset1:Trait1,Dataset2:Trait2", n_samples="100") + results_path="~/results", mapping_method="gemma", mapping_scale="physic", + score_type="-logP", transform="qnorm", + covariates="Dataset1:Trait1,Dataset2:Trait2", + n_samples="100", vals_hash="") write_calls = [ mock.call('Time/Date: 09/01/19 / 10:12:12\n'), mock.call('Population: Human GP1_\n'), mock.call( - 'Data Set: dataser_1\n'), - mock.call('N Samples: 100\n'), mock.call( - 'Transform - Quantile Normalized\n'), + 'Data Set: dataset_1\n'), + mock.call('Trait: Test Name\n'), + mock.call('Trait Hash: \n'), + mock.call('N Samples: 100\n'), + mock.call('Mapping Tool: gemma\n'), + mock.call('Transform - Quantile Normalized\n'), mock.call('Gene Symbol: IGFI\n'), mock.call( 'Location: X1 @ 123313 Mb\n'), mock.call('Cofactors (dataset - trait):\n'), mock.call('Trait1 - Dataset1\n'), mock.call('Trait2 - Dataset2\n'), mock.call('\n'), mock.call('Name,Chr,'), - mock.call('Mb,-log(p)'), mock.call('Cm,-log(p)'), + mock.call('Mb,-logP'), mock.call(',Additive'), mock.call(',Dominance'), mock.call('\n'), mock.call('MK1,C1,'), - mock.call('12000,'), mock.call('1,'), - mock.call('3'), mock.call(',VA'), - mock.call(',TT'), mock.call('\n'), - mock.call('MK2,C2,'), mock.call('10000,'), - mock.call('15,'), mock.call('7'), + mock.call('12000,'), mock.call('3'), + mock.call(',VA'), mock.call(',TT'), + mock.call('\n'), mock.call('MK2,C2,'), + mock.call('10000,'), mock.call('7'), mock.call('\n'), mock.call('MK1,C3,'), - mock.call('1,'), mock.call('45,'), - mock.call('7'), mock.call(',VE'), - mock.call(',Tt') - + mock.call('1,'), mock.call('7'), + mock.call(',VE'), mock.call(',Tt') ] mock_open.assert_called_once_with("~/results", "w+") filehandler = mock_open() @@ -232,25 +234,20 @@ class TestRunMapping(unittest.TestCase): "c1": "c1_value", "c2": "c2_value", "w1": "w1_value" - }, "S2": { "w1": "w2_value", "w2": "w2_value" - }, "S3": { "c1": "c1_value", "c2": "c2_value" - }, - }}) - results = get_perm_strata(this_trait={}, sample_list=sample_list, categorical_vars=categorical_vars, used_samples=used_samples) - self.assertEqual(results, [2, 1]) + self.assertEqual(results, [1, 1]) def test_get_chr_length(self): """test for getting chromosome length""" diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index 9b2c6735..d4256a46 100644 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -139,7 +139,7 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab max_D = max(data) min_D = min(data) # add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong - if max_D == float('inf') or max_D > webqtlConfig.MAXLRS: + if (max_D == float('inf') or max_D > webqtlConfig.MAXLRS) and min_D < webqtlConfig.MAXLRS: max_D = webqtlConfig.MAXLRS # maximum LRS value xLow, xTop, stepX = detScale(min_D, max_D) @@ -156,7 +156,7 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab j += step for i, item in enumerate(data): - if item == float('inf') or item > webqtlConfig.MAXLRS: + if (item == float('inf') or item > webqtlConfig.MAXLRS) and min_D < webqtlConfig.MAXLRS: item = webqtlConfig.MAXLRS # maximum LRS value j = int((item - xLow) / step) Count[j] += 1 diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index ff125bd2..de9dde46 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -127,22 +127,20 @@ def check_verification_code(code): def get_user_groups(user_id): - # ZS: Get the groups where a user is an admin or a member and + # Get the groups where a user is an admin or a member and # return lists corresponding to those two sets of groups - admin_group_ids = [] # ZS: Group IDs where user is an admin - user_group_ids = [] # ZS: Group IDs where user is a regular user + admin_group_ids = [] # Group IDs where user is an admin + user_group_ids = [] # Group IDs where user is a regular user groups_list = Redis.hgetall("groups") - for key in groups_list: + for group_id, group_details in groups_list.items(): try: - group_ob = json.loads(groups_list[key]) - group_admins = set([this_admin.encode( - 'utf-8') if this_admin else None for this_admin in group_ob['admins']]) - group_members = set([this_member.encode( - 'utf-8') if this_member else None for this_member in group_ob['members']]) + _details = json.loads(group_details) + group_admins = set([this_admin if this_admin else None for this_admin in _details['admins']]) + group_members = set([this_member if this_member else None for this_member in _details['members']]) if user_id in group_admins: - admin_group_ids.append(group_ob['id']) + admin_group_ids.append(group_id) elif user_id in group_members: - user_group_ids.append(group_ob['id']) + user_group_ids.append(group_id) else: continue except: diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py index 56d0af6f..778fb64d 100644 --- a/wqflask/utility/startup_config.py +++ b/wqflask/utility/startup_config.py @@ -20,8 +20,12 @@ def app_config(): import os app.config['SECRET_KEY'] = str(os.urandom(24)) mode = WEBSERVER_MODE - if mode == "DEV" or mode == "DEBUG": + if mode in ["DEV", "DEBUG"]: app.config['TEMPLATES_AUTO_RELOAD'] = True + if mode == "DEBUG": + from flask_debugtoolbar import DebugToolbarExtension + app.debug = True + toolbar = DebugToolbarExtension(app) print("==========================================") diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py index f7c06a46..a18bceaf 100644 --- a/wqflask/wqflask/correlation/correlation_gn3_api.py +++ b/wqflask/wqflask/correlation/correlation_gn3_api.py @@ -148,14 +148,9 @@ def lit_for_trait_list(corr_results, this_dataset, this_trait): def fetch_sample_data(start_vars, this_trait, this_dataset, target_dataset): sample_data = process_samples( - start_vars, this_dataset.group.samplelist) + start_vars, this_dataset.group.all_samples_ordered()) - sample_data = test_process_data(this_trait, this_dataset, start_vars) - - if target_dataset.type == "ProbeSet": - target_dataset.get_probeset_data(list(sample_data.keys())) - else: - target_dataset.get_trait_data(list(sample_data.keys())) + target_dataset.get_trait_data(list(sample_data.keys())) this_trait = retrieve_sample_data(this_trait, this_dataset) this_trait_data = { "trait_sample_data": sample_data, diff --git a/wqflask/wqflask/decorators.py b/wqflask/wqflask/decorators.py index f0978fd3..54aa6795 100644 --- a/wqflask/wqflask/decorators.py +++ b/wqflask/wqflask/decorators.py @@ -1,14 +1,36 @@ """This module contains gn2 decorators""" from flask import g +from typing import Dict from functools import wraps +from utility.hmac import hmac_creation +import json +import requests -def admin_login_required(f): + +def edit_access_required(f): """Use this for endpoints where admins are required""" @wraps(f) def wrap(*args, **kwargs): - if g.user_session.record.get(b"user_email_address") not in [ - b"labwilliams@gmail.com"]: + resource_id: str = "" + if kwargs.get("inbredset_id"): # data type: dataset-publish + resource_id = hmac_creation("dataset-publish:" + f"{kwargs.get('inbredset_id')}:" + f"{kwargs.get('name')}") + if kwargs.get("dataset_name"): # data type: dataset-probe + resource_id = hmac_creation("dataset-probeset:" + f"{kwargs.get('dataset_name')}") + response: Dict = {} + try: + _user_id = g.user_session.record.get(b"user_id", + "").decode("utf-8") + response = json.loads( + requests.get("http://localhost:8080/" + "available?resource=" + f"{resource_id}&user={_user_id}").content) + except: + response = {} + if "edit" not in response.get("data", []): return "You need to be admin", 401 return f(*args, **kwargs) return wrap diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index f941267e..6254b9b9 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -24,6 +24,7 @@ # # Last updated by Zach 12/14/2010 +import datetime import string from math import * from PIL import Image @@ -271,6 +272,7 @@ class DisplayMappingResults: # Needing for form submission when doing single chr # mapping or remapping after changing options self.sample_vals = start_vars['sample_vals'] + self.vals_hash= start_vars['vals_hash'] self.sample_vals_dict = json.loads(self.sample_vals) self.transform = start_vars['transform'] @@ -355,8 +357,7 @@ class DisplayMappingResults: if 'use_loco' in list(start_vars.keys()) and self.mapping_method == "gemma": self.use_loco = start_vars['use_loco'] - if 'reaper_version' in list(start_vars.keys()) and self.mapping_method == "reaper": - self.reaper_version = start_vars['reaper_version'] + if self.mapping_method == "reaper": if 'output_files' in start_vars: self.output_files = ",".join( [(the_file if the_file is not None else "") for the_file in start_vars['output_files']]) @@ -651,7 +652,7 @@ class DisplayMappingResults: btminfo.append( 'Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.') - def plotIntMapping(self, canvas, offset=(80, 120, 90, 100), zoom=1, startMb=None, endMb=None, showLocusForm=""): + def plotIntMapping(self, canvas, offset=(80, 120, 110, 100), zoom=1, startMb=None, endMb=None, showLocusForm=""): im_drawer = ImageDraw.Draw(canvas) # calculating margins xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset @@ -661,7 +662,7 @@ class DisplayMappingResults: if self.legendChecked: yTopOffset += 10 if self.covariates != "" and self.controlLocus and self.doControl != "false": - yTopOffset += 20 + yTopOffset += 25 if len(self.transform) > 0: yTopOffset += 5 else: @@ -1195,43 +1196,47 @@ class DisplayMappingResults: dataset_label = "%s - %s" % (self.dataset.group.name, self.dataset.fullname) - string1 = 'Dataset: %s' % (dataset_label) + + self.current_datetime = datetime.datetime.now().strftime("%b %d %Y %H:%M:%S") + string1 = 'UTC Timestamp: %s' % (self.current_datetime) + string2 = 'Dataset: %s' % (dataset_label) + string3 = 'Trait Hash: %s' % (self.vals_hash) if self.genofile_string == "": - string2 = 'Genotype File: %s.geno' % self.dataset.group.name + string4 = 'Genotype File: %s.geno' % self.dataset.group.name else: - string2 = 'Genotype File: %s' % self.genofile_string + string4 = 'Genotype File: %s' % self.genofile_string.split(":")[1] - string4 = '' + string6 = '' if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam": if self.use_loco == "True": - string3 = 'Using GEMMA mapping method with LOCO and ' + string5 = 'Using GEMMA mapping method with LOCO and ' else: - string3 = 'Using GEMMA mapping method with ' + string5 = 'Using GEMMA mapping method with ' if self.covariates != "": - string3 += 'the cofactors below:' + string5 += 'the cofactors below:' cofactor_names = ", ".join( [covar.split(":")[0] for covar in self.covariates.split(",")]) - string4 = cofactor_names + string6 = cofactor_names else: - string3 += 'no cofactors' + string5 += 'no cofactors' elif self.mapping_method == "rqtl_plink" or self.mapping_method == "rqtl_geno": - string3 = 'Using R/qtl mapping method with ' + string5 = 'Using R/qtl mapping method with ' if self.covariates != "": - string3 += 'the cofactors below:' + string5 += 'the cofactors below:' cofactor_names = ", ".join( [covar.split(":")[0] for covar in self.covariates.split(",")]) - string4 = cofactor_names + string6 = cofactor_names elif self.controlLocus and self.doControl != "false": - string3 += '%s as control' % self.controlLocus + string5 += '%s as control' % self.controlLocus else: - string3 += 'no cofactors' + string5 += 'no cofactors' else: - string3 = 'Using Haldane mapping function with ' + string5 = 'Using Haldane mapping function with ' if self.controlLocus and self.doControl != "false": - string3 += '%s as control' % self.controlLocus + string5 += '%s as control' % self.controlLocus else: - string3 += 'no control for other QTLs' + string5 += 'no control for other QTLs' y_constant = 10 if self.this_trait.name: @@ -1243,24 +1248,26 @@ class DisplayMappingResults: if self.this_trait.symbol: identification += "Trait: %s - %s" % ( - self.this_trait.name, self.this_trait.symbol) + self.this_trait.display_name, self.this_trait.symbol) elif self.dataset.type == "Publish": if self.this_trait.post_publication_abbreviation: identification += "Trait: %s - %s" % ( - self.this_trait.name, self.this_trait.post_publication_abbreviation) + self.this_trait.display_name, self.this_trait.post_publication_abbreviation) elif self.this_trait.pre_publication_abbreviation: identification += "Trait: %s - %s" % ( - self.this_trait.name, self.this_trait.pre_publication_abbreviation) + self.this_trait.display_name, self.this_trait.pre_publication_abbreviation) else: - identification += "Trait: %s" % (self.this_trait.name) + identification += "Trait: %s" % (self.this_trait.display_name) else: - identification += "Trait: %s" % (self.this_trait.name) + identification += "Trait: %s" % (self.this_trait.display_name) identification += " with %s samples" % (self.n_samples) d = 4 + max( im_drawer.textsize(identification, font=labelFont)[0], im_drawer.textsize(string1, font=labelFont)[0], - im_drawer.textsize(string2, font=labelFont)[0]) + im_drawer.textsize(string2, font=labelFont)[0], + im_drawer.textsize(string3, font=labelFont)[0], + im_drawer.textsize(string4, font=labelFont)[0]) im_drawer.text( text=identification, xy=(xLeftOffset, y_constant * fontZoom), font=labelFont, @@ -1269,7 +1276,9 @@ class DisplayMappingResults: else: d = 4 + max( im_drawer.textsize(string1, font=labelFont)[0], - im_drawer.textsize(string2, font=labelFont)[0]) + im_drawer.textsize(string2, font=labelFont)[0], + im_drawer.textsize(string3, font=labelFont)[0], + im_drawer.textsize(string4, font=labelFont)[0]) if len(self.transform) > 0: transform_text = "Transform - " @@ -1296,14 +1305,22 @@ class DisplayMappingResults: text=string2, xy=(xLeftOffset, y_constant * fontZoom), font=labelFont, fill=labelColor) y_constant += 15 - if string3 != '': + im_drawer.text( + text=string3, xy=(xLeftOffset, y_constant * fontZoom), + font=labelFont, fill=labelColor) + y_constant += 15 + im_drawer.text( + text=string4, xy=(xLeftOffset, y_constant * fontZoom), + font=labelFont, fill=labelColor) + y_constant += 15 + if string4 != '': im_drawer.text( - text=string3, xy=(xLeftOffset, y_constant * fontZoom), + text=string5, xy=(xLeftOffset, y_constant * fontZoom), font=labelFont, fill=labelColor) y_constant += 15 - if string4 != '': + if string5 != '': im_drawer.text( - text=string4, xy=(xLeftOffset, y_constant * fontZoom), + text=string6, xy=(xLeftOffset, y_constant * fontZoom), font=labelFont, fill=labelColor) def drawGeneBand(self, canvas, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None): @@ -2113,7 +2130,7 @@ class DisplayMappingResults: thisChr.append( [_locus.name, _locus.cM - Locus0CM]) else: - for j in (0, nLoci / 4, nLoci / 2, nLoci * 3 / 4, -1): + for j in (0, round(nLoci / 4), round(nLoci / 2), round(nLoci * 3 / 4), -1): while _chr[j].name == ' - ': j += 1 if _chr[j].cM != preLpos: diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py index 4d6715ba..801674e1 100644 --- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py +++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py @@ -178,101 +178,6 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename): return marker_obs, permu_vals, bootstrap_vals -def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot): - genotype = dataset.group.read_genotype_file(use_reaper=True) - - if manhattan_plot != True: - genotype = genotype.addinterval() - - trimmed_samples = [] - trimmed_values = [] - for i in range(0, len(samples_before)): - try: - trimmed_values.append(float(trait_vals[i])) - trimmed_samples.append(str(samples_before[i])) - except: - pass - - perm_output = [] - bootstrap_results = [] - - if num_perm < 100: - suggestive = 0 - significant = 0 - else: - perm_output = genotype.permutation( - strains=trimmed_samples, trait=trimmed_values, nperm=num_perm) - suggestive = perm_output[int(num_perm * 0.37 - 1)] - significant = perm_output[int(num_perm * 0.95 - 1)] - # highly_significant = perm_output[int(num_perm*0.99-1)] #ZS: Currently not used, but leaving it here just in case - - json_data['suggestive'] = suggestive - json_data['significant'] = significant - - if control_marker != "" and do_control == "true": - reaper_results = genotype.regression(strains=trimmed_samples, - trait=trimmed_values, - control=str(control_marker)) - if bootCheck: - control_geno = [] - control_geno2 = [] - _FIND = 0 - for _chr in genotype: - for _locus in _chr: - if _locus.name == control_marker: - control_geno2 = _locus.genotype - _FIND = 1 - break - if _FIND: - break - if control_geno2: - _prgy = list(genotype.prgy) - for _strain in trimmed_samples: - _idx = _prgy.index(_strain) - control_geno.append(control_geno2[_idx]) - - bootstrap_results = genotype.bootstrap(strains=trimmed_samples, - trait=trimmed_values, - control=control_geno, - nboot=num_bootstrap) - else: - reaper_results = genotype.regression(strains=trimmed_samples, - trait=trimmed_values) - - if bootCheck: - bootstrap_results = genotype.bootstrap(strains=trimmed_samples, - trait=trimmed_values, - nboot=num_bootstrap) - - json_data['chr'] = [] - json_data['pos'] = [] - json_data['lod.hk'] = [] - json_data['markernames'] = [] - # if self.additive: - # self.json_data['additive'] = [] - - # Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary - qtl_results = [] - for qtl in reaper_results: - reaper_locus = qtl.locus - # ZS: Convert chr to int - converted_chr = reaper_locus.chr - if reaper_locus.chr != "X" and reaper_locus.chr != "X/Y": - converted_chr = int(reaper_locus.chr) - json_data['chr'].append(converted_chr) - json_data['pos'].append(reaper_locus.Mb) - json_data['lod.hk'].append(qtl.lrs) - json_data['markernames'].append(reaper_locus.name) - # if self.additive: - # self.json_data['additive'].append(qtl.additive) - locus = {"name": reaper_locus.name, "chr": reaper_locus.chr, - "cM": reaper_locus.cM, "Mb": reaper_locus.Mb} - qtl = {"lrs_value": qtl.lrs, "chr": converted_chr, "Mb": reaper_locus.Mb, - "cM": reaper_locus.cM, "name": reaper_locus.name, "additive": qtl.additive, "dominance": qtl.dominance} - qtl_results.append(qtl) - return qtl_results, json_data, perm_output, suggestive, significant, bootstrap_results - - def natural_sort(marker_list): """ Function to naturally sort numbers + strings, adopted from user Mark Byers here: https://stackoverflow.com/questions/4836710/does-python-have-a-built-in-function-for-string-natural-sort diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index 09afb8d1..1dca1b1b 100644 --- a/wqflask/wqflask/marker_regression/rqtl_mapping.py +++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py @@ -39,7 +39,7 @@ def run_rqtl(trait_name, vals, samples, dataset, mapping_scale, model, method, n } if do_control == "true" and control_marker: - post_data["control_marker"] = control_marker + post_data["control"] = control_marker if not manhattan_plot: post_data["interval"] = True @@ -61,6 +61,7 @@ def get_hash_of_textio(the_file: TextIO) -> str: the_file.seek(0) hash_of_file = hashlib.md5(the_file.read().encode()).hexdigest() + hash_of_file = hash_of_file.replace("/", "_") # Replace / with _ to prevent issue with filenames being translated to directories return hash_of_file @@ -89,7 +90,7 @@ def write_phenotype_file(trait_name: str, for i, sample in enumerate(samples): this_row = [sample] if vals[i] != "x": - this_row.append(vals[i]) + this_row.append(str(round(float(vals[i]), 3))) else: this_row.append("NA") for cofactor in cofactor_data: @@ -126,7 +127,7 @@ def cofactors_to_dict(cofactors: str, dataset_ob, samples) -> Dict: sample_data = trait_ob.data for index, sample in enumerate(samples): if sample in sample_data: - sample_value = sample_data[sample].value + sample_value = str(round(float(sample_data[sample].value), 3)) cofactor_dict[cofactor_name].append(sample_value) else: cofactor_dict[cofactor_name].append("NA") diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index f601201b..80094057 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -75,6 +75,7 @@ class RunMapping: self.vals = [] self.samples = [] self.sample_vals = start_vars['sample_vals'] + self.vals_hash = start_vars['vals_hash'] sample_val_dict = json.loads(self.sample_vals) samples = sample_val_dict.keys() if (len(genofile_samplelist) != 0): @@ -103,9 +104,7 @@ class RunMapping: if "results_path" in start_vars: self.mapping_results_path = start_vars['results_path'] else: - mapping_results_filename = self.dataset.group.name + "_" + \ - ''.join(random.choice(string.ascii_uppercase + string.digits) - for _ in range(6)) + mapping_results_filename = "_".join([self.dataset.group.name, self.mapping_method, self.vals_hash]).replace("/", "_") self.mapping_results_path = "{}{}.csv".format( webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename) @@ -220,7 +219,7 @@ class RunMapping: elif self.mapping_method == "rqtl_plink": results = self.run_rqtl_plink() elif self.mapping_method == "rqtl_geno": - perm_strata = [] + self.perm_strata = [] if "perm_strata" in start_vars and "categorical_vars" in start_vars: self.categorical_vars = start_vars["categorical_vars"].split( ",") @@ -229,7 +228,7 @@ class RunMapping: sample_names=self.samples, this_trait=self.this_trait) - perm_strata = get_perm_strata( + self.perm_strata = get_perm_strata( self.this_trait, primary_samples, self.categorical_vars, self.samples) self.score_type = "LOD" self.control_marker = start_vars['control_marker'] @@ -243,10 +242,10 @@ class RunMapping: # self.pair_scan = True if self.permCheck and self.num_perm > 0: self.perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl( - self.this_trait.name, self.vals, self.samples, self.dataset, self.mapping_scale, self.model, self.method, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates) + self.this_trait.name, self.vals, self.samples, self.dataset, self.mapping_scale, self.model, self.method, self.num_perm, self.perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates) else: results = rqtl_mapping.run_rqtl(self.this_trait.name, self.vals, self.samples, self.dataset, self.mapping_scale, self.model, self.method, - self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates) + self.num_perm, self.perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates) elif self.mapping_method == "reaper": if "startMb" in start_vars: # ZS: Check if first time page loaded, so it can default to ON if "additiveCheck" in start_vars: @@ -272,47 +271,32 @@ class RunMapping: self.bootCheck = False self.num_bootstrap = 0 - self.reaper_version = start_vars['reaper_version'] - self.control_marker = start_vars['control_marker'] self.do_control = start_vars['do_control'] logger.info("Running qtlreaper") - if self.reaper_version == "new": - self.first_run = True - self.output_files = None - # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc) - if 'first_run' in start_vars: - self.first_run = False - if 'output_files' in start_vars: - self.output_files = start_vars['output_files'].split( - ",") - - results, self.perm_output, self.suggestive, self.significant, self.bootstrap_results, self.output_files = qtlreaper_mapping.run_reaper(self.this_trait, - self.dataset, - self.samples, - self.vals, - self.json_data, - self.num_perm, - self.bootCheck, - self.num_bootstrap, - self.do_control, - self.control_marker, - self.manhattan_plot, - self.first_run, - self.output_files) - else: - results, self.json_data, self.perm_output, self.suggestive, self.significant, self.bootstrap_results = qtlreaper_mapping.run_original_reaper(self.this_trait, - self.dataset, - self.samples, - self.vals, - self.json_data, - self.num_perm, - self.bootCheck, - self.num_bootstrap, - self.do_control, - self.control_marker, - self.manhattan_plot) + self.first_run = True + self.output_files = None + # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc) + if 'first_run' in start_vars: + self.first_run = False + if 'output_files' in start_vars: + self.output_files = start_vars['output_files'].split( + ",") + + results, self.perm_output, self.suggestive, self.significant, self.bootstrap_results, self.output_files = qtlreaper_mapping.run_reaper(self.this_trait, + self.dataset, + self.samples, + self.vals, + self.json_data, + self.num_perm, + self.bootCheck, + self.num_bootstrap, + self.do_control, + self.control_marker, + self.manhattan_plot, + self.first_run, + self.output_files) elif self.mapping_method == "plink": self.score_type = "-logP" self.manhattan_plot = True @@ -422,7 +406,8 @@ class RunMapping: with Bench("Exporting Results"): export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, - self.mapping_scale, self.score_type, self.transform, self.covariates, self.n_samples) + self.mapping_method, self.mapping_scale, self.score_type, + self.transform, self.covariates, self.n_samples, self.vals_hash) with Bench("Trimming Markers for Figure"): if len(self.qtl_results) > 30000: @@ -540,14 +525,21 @@ class RunMapping: return trimmed_genotype_data -def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type, transform, covariates, n_samples): +def export_mapping_results(dataset, trait, markers, results_path, mapping_method, mapping_scale, score_type, transform, covariates, n_samples, vals_hash): + if mapping_scale == "physic": + scale_string = "Mb" + else: + scale_string = "cM" with open(results_path, "w+") as output_file: output_file.write( "Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n") output_file.write( "Population: " + dataset.group.species.title() + " " + dataset.group.name + "\n") output_file.write("Data Set: " + dataset.fullname + "\n") + output_file.write("Trait: " + trait.display_name + "\n") + output_file.write("Trait Hash: " + vals_hash + "\n") output_file.write("N Samples: " + str(n_samples) + "\n") + output_file.write("Mapping Tool: " + str(mapping_method) + "\n") if len(transform) > 0: transform_text = "Transform - " if transform == "qnorm": @@ -577,10 +569,7 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, output_file.write("Name,Chr,") if score_type.lower() == "-logP": score_type = "-logP" - if 'Mb' in markers[0]: - output_file.write("Mb," + score_type) - if 'cM' in markers[0]: - output_file.write("Cm," + score_type) + output_file.write(scale_string + "," + score_type) if "additive" in list(markers[0].keys()): output_file.write(",Additive") if "dominance" in list(markers[0].keys()): @@ -588,11 +577,8 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, output_file.write("\n") for i, marker in enumerate(markers): output_file.write(marker['name'] + "," + str(marker['chr']) + ",") - if 'Mb' in marker: - output_file.write(str(marker['Mb']) + ",") - if 'cM' in marker: - output_file.write(str(marker['cM']) + ",") - if "lod_score" in marker.keys(): + output_file.write(str(marker[scale_string]) + ",") + if score_type == "-logP": output_file.write(str(marker['lod_score'])) else: output_file.write(str(marker['lrs_value'])) @@ -765,9 +751,9 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples): if sample in list(sample_list.sample_attribute_values.keys()): combined_string = "" for var in categorical_vars: - if var.lower() in sample_list.sample_attribute_values[sample]: + if var in sample_list.sample_attribute_values[sample]: combined_string += str( - sample_list.sample_attribute_values[sample][var.lower()]) + sample_list.sample_attribute_values[sample][var]) else: combined_string += "NA" else: diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py index b28c1b04..c54dd0b3 100644 --- a/wqflask/wqflask/resource_manager.py +++ b/wqflask/wqflask/resource_manager.py @@ -8,8 +8,6 @@ from wqflask import app from utility.authentication_tools import check_owner_or_admin from utility.redis_tools import get_resource_info, get_group_info, get_groups_like_unique_column, get_user_id, get_user_by_unique_column, get_users_like_unique_column, add_access_mask, add_resource, change_resource_owner -from utility.logger import getLogger -logger = getLogger(__name__) @app.route("/resources/manage", methods=('GET', 'POST')) diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index 92cea550..ae30aa59 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -32,7 +32,7 @@ class SampleList: for counter, sample_name in enumerate(sample_names, 1): sample_name = sample_name.replace("_2nd_", "") - # ZS: self.this_trait will be a list if it is a Temp trait + # self.this_trait will be a list if it is a Temp trait if isinstance(self.this_trait, list): sample = webqtlCaseData.webqtlCaseData(name=sample_name) if counter <= len(self.this_trait): @@ -47,7 +47,7 @@ class SampleList: name=sample_name, value=float(self.this_trait[counter - 1])) else: - # ZS - If there's no value for the sample/strain, + # If there's no value for the sample/strain, # create the sample object (so samples with no value # are still displayed in the table) try: @@ -63,29 +63,29 @@ class SampleList: sample.this_id = str(counter) - # ZS: For extra attribute columns; currently only used by + # For extra attribute columns; currently only used by # several datasets if self.sample_attribute_values: sample.extra_attributes = self.sample_attribute_values.get( sample_name, {}) - # ZS: Add a url so RRID case attributes can be displayed as links - if 'rrid' in sample.extra_attributes: + # Add a url so RRID case attributes can be displayed as links + if '36' in sample.extra_attributes: if self.dataset.group.species == "mouse": - if len(sample.extra_attributes['rrid'].split(":")) > 1: - the_rrid = sample.extra_attributes['rrid'].split(":")[ + if len(sample.extra_attributes['36'].split(":")) > 1: + the_rrid = sample.extra_attributes['36'].split(":")[ 1] - sample.extra_attributes['rrid'] = [ - sample.extra_attributes['rrid']] - sample.extra_attributes['rrid'].append( + sample.extra_attributes['36'] = [ + sample.extra_attributes['36']] + sample.extra_attributes['36'].append( webqtlConfig.RRID_MOUSE_URL % the_rrid) elif self.dataset.group.species == "rat": - if len(str(sample.extra_attributes['rrid'])): - the_rrid = sample.extra_attributes['rrid'].split("_")[ + if len(str(sample.extra_attributes['36'])): + the_rrid = sample.extra_attributes['36'].split("_")[ 1] - sample.extra_attributes['rrid'] = [ - sample.extra_attributes['rrid']] - sample.extra_attributes['rrid'].append( + sample.extra_attributes['36'] = [ + sample.extra_attributes['36']] + sample.extra_attributes['36'].append( webqtlConfig.RRID_RAT_URL % the_rrid) self.sample_list.append(sample) @@ -124,17 +124,19 @@ class SampleList: # Get attribute names and distinct values for each attribute results = g.db.execute(''' - SELECT DISTINCT CaseAttribute.Id, CaseAttribute.Name, CaseAttributeXRefNew.Value + SELECT DISTINCT CaseAttribute.Id, CaseAttribute.Name, CaseAttribute.Description, CaseAttributeXRefNew.Value FROM CaseAttribute, CaseAttributeXRefNew WHERE CaseAttributeXRefNew.CaseAttributeId = CaseAttribute.Id AND CaseAttributeXRefNew.InbredSetId = %s - ORDER BY lower(CaseAttribute.Name)''', (str(self.dataset.group.id),)) + ORDER BY CaseAttribute.Id''', (str(self.dataset.group.id),)) self.attributes = {} - for attr, values in itertools.groupby(results.fetchall(), lambda row: (row.Id, row.Name)): - key, name = attr + for attr, values in itertools.groupby(results.fetchall(), lambda row: (row.Id, row.Name, row.Description)): + key, name, description = attr self.attributes[key] = Bunch() + self.attributes[key].id = key self.attributes[key].name = name + self.attributes[key].description = description self.attributes[key].distinct_values = [ item.Value for item in values] self.attributes[key].distinct_values = natural_sort( @@ -168,10 +170,13 @@ class SampleList: for sample_name, items in itertools.groupby(results.fetchall(), lambda row: row.SampleName): attribute_values = {} + # Make a list of attr IDs without values (that have values for other samples) + valueless_attr_ids = [self.attributes[key].id for key in self.attributes.keys()] for item in items: + valueless_attr_ids.remove(item.Id) attribute_value = item.Value - # ZS: If it's an int, turn it into one for sorting + # If it's an int, turn it into one for sorting # (for example, 101 would be lower than 80 if # they're strings instead of ints) try: @@ -179,8 +184,10 @@ class SampleList: except ValueError: pass - attribute_values[self.attributes[item.Id].name.lower( - )] = attribute_value + attribute_values[str(item.Id)] = attribute_value + for attr_id in valueless_attr_ids: + attribute_values[str(attr_id)] = "" + self.sample_attribute_values[sample_name] = attribute_values def get_first_attr_col(self): diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index c07430dd..c4d1ae1c 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -1,3 +1,5 @@ +from typing import Dict + import string import datetime import uuid @@ -176,11 +178,11 @@ class ShowTrait: self.sample_group_types['samples_primary'] = self.dataset.group.name sample_lists = [group.sample_list for group in self.sample_groups] - categorical_var_list = [] + self.categorical_var_list = [] self.numerical_var_list = [] if not self.temp_trait: # ZS: Only using first samplelist, since I think mapping only uses those samples - categorical_var_list = get_categorical_variables( + self.categorical_var_list = get_categorical_variables( self.this_trait, self.sample_groups[0]) self.numerical_var_list = get_numerical_variables( self.this_trait, self.sample_groups[0]) @@ -192,6 +194,8 @@ class ShowTrait: [self.dataset.species.chromosomes.chromosomes[this_chr].name, i]) self.genofiles = self.dataset.group.get_genofiles() + study_samplelist_json = self.dataset.group.get_study_samplelists() + self.study_samplelists = [study["title"] for study in study_samplelist_json] # ZS: No need to grab scales from .geno file unless it's using # a mapping method that reads .geno files @@ -280,10 +284,11 @@ class ShowTrait: hddn['selected_chr'] = -1 hddn['mapping_display_all'] = True hddn['suggestive'] = 0 + hddn['study_samplelists'] = json.dumps(study_samplelist_json) hddn['num_perm'] = 0 hddn['categorical_vars'] = "" - if categorical_var_list: - hddn['categorical_vars'] = ",".join(categorical_var_list) + if self.categorical_var_list: + hddn['categorical_vars'] = ",".join(self.categorical_var_list) hddn['manhattan_plot'] = "" hddn['control_marker'] = "" if not self.temp_trait: @@ -295,7 +300,7 @@ class ShowTrait: hddn['compare_traits'] = [] hddn['export_data'] = "" hddn['export_format'] = "excel" - if len(self.scales_in_geno) < 2: + if len(self.scales_in_geno) < 2 and bool(self.scales_in_geno): hddn['mapping_scale'] = self.scales_in_geno[list( self.scales_in_geno.keys())[0]][0][0] @@ -318,7 +323,7 @@ class ShowTrait: has_num_cases=self.has_num_cases, attributes=self.sample_groups[0].attributes, categorical_attr_exists=self.categorical_attr_exists, - categorical_vars=",".join(categorical_var_list), + categorical_vars=",".join(self.categorical_var_list), num_values=self.num_values, qnorm_values=self.qnorm_vals, zscore_values=self.z_scores, @@ -520,6 +525,9 @@ class ShowTrait: sample_group_type='primary', header="%s Only" % (self.dataset.group.name)) self.sample_groups = (primary_samples,) + print("\nttttttttttttttttttttttttttttttttttttttttttttt\n") + print(self.sample_groups) + print("\nttttttttttttttttttttttttttttttttttttttttttttt\n") self.primary_sample_names = primary_sample_names self.dataset.group.allsamples = all_samples_ordered @@ -693,7 +701,7 @@ def get_categorical_variables(this_trait, sample_list) -> list: if len(sample_list.attributes) > 0: for attribute in sample_list.attributes: if len(sample_list.attributes[attribute].distinct_values) < 10: - categorical_var_list.append(sample_list.attributes[attribute].name) + categorical_var_list.append(str(sample_list.attributes[attribute].id)) return categorical_var_list @@ -799,3 +807,41 @@ def get_scales_from_genofile(file_location): return [["physic", "Mb"], ["morgan", "cM"]] else: return [["physic", "Mb"]] + + + +def get_diff_of_vals(new_vals: Dict, trait_id: str) -> Dict: + """ Get the diff between current sample values and the values in the DB + + Given a dict of the changed values and the trait/dataset ID, return a Dict + with keys corresponding to each sample with a changed value and a value + that is a dict with keys for the old_value and new_value + + """ + + trait_name = trait_id.split(":")[0] + dataset_name = trait_id.split(":")[1] + trait_ob = create_trait(name=trait_name, dataset_name=dataset_name) + + old_vals = {sample : trait_ob.data[sample].value for sample in trait_ob.data} + + shared_samples = set.union(set(new_vals.keys()), set(old_vals.keys())) + + diff_dict = {} + for sample in shared_samples: + try: + new_val = round(float(new_vals[sample]), 3) + except: + new_val = "x" + try: + old_val = round(float(old_vals[sample]), 3) + except: + old_val = "x" + + if new_val != old_val: + diff_dict[sample] = { + "new_val": new_val, + "old_val": old_val + } + + return diff_dict diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css index 782dabc2..b0514e01 100644 --- a/wqflask/wqflask/static/new/css/show_trait.css +++ b/wqflask/wqflask/static/new/css/show_trait.css @@ -260,3 +260,33 @@ input.trait-value-input { div.inline-div { display: inline; } + +/* div.colorbox_border { + border: 1px solid grey; +} */ +div#cboxContent { + /* box-shadow: + 0 2.8px 2.2px rgba(0, 0, 0, 0.034), + 0 6.7px 5.3px rgba(0, 0, 0, 0.048), + 0 12.5px 10px rgba(0, 0, 0, 0.06), + 0 22.3px 17.9px rgba(0, 0, 0, 0.072), + 0 41.8px 33.4px rgba(0, 0, 0, 0.086), + 0 100px 80px rgba(0, 0, 0, 0.12) */ + + padding: 10px 10px 5px 10px; + + -moz-box-shadow: 3px 3px 5px #535353; + -webkit-box-shadow: 3px 3px 5px #535353; + box-shadow: 3px 3px 5px #535353; + + -moz-border-radius: 6px 6px 6px 6px; + -webkit-border-radius: 6px; + border-radius: 6px 6px 6px 6px; + + /* border: 2px solid grey; */ +} + +#cboxClose { + margin-right: 5px; + margin-bottom: 2px; +} diff --git a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js index 3e414034..00025a32 100644 --- a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js +++ b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js @@ -65,10 +65,8 @@ if ( ! $.fn.DataTable.isDataTable( '#collection_table' ) ) { collection_click = function() { var this_collection_url; - console.log("Clicking on:", $(this)); this_collection_url = $(this).find('.collection_name').prop("href"); this_collection_url += "&json"; - console.log("this_collection_url", this_collection_url); collection_list = $("#collections_holder").html(); return $.ajax({ dataType: "json", @@ -79,32 +77,57 @@ collection_click = function() { submit_click = function() { var covariates_string = ""; - var covariates_display_string = ""; + var covariates_as_set = new Set(); + $(".selected-covariates:first option").each(function() { + if ($(this).val() != ""){ + covariates_as_set.add($(this).val() + "," + $(this).text()); + } + }); $('#collections_holder').find('input[type=checkbox]:checked').each(function() { var this_dataset, this_trait; this_trait = $(this).parents('tr').find('.trait').text(); this_trait_display = $(this).parents('tr').find('.trait').data("display_name"); this_description = $(this).parents('tr').find('.description').text(); - console.log("this_trait is:", this_trait_display); this_dataset = $(this).parents('tr').find('.dataset').data("dataset"); - console.log("this_dataset is:", this_dataset); - covariates_string += this_trait + ":" + this_dataset + "," - //this_covariate_display_string = this_trait + ": " + this_description this_covariate_display_string = this_trait_display if (this_covariate_display_string.length > 50) { this_covariate_display_string = this_covariate_display_string.substring(0, 45) + "..." } - covariates_display_string += this_covariate_display_string + "\n" + covariates_as_set.add(this_trait + ":" + this_dataset + "," + this_covariate_display_string) + }); + + covariates_as_list = Array.from(covariates_as_set) + + // Removed the starting "No covariates selected" option before adding options for each covariate + if (covariates_as_list.length > 0){ + $(".selected-covariates option[value='']").each(function() { + $(this).remove(); + }); + } + + $(".selected-covariates option").each(function() { + $(this).remove(); }); - // Trim the last newline from display_string - covariates_display_string = covariates_display_string.replace(/\n$/, "") - // Trim the last comma - covariates_string = covariates_string.substring(0, covariates_string.length - 1) - //covariates_display_string = covariates_display_string.substring(0, covariates_display_string.length - 2) + covariate_list_for_form = [] + $.each(covariates_as_list, function (index, value) { + option_value = value.split(",")[0] + option_text = value.split(",")[1] + $(".selected-covariates").append($("<option/>", { + value: option_value, + text: option_text + })) + covariate_list_for_form.push(option_value) + }); - $("input[name=covariates]").val(covariates_string) - $(".selected-covariates").val(covariates_display_string) + $("input[name=covariates]").val(covariate_list_for_form.join(",")); + + cofactor_count = $(".selected-covariates:first option").length; + if (cofactor_count > 10){ + $(".selected-covariates").attr("size", 10); + } else { + $(".selected-covariates").attr("size", cofactor_count); + } return $.colorbox.close(); }; @@ -186,9 +209,8 @@ color_by_trait = function(trait_sample_data, textStatus, jqXHR) { process_traits = function(trait_data, textStatus, jqXHR) { var the_html, trait, _i, _len; console.log('in process_traits with trait_data:', trait_data); - the_html = "<button id='back_to_collections' class='btn btn-inverse btn-small'>"; - the_html += "<i class='icon-white icon-arrow-left'></i> Back </button>"; - the_html += " <button id='submit' class='btn btn-primary btn-small'> Submit </button>"; + the_html = "<button class='btn btn-success btn-small submit'> Submit </button>"; + the_html += "<button id='back_to_collections' class='btn btn-inverse btn-small' style='float: right;'>Back</button>"; the_html += "<table id='collection_table' style='padding-top: 10px;' class='table table-hover'>"; the_html += "<thead><tr><th></th><th>Record</th><th>Data Set</th><th>Description</th></tr></thead>"; the_html += "<tbody>"; @@ -221,6 +243,6 @@ back_to_collections = function() { }; $(".collection_line").on("click", collection_click); -$("#submit").on("click", submit_click); +$(".submit").on("click", submit_click); $(".trait").on("click", trait_click); -$("#back_to_collections").on("click", back_to_collections);
\ No newline at end of file +$("#back_to_collections").on("click", back_to_collections); diff --git a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js index 6ca92fb6..0a060cdc 100644 --- a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js +++ b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js @@ -93,15 +93,15 @@ build_columns = function() { ); } - attr_keys = Object.keys(js_data.attributes).sort((a, b) => (js_data.attributes[a].name.toLowerCase() > js_data.attributes[b].name.toLowerCase()) ? 1 : -1) + attr_keys = Object.keys(js_data.attributes).sort((a, b) => (js_data.attributes[a].id > js_data.attributes[b].id) ? 1 : -1) for (i = 0; i < attr_keys.length; i++){ column_list.push( { - 'title': "<div style='text-align: " + js_data.attributes[attr_keys[i]].alignment + "'>" + js_data.attributes[attr_keys[i]].name + "</div>", + 'title': "<div title='" + js_data.attributes[attr_keys[i]].description + "' style='text-align: " + js_data.attributes[attr_keys[i]].alignment + "'>" + js_data.attributes[attr_keys[i]].name + "</div>", 'type': "natural", 'data': null, 'render': function(data, type, row, meta) { - attr_name = Object.keys(data.extra_attributes).sort()[meta.col - data.first_attr_col] + attr_name = Object.keys(data.extra_attributes).sort((a, b) => (parseInt(a) > parseInt(b)) ? 1 : -1)[meta.col - data.first_attr_col] if (attr_name != null && attr_name != undefined){ if (Array.isArray(data.extra_attributes[attr_name])){ @@ -130,6 +130,7 @@ var primary_table = $('#samples_primary').DataTable( { $(row).addClass("value_se"); if (data.outlier) { $(row).addClass("outlier"); + $(row).attr("style", "background-color: orange;"); } $('td', row).eq(1).addClass("column_name-Index") $('td', row).eq(2).addClass("column_name-Sample") @@ -189,6 +190,7 @@ if (js_data.sample_lists.length > 1){ $(row).addClass("value_se"); if (data.outlier) { $(row).addClass("outlier"); + $(row).attr("style", "background-color: orange;"); } $('td', row).eq(1).addClass("column_name-Index") $('td', row).eq(2).addClass("column_name-Sample") diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 77ef1720..f050d4ae 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -98,11 +98,54 @@ sample_group_types = js_data.sample_group_types; $(".select_covariates").click(function () { open_covariate_selection(); }); + $(".remove_covariates").click(function () { - $("input[name=covariates]").val("") - $(".selected-covariates").val("") + $(".selected-covariates option:selected").each(function() { + this_val = $(this).val(); + $(".selected-covariates option").each(function(){ + if ($(this).val() == this_val){ + $(this).remove(); + } + }) + cofactor_count = $(".selected-covariates:first option").length + if (cofactor_count > 2 && cofactor_count < 11){ + $(".selected-covariates").each(function() { + $(this).attr("size", $(".selected-covariates:first option").length) + }); + } else if (cofactor_count > 10) { + $(".selected-covariates").each(function() { + $(this).attr("size", 10) + }); + } else { + $(".selected-covariates").each(function() { + $(this).attr("size", 2) + }); + } + if (cofactor_count == 0){ + $(".selected-covariates").each(function() { + $(this).append($("<option/>", { + value: "", + text: "No covariates selected" + })) + }) + } + }); + + covariates_list = []; + $(".selected-covariates:first option").each(function() { + covariates_list.push($(this).val()); + }) + $("input[name=covariates]").val(covariates_list.join(",")) }); +$(".remove_all_covariates").click(function() { + $(".selected-covariates option").each(function() { + $(this).remove(); + }); + $(".selected-covariates").attr("size", 2) + $("input[name=covariates]").val(""); +}) + open_trait_selection = function() { return $('#collections_holder').load('/collections/list?color_by_trait #collections_list', (function(_this) { return function() { @@ -608,13 +651,14 @@ $(".corr_compute").on("click", (function(_this) { create_value_dropdown = function(value) { return "<option val=" + value + ">" + value + "</option>"; }; + populate_sample_attributes_values_dropdown = function() { var attribute_info, key, sample_attributes, selected_attribute, value, _i, _len, _ref, _ref1, _results; $('#attribute_values').empty(); sample_attributes = []; var attributes_as_list = Object.keys(js_data.attributes).map(function(key) { - return [key, js_data.attributes[key].name.toLowerCase()]; + return [key, js_data.attributes[key].id]; }); attributes_as_list.sort(function(first, second) { @@ -628,7 +672,7 @@ populate_sample_attributes_values_dropdown = function() { }); for (i=0; i < attributes_as_list.length; i++) { - attribute_info = js_data.attributes[attributes_as_list[i][0]] + attribute_info = js_data.attributes[attributes_as_list[i][1]] sample_attributes.push(attribute_info.distinct_values); } @@ -667,11 +711,13 @@ block_by_attribute_value = function() { let exclude_val_nodes = table_api.column(attribute_start_pos + parseInt(exclude_column)).nodes().to$(); for (i = 0; i < exclude_val_nodes.length; i++) { - let this_col_value = exclude_val_nodes[i].childNodes[0].data; - let this_val_node = val_nodes[i].childNodes[0]; + if (exclude_val_nodes[i].hasChildNodes()) { + let this_col_value = exclude_val_nodes[i].childNodes[0].data; + let this_val_node = val_nodes[i].childNodes[0]; - if (this_col_value == exclude_by_value){ - this_val_node.value = "x"; + if (this_col_value == exclude_by_value){ + this_val_node.value = "x"; + } } } @@ -713,10 +759,34 @@ block_by_index = function() { for (_k = 0, _len1 = index_list.length; _k < _len1; _k++) { index = index_list[_k]; val_nodes[index - 1].childNodes[0].value = "x"; - } }; +filter_by_study = function() { + let this_study = $('#filter_study').val(); + + let study_sample_data = JSON.parse($('input[name=study_samplelists]').val()) + let filter_samples = study_sample_data[parseInt(this_study)]['samples'] + + if ($('#filter_study_group').length){ + let block_group = $('#filter_study_group').val(); + if (block_group === "other") { + table_api = $('#samples_other').DataTable(); + } else { + table_api = $('#samples_primary').DataTable(); + } + } + + let sample_nodes = table_api.column(2).nodes().to$(); + let val_nodes = table_api.column(3).nodes().to$(); + for (i = 0; i < sample_nodes.length; i++) { + this_sample = sample_nodes[i].childNodes[0].innerText; + if (!filter_samples.includes(this_sample)){ + val_nodes[i].childNodes[0].value = "x"; + } + } +} + filter_by_value = function() { let filter_logic = $('#filter_logic').val(); let filter_column = $('#filter_column').val(); @@ -748,7 +818,7 @@ filter_by_value = function() { var this_col_value = filter_val_nodes[i].childNodes[0].value; } else { if (filter_val_nodes[i].childNodes[0] !== undefined){ - var this_col_value = filter_val_nodes[i].childNodes[0].data; + var this_col_value = filter_val_nodes[i].innerText; } else { continue } @@ -1690,6 +1760,11 @@ $('#block_by_index').click(function(){ edit_data_change(); }); +$('#filter_by_study').click(function(){ + filter_by_study(); + edit_data_change(); +}) + $('#filter_by_value').click(function(){ filter_by_value(); edit_data_change(); diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js index 09e9d024..e42fe8c4 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -141,11 +141,11 @@ $('input[name=display_all]').change((function(_this) { })(this)); //ZS: This is a list of inputs to be passed to the loading page, since not all inputs on the trait page are relevant to mapping -var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', 'sample_vals', - 'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results', - 'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'do_control', 'genofile', - 'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', - 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples'] +var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', + 'sample_vals', 'vals_hash', 'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', + 'num_bootstrap', 'bootCheck', 'bootstrap_results', 'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', + 'do_control', 'genofile', 'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', + 'haplotypeAnalystCheck', 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'primary_samples'] $(".rqtl-geno-tab, #rqtl_geno_compute").on("click", (function(_this) { return function() { diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html index c0b99e75..692a7abc 100644 --- a/wqflask/wqflask/templates/admin/group_manager.html +++ b/wqflask/wqflask/templates/admin/group_manager.html @@ -81,7 +81,7 @@ <tr> <td><input type="checkbox" name="read" value="{{ group.id }}"></td> <td>{{ loop.index }}</td> - <td>{{ group.name }}</td> + <td><a href="/groups/view?id={{ group.id }}">{{ group.name }}</a></td> <td>{{ group.admins|length + group.members|length }}</td> <td>{{ group.created_timestamp }}</td> <td>{{ group.changed_timestamp }}</td> diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 049ebe6d..14e6bc88 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -87,6 +87,7 @@ <li><a href="https://systems-genetics.org/">Systems Genetics PheWAS</a></li> <li><a href="http://ucscbrowser.genenetwork.org/">Genome Browser</a></li> <li><a href="http://power.genenetwork.org">BXD Power Calculator</a></li> + <li><a href="http://notebook.genenetwork.org/">Jupyter Notebook Launcher</a></li> <li><a href="http://datafiles.genenetwork.org">Interplanetary File System</a></li> </ul> </li> diff --git a/wqflask/wqflask/templates/collections/add.html b/wqflask/wqflask/templates/collections/add.html index 0398c6e4..8640fdb8 100644 --- a/wqflask/wqflask/templates/collections/add.html +++ b/wqflask/wqflask/templates/collections/add.html @@ -5,7 +5,7 @@ or add to an existing collection.</p> </div> <div class="modal-body" style="margin-left: 20px;"> - <form action="/collections/new" target="_blank" data-validate="parsley" id="add_form"> + <form action="/collections/new" target="_blank" data-validate="parsley" id="add_form" class="form-inline"> {% if traits is defined %} <input type="hidden" name="traits" value="{{ traits }}" /> {% else %} @@ -14,10 +14,8 @@ {% if collections|length > 0 %} <fieldset> <legend>1. Add to an existing collection</legend> - <div style="margin-left: 20px;"> - <!--<label>Existing collection name:</label>--> - <select name="existing_collection" class="form-control"> - <!--<option selected disabled>Select Collection</option>--> + <div style="margin-left: 20px;"> + <select name="existing_collection" class="form-control" style="width: 80%;"> {% for col in collections %} {% if loop.index == 1 %} <option value="{{ col.id }}:{{ col.name }}" selected>{{ col.name }}</option> @@ -26,8 +24,9 @@ {% endif %} {% endfor %} </select> - <br /> - <button type="submit" name="add_to_existing" class="btn btn-primary">Add to existing collection</button> + <input type="button" style="display: inline;" id="make_default" value="Make Default"> + <br><br> + <button type="submit" name="add_to_existing" class="btn btn-primary">Add</button> </div> </fieldset> {% endif %} @@ -35,7 +34,6 @@ <fieldset> <legend>{% if collections|length > 0 %}2. {% else %}{% endif %}Create a new collection</legend> <div style="margin-left: 20px;"> - <!--<label>Collection name:</label>--> <input type="text" name="new_collection" placeholder=" Name of new collection..." data-trigger="change" data-minlength="5" data-maxlength="50" style="width: 100%"> <button type="submit" name="create_new" class="btn btn-primary" style="margin-top: 20px;">Create collection</button> @@ -54,6 +52,21 @@ parent.jQuery.colorbox.close(); }); + make_default = function() { + alert("The current collection is now your default collection.") + let uc_id = $('[name=existing_collection] option:selected').val().split(":")[0] + $.cookie('default_collection', uc_id, { + expires: 365, + path: '/' + }); + + let default_collection_id = $.cookie('default_collection'); + }; + + $("#make_default").on("click", function(){ + make_default(); + }); + apply_default = function() { let default_collection_id = $.cookie('default_collection'); if (default_collection_id) { diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html index 9ec98ab1..a3090bcf 100644 --- a/wqflask/wqflask/templates/collections/view.html +++ b/wqflask/wqflask/templates/collections/view.html @@ -49,7 +49,7 @@ <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Select Top ..."> <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button> <button id="remove" class="btn btn-danger" data-url="/collections/remove" type="button" disabled><i class="icon-minus-sign"></i> Delete Rows</button> - <button id="delete" class="btn btn-danger submit_special" data-url="/collections/delete" title="Delete this collection" > Delete Collection</button> + <button id="delete" class="btn btn-danger submit_special" data-url="/collections/delete" type="button" title="Delete this collection" > Delete Collection</button> </form> </div> <div style="margin-top: 10px; margin-bottom: 5px;"> diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html index 6d6136ac..ccf810b0 100644 --- a/wqflask/wqflask/templates/loading.html +++ b/wqflask/wqflask/templates/loading.html @@ -12,6 +12,8 @@ {% if start_vars.tool_used == "Mapping" %} <h1>Computing the Maps</h1> <br> + <b>Time Elapsed:</b> <span class="timer"></span> + <br> <b>Trait Metadata</b> <br> species = <b><i>{{ start_vars.species[0] | upper }}{{ start_vars.species[1:] }}</i></b> @@ -25,6 +27,8 @@ <br> transformation = <b><i>{{ start_vars.transform }}</i></b> {% endif %} + <br> + hash of sample values = <b><i>{{ start_vars.vals_hash }}</i></b> <br><br> <b>Mapping Metadata</b> <br> @@ -68,6 +72,29 @@ <div style="text-align: center;"> <img align="center" src="/static/gif/89.gif"> </div> + {% if start_vars.vals_diff|length != 0 and start_vars.transform == "" %} + <br><br> + <button id="show_full_diff">Show Full Diff</button> + <br> + <div id="diff_table_container" style="display: none; height:200px; overflow:auto;"> + <table class="table table-hover"> + <thead> + <th>Sample</th> + <th>New Value</th> + <th>Old Value</th> + </thead> + <tbody> + {% for sample in start_vars.vals_diff %} + <tr> + <td>{{ sample }}</td> + <td>{{ start_vars.vals_diff[sample].new_val }}</td> + <td>{{ start_vars.vals_diff[sample].old_val }}</td> + </tr> + {% endfor %} + </tbody> + </table> + </div> + {% endif %} </div> </div> </div> @@ -76,6 +103,30 @@ <script src="{{ url_for('js', filename='jquery/jquery.min.js') }}" type="text/javascript"></script> <script src="{{ url_for('js', filename='bootstrap/js/bootstrap.min.js') }}" type="text/javascript"></script> <script type="text/javascript"> +$('#show_full_diff').click(function() { + if ($('#diff_table_container').is(':visible')){ + $('#diff_table_container').hide(); + } else { + $('#diff_table_container').show(); + } +}) + +var start = new Date; + +setInterval(function() { + minutes = Math.floor((new Date - start) / 1000 / 60) + seconds = Math.round(((new Date - start) / 1000) % 60) + if (seconds < 10 && minutes >= 1){ + seconds_text = "0" + seconds.toString() + } else { + seconds_text = seconds.toString() + } + if (minutes < 1) { + $('.timer').text(seconds_text + " seconds"); + } else { + $('.timer').text(minutes.toString() + ":" + seconds_text); + } +}, 100); $("#loading_form").attr("action", "{{ start_vars.form_url }}"); setTimeout(function(){ $("#loading_form").submit()}, 350); diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index 35d8a157..f2d11e89 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -34,6 +34,7 @@ <input type="hidden" name="results_path" value="{{ mapping_results_path }}"> <input type="hidden" name="method" value="{{ mapping_method }}"> <input type="hidden" name="sample_vals" value="{{ sample_vals }}"> + <input type="hidden" name="vals_hash" value="{{ vals_hash }}"> <input type="hidden" name="n_samples" value="{{ n_samples }}"> <input type="hidden" name="maf" value="{{ maf }}"> <input type="hidden" name="use_loco" value="{{ use_loco }}"> @@ -44,7 +45,12 @@ {% endif %} <input type="hidden" name="num_perm" value="{{ nperm }}"> <input type="hidden" name="perm_info" value=""> - <input type="hidden" name="perm_strata" value="{{ perm_strata }}"> + {% if categorical_vars is defined %} + <input type="hidden" name="categorical_vars" value="{{ categorical_vars|join(',') }}"> + {% endif %} + {% if perm_strata is defined %} + <input type="hidden" name="perm_strata" value="True"> + {% endif %} <input type="hidden" name="num_bootstrap" value="{{ nboot }}"> <input type="hidden" name="do_control" value="{{ doControl }}"> <input type="hidden" name="control_marker" value="{{ controlLocus }}"> @@ -62,15 +68,16 @@ <h2>Map Viewer: Whole Genome</h2><br> <b>Population:</b> {{ dataset.group.species|capitalize }} {{ dataset.group.name }}<br> <b>Database:</b> {{ dataset.fullname }}<br> - {% if dataset.type == "ProbeSet" %}<b>Trait ID:</b>{% else %}<b>Record ID:</b>{% endif %} <a href="/show_trait?trait_id={{ this_trait.name }}&dataset={{ dataset.name }}">{{ this_trait.name }}</a><br> + {% if dataset.type == "ProbeSet" %}<b>Trait ID:</b>{% else %}<b>Record ID:</b>{% endif %} <a href="/show_trait?trait_id={{ this_trait.name }}&dataset={{ dataset.name }}">{{ this_trait.display_name }}</a><br> + <b>Trait Hash: </b> {{ vals_hash }}<br> {% if dataset.type == "ProbeSet" %} <b>Gene Symbol:</b> <i>{{ this_trait.symbol }}</i><br> <b>Location:</b> Chr {{ this_trait.chr }} @ {{ this_trait.mb }} Mb<br> {% endif %} - {% if genofile_string is defined %} - <b>Genotypes:</b> {{ genofile_string.split(":")[1] }} + {% if genofile_string != "" %} + <b>Genotypes:</b> {{ genofile_string.split(":")[1] }}<br> {% endif %} - <br> + <b>Current Date/Time:</b> {{ current_datetime }}<br> <br> <a class="export_mapping_results" href="#" target="_blank" >Download Full Results</a> </div> @@ -524,7 +531,7 @@ }); {% endif %} - {% if mapping_method != "gemma" and mapping_method != "plink" %} + {% if mapping_method != "gemma" and mapping_method != "plink" and nperm > 0 and permChecked == "ON" %} $('#download_perm').click(function(){ perm_info_dict = { perm_data: js_data.perm_results, diff --git a/wqflask/wqflask/templates/new_security/_scripts.html b/wqflask/wqflask/templates/new_security/_scripts.html deleted file mode 100644 index 5fefe305..00000000 --- a/wqflask/wqflask/templates/new_security/_scripts.html +++ /dev/null @@ -1 +0,0 @@ -<!--<script type="text/javascript" src="/static/new/javascript/login.js"></script>--> diff --git a/wqflask/wqflask/templates/new_security/forgot_password.html b/wqflask/wqflask/templates/new_security/forgot_password.html index e5c42a45..60a221da 100644 --- a/wqflask/wqflask/templates/new_security/forgot_password.html +++ b/wqflask/wqflask/templates/new_security/forgot_password.html @@ -48,6 +48,5 @@ {% endblock %} {% block js %} - {% include "new_security/_scripts.html" %} {% endblock %} diff --git a/wqflask/wqflask/templates/new_security/forgot_password_step2.html b/wqflask/wqflask/templates/new_security/forgot_password_step2.html index b4bf41c7..1835fd4c 100644 --- a/wqflask/wqflask/templates/new_security/forgot_password_step2.html +++ b/wqflask/wqflask/templates/new_security/forgot_password_step2.html @@ -20,7 +20,6 @@ {% endblock %} {% block js %} - {% include "new_security/_scripts.html" %} <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn/zxcvbn.js') }}"></script> <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script> {% endblock %} diff --git a/wqflask/wqflask/templates/new_security/login_user.html b/wqflask/wqflask/templates/new_security/login_user.html index 095036f0..88eab6bc 100644 --- a/wqflask/wqflask/templates/new_security/login_user.html +++ b/wqflask/wqflask/templates/new_security/login_user.html @@ -114,31 +114,5 @@ label.error,div.error{ {% endblock %} {% block js %} - <!-- Disable plugin, see https://github.com/genenetwork/genenetwork2/issues/310 - - <script type="text/javascript" src="/static/new/packages/ValidationPlugin/dist/jquery.validate.min.js"></script> - <script> - $(document).ready(function () { - $("#loginUserForm").validate({ - onkeyup: false, - onsubmit: true, - onfocusout: function(element) { $(element).valid(); }, - rules: { - email_address: { - required: true, - email: true - }, - password: { - required: true - } - } - }); - }); - - </script> - - --> - - {% include "new_security/_scripts.html" %} {% endblock %} diff --git a/wqflask/wqflask/templates/new_security/password_reset.html b/wqflask/wqflask/templates/new_security/password_reset.html index 684c12b1..e21f075c 100644 --- a/wqflask/wqflask/templates/new_security/password_reset.html +++ b/wqflask/wqflask/templates/new_security/password_reset.html @@ -73,7 +73,6 @@ {% block js %} - {% include "new_security/_scripts.html" %} <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn/zxcvbn.js') }}"></script> <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script> {% endblock %} diff --git a/wqflask/wqflask/templates/new_security/register_user.html b/wqflask/wqflask/templates/new_security/register_user.html index 3ae4488b..c2895517 100644 --- a/wqflask/wqflask/templates/new_security/register_user.html +++ b/wqflask/wqflask/templates/new_security/register_user.html @@ -100,7 +100,6 @@ {% block js %} - {% include "new_security/_scripts.html" %} <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn/zxcvbn.js') }}"></script> <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script> {% endblock %} diff --git a/wqflask/wqflask/templates/new_security/registered.html b/wqflask/wqflask/templates/new_security/registered.html index f2f58ec1..29889a97 100644 --- a/wqflask/wqflask/templates/new_security/registered.html +++ b/wqflask/wqflask/templates/new_security/registered.html @@ -19,7 +19,6 @@ {% block js %} - {% include "new_security/_scripts.html" %} <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn/zxcvbn.js') }}"></script> <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script> {% endblock %} diff --git a/wqflask/wqflask/templates/new_security/thank_you.html b/wqflask/wqflask/templates/new_security/thank_you.html index 0ff7ee8d..d4f5e574 100644 --- a/wqflask/wqflask/templates/new_security/thank_you.html +++ b/wqflask/wqflask/templates/new_security/thank_you.html @@ -18,7 +18,6 @@ {% endblock %} {% block js %} - {% include "new_security/_scripts.html" %} <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn/zxcvbn.js') }}"></script> <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script> {% endblock %} diff --git a/wqflask/wqflask/templates/new_security/verification_still_needed.html b/wqflask/wqflask/templates/new_security/verification_still_needed.html index dc0f9e68..1f91fd8d 100644 --- a/wqflask/wqflask/templates/new_security/verification_still_needed.html +++ b/wqflask/wqflask/templates/new_security/verification_still_needed.html @@ -21,7 +21,6 @@ {% endblock %} {% block js %} - {% include "new_security/_scripts.html" %} <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn/zxcvbn.js') }}"></script> <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script> {% endblock %} diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 7ec335d5..c499aa8f 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -53,6 +53,7 @@ A total of {{ results|count }} records were found. </p> + {% if results|count > 0 %} {% if go_term is not none %} <p><b>The associated genes include:</b><br><br>{% for word in search_terms %}{{ word.search_term[0] }}{% endfor %}</p> {% endif %} @@ -133,8 +134,11 @@ </div> </div> {% endif %} + {% else %} + <br> + <button type="button" onclick="window.location.href='/'">Return To Index Page</button> + {% endif %} </div> - <div id="myModal"></div> <!-- End of body --> @@ -171,6 +175,7 @@ return params; }; + {% if results|count > 0 %} //ZS: Need to make sort by symbol, also need to make sure blank symbol fields at the bottom and symbols starting with numbers below letters trait_table = $('#trait_table').DataTable( { 'drawCallback': function( settings ) { @@ -412,6 +417,7 @@ var table = $('#trait_table').DataTable(); table.colReorder.reset() }); + {% endif %} submit_special = function(url) { $("#trait_submission_form").attr("action", url); diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index 3dbf5f57..f3fa1332 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -254,8 +254,6 @@ } ); {% endif %} - $('#samples_primary, #samples_other').find("tr.outlier").css('background-color', 'orange') - $('.edit_sample_checkbox:checkbox').change(function() { if ($(this).is(":checked")) { if (!$(this).closest('tr').hasClass('selected')) { diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index bb30c54c..2a21dd24 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -236,12 +236,15 @@ <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}', '_blank')">Go to GN1</button> {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %} {% if this_trait.dataset.type == 'Publish' %} - <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('/trait/{{ this_trait.name }}/edit/{{ this_trait.dataset.id }}', '_blank')">Edit</button> + <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('/trait/{{ this_trait.name }}/edit/inbredset-id/{{ this_trait.dataset.id }}', '_blank')">Edit</button> {% endif %} {% if this_trait.dataset.type == 'ProbeSet' %} <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('/trait/edit/probeset-name/{{ this_trait.name }}', '_blank')">Edit</button> {% endif %} + {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %} + <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('./resources/manage?resource_id={{ resource_id }}', '_blank')">Edit Privileges</button> + {% endif %} {% endif %} </div> </div> diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index 3dd44c85..3af94ed6 100755 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -74,17 +74,20 @@ No collections available. Please add traits to a collection to use them as covariates. {% else %} <div class="select-covar-div"> - <button type="button" class="btn btn-default select-covar-button select_covariates">Select</button> + <button type="button" class="btn btn-success select-covar-button select_covariates">Select</button> <button type="button" class="btn btn-default select-covar-button remove_covariates">Remove</button> + <button type="button" class="btn btn-danger select-covar-button remove_all_covariates">Clear</button> </div> - <textarea rows="3" cols="50" readonly placeholder="No covariates selected" class="selected-covariates"></textarea> + <select size="2" name="selected_covariates_gemma" class="form-control selected-covariates" multiple> + <option value="">No covariates selected</option> + </select> {% endif %} </div> </div> <div class="mapping_method_fields form-group"> <label class="col-xs-3 control-label"></label> <div class="col-xs-6"> - <button id="gemma_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression" value="Compute">Compute</button> + <button id="gemma_compute" type="button" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression" value="Compute">Compute</button> </div> </div> </div> @@ -93,15 +96,6 @@ <div class="tab-pane" id="interval_mapping"> <div class="form-horizontal section-form-div"> <div class="mapping_method_fields form-group"> - <label for="reaper_version" class="col-xs-3 control-label">Version<sup><a href="https://github.com/chfi/rust-qtlreaper" target="_blank" title="'New' is the new qtlreaper implementation written in RUST by Christian Fischer. 'Original' corresponds to the original version written in C.">?</a></sup></label> - <div class="col-xs-3 controls"> - <select name="reaper_version" class="form-control reaper-ver-select"> - <option value="new">New</option> - <option value="original">Original</option> - </select> - </div> - </div> - <div class="mapping_method_fields form-group"> <label for="chr_select" class="col-xs-3 control-label">Chromosome</label> <div class="col-xs-2 controls"> <select id="chr_reaper" class="form-control chr-select"> @@ -187,7 +181,7 @@ <div class="mapping_method_fields form-group"> <label class="col-xs-3 control-label"></label> <div class="col-xs-6"> - <button id="interval_mapping_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping" value="Compute">Compute</button> + <button id="interval_mapping_compute" type="button" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping" value="Compute">Compute</button> </div> </div> </div> @@ -226,6 +220,17 @@ </select> </div> </div> + {% else %} + <div class="mapping_method_fields form-group"> + <label for="scale_select" class="col-xs-3 control-label">Map Scale</label> + <div class="col-xs-2 controls"> + <select id="scale_rqtl_geno" class="form-control scale-select"> + {% for item in scales_in_geno[dataset.group.name + ".geno"] %} + <option value="{{ item[0] }}">{{ item[1] }}</option> + {% endfor %} + </select> + </div> + </div> {% endif %} <div class="mapping_method_fields form-group"> <label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label> @@ -249,21 +254,6 @@ </div> {% endif %} <div class="mapping_method_fields form-group"> - <label for="control_for" class="col-xs-3 control-label">Control for</label> - <div class="col-xs-6 controls"> - <input name="control_rqtl_geno" value="{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != '' %}{{ nearest_marker }}{% endif %}" type="text" class="form-control cofactor-input" /> - <label class="radio-inline"> - <input type="radio" name="do_control_rqtl" value="true"> - Yes - </label> - <label class="radio-inline"> - <input type="radio" name="do_control_rqtl" value="false" checked=""> - No - </label> - </div> - </div> - - <div class="mapping_method_fields form-group"> <label for="mapmodel_rqtl_geno" class="col-xs-3 control-label">Model</label> <div class="col-xs-4 controls"> <select id="mapmodel_rqtl_geno" name="mapmodel_rqtl_geno" class="form-control"> @@ -317,17 +307,20 @@ No collections available. Please add traits to a collection to use them as covariates. {% else %} <div class="select-covar-div"> - <button type="button" class="btn btn-default select-covar-button select_covariates">Select</button> + <button type="button" class="btn btn-success select-covar-button select_covariates">Select</button> <button type="button" class="btn btn-default select-covar-button remove_covariates">Remove</button> + <button type="button" class="btn btn-danger select-covar-button remove_all_covariates">Clear</button> </div> - <textarea rows="3" cols="50" readonly placeholder="No covariates selected" class="selected-covariates"></textarea> + <select size="2" name="selected_covariates_rqtl" class="form-control selected-covariates" multiple> + <option value="">No covariates selected</option> + </select> {% endif %} </div> </div> <div class="mapping_method_fields form-group"> <label class="col-xs-3 control-label"></label> <div class="col-xs-6 controls"> - <button id="rqtl_geno_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression" value="Compute">Compute</button> + <button id="rqtl_geno_compute" type="button" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression" value="Compute">Compute</button> </div> </div> </div> diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html index 20f78b48..5e6ed2cf 100644 --- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html +++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html @@ -25,7 +25,7 @@ <label for="exclude_column">Block samples by group:</label> <select id="exclude_column" size=1> {% for attribute in sample_groups[0].attributes %} - {% if sample_groups[0].attributes[attribute].distinct_values|length <= 10 %} + {% if sample_groups[0].attributes[attribute].distinct_values|length <= 10 and sample_groups[0].attributes[attribute].distinct_values|length > 1 %} <option value="{{ loop.index }}"> {{ sample_groups[0].attributes[attribute].name }} </option> @@ -45,6 +45,27 @@ <input type="button" id="exclude_by_attr" class="btn btn-danger" value="Block"> </div> {% endif %} + {% if study_samplelists|length > 0 %} + <div id="filterMenuSpan" class="input-append block-div-2"> + <label for="filter_study_select">Filter samples by study: </label> + <select id="filter_study"> + {% for study in study_samplelists %} + <option value="{{ loop.index - 1 }}">{{ study }}</option> + {% endfor %} + </select> + {% if sample_groups|length != 1 %} + <select id="filter_study_group" size="1"> + <option value="primary"> + {{ sample_group_types['samples_primary'] }} + </option> + <option value="other"> + {{ sample_group_types['samples_other'] }} + </option> + </select> + {% endif %} + <input type="button" id="filter_by_study" class="btn btn-danger" value="Filter"> + </div> + {% endif %} <div id="filterMenuSpan" class="input-append block-div-2"> <label for="filter_samples_field">Filter samples by {% if (numerical_var_list|length == 0) and (not js_data.se_exists) %}value{% endif %} </label> {% if (numerical_var_list|length > 0) or js_data.se_exists %} @@ -53,10 +74,12 @@ {% if js_data.se_exists %} <option value="stderr">SE</option> {% endif %} - {% for attribute in numerical_var_list %} + {% for attribute in sample_groups[0].attributes %} + {% if sample_groups[0].attributes[attribute].name in numerical_var_list %} <option value="{{ loop.index }}"> - {{ attribute }} + {{ sample_groups[0].attributes[attribute].name }} </option> + {% endif %} {% endfor %} </select> {% endif %} diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index a462b31a..b0da1f21 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -28,6 +28,7 @@ from zipfile import ZIP_DEFLATED from wqflask import app from gn3.commands import run_cmd +from gn3.computations.gemma import generate_hash_of_string from gn3.db import diff_from_dict from gn3.db import fetchall from gn3.db import fetchone @@ -63,6 +64,7 @@ from wqflask import server_side from base.data_set import create_dataset # Used by YAML in marker_regression from wqflask.show_trait import show_trait from wqflask.show_trait import export_trait_data +from wqflask.show_trait.show_trait import get_diff_of_vals from wqflask.heatmap import heatmap from wqflask.external_tools import send_to_bnw from wqflask.external_tools import send_to_webgestalt @@ -84,7 +86,7 @@ from wqflask.export_traits import export_search_results_csv from wqflask.gsearch import GSearch from wqflask.update_search_results import GSearch as UpdateGSearch from wqflask.docs import Docs, update_text -from wqflask.decorators import admin_login_required +from wqflask.decorators import edit_access_required from wqflask.db_info import InfoPage from utility import temp_data @@ -159,28 +161,37 @@ def shutdown_session(exception=None): @app.errorhandler(Exception) -def handle_bad_request(e): +def handle_generic_exceptions(e): + import werkzeug err_msg = str(e) - logger.error(err_msg) - logger.error(request.url) - # get the stack trace and send it to the logger - exc_type, exc_value, exc_traceback = sys.exc_info() - logger.error(traceback.format_exc()) now = datetime.datetime.utcnow() time_str = now.strftime('%l:%M%p UTC %b %d, %Y') - formatted_lines = [request.url - + " (" + time_str + ")"] + traceback.format_exc().splitlines() - + # get the stack trace and send it to the logger + exc_type, exc_value, exc_traceback = sys.exc_info() + formatted_lines = {f"{request.url} ({time_str}) " + f" {traceback.format_exc().splitlines()}"} + + _message_templates = { + werkzeug.exceptions.NotFound: ("404: Not Found: " + f"{time_str}: {request.url}"), + werkzeug.exceptions.BadRequest: ("400: Bad Request: " + f"{time_str}: {request.url}"), + werkzeug.exceptions.RequestTimeout: ("408: Request Timeout: " + f"{time_str}: {request.url}")} + # Default to the lengthy stack trace! + logger.error(_message_templates.get(exc_type, + formatted_lines)) # Handle random animations # Use a cookie to have one animation on refresh animation = request.cookies.get(err_msg[:32]) if not animation: - list = [fn for fn in os.listdir( - "./wqflask/static/gif/error") if fn.endswith(".gif")] - animation = random.choice(list) + animation = random.choice([fn for fn in os.listdir( + "./wqflask/static/gif/error") if fn.endswith(".gif")]) resp = make_response(render_template("error.html", message=err_msg, - stack=formatted_lines, error_image=animation, version=GN_VERSION)) + stack=formatted_lines, + error_image=animation, + version=GN_VERSION)) # logger.error("Set cookie %s with %s" % (err_msg, animation)) resp.set_cookie(err_msg[:32], animation) @@ -372,7 +383,6 @@ def wcgna_results(): results = run_wgcna(dict(request.form)) return render_template("test_wgcna_results.html", **results) - @app.route("/ctl_setup", methods=('POST',)) def ctl_setup(): # We are going to get additional user input for the analysis @@ -382,20 +392,6 @@ def ctl_setup(): return render_template("ctl_setup.html", **request.form) -# @app.route("/ctl_results", methods=('POST',)) -# def ctl_results(): -# logger.info("In ctl, request.form is:", request.form) -# logger.info(request.url) -# # Start R, load the package and pointers and create the analysis -# ctl = ctl_analysis.CTL() -# # Start the analysis, a ctlA object should be a separate long running thread -# ctlA = ctl.run_analysis(request.form) -# # After the analysis is finished store the result -# result = ctl.process_results(ctlA) -# # Display them using the template -# return render_template("ctl_results.html", **result) - - @app.route("/intro") def intro(): doc = Docs("intro", request.args) @@ -430,9 +426,9 @@ def submit_trait_form(): version=GN_VERSION) -@app.route("/trait/<name>/edit/phenotype-id/<phenotype_id>") -@admin_login_required -def edit_phenotype(name, phenotype_id): +@app.route("/trait/<name>/edit/inbredset-id/<inbredset_id>") +@edit_access_required +def edit_phenotype(name, inbredset_id): conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"), user=current_app.config.get("DB_USER"), passwd=current_app.config.get("DB_PASS"), @@ -441,7 +437,7 @@ def edit_phenotype(name, phenotype_id): conn=conn, table="PublishXRef", where=PublishXRef(id_=name, - phenotype_id=phenotype_id)) + inbred_set_id=inbredset_id)) phenotype_ = fetchone( conn=conn, table="Phenotype", @@ -488,7 +484,7 @@ def edit_phenotype(name, phenotype_id): @app.route("/trait/edit/probeset-name/<dataset_name>") -# @admin_login_required +@edit_access_required def edit_probeset(dataset_name): conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"), user=current_app.config.get("DB_USER"), @@ -531,7 +527,7 @@ def edit_probeset(dataset_name): @app.route("/trait/update", methods=["POST"]) -@admin_login_required +@edit_access_required def update_phenotype(): conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"), user=current_app.config.get("DB_USER"), @@ -653,11 +649,11 @@ def update_phenotype(): json_data=json.dumps(diff_data))) flash(f"Diff-data: \n{diff_data}\nhas been uploaded", "success") return redirect(f"/trait/{data_.get('dataset-name')}" - f"/edit/phenotype-id/{data_.get('phenotype-id')}") + f"/edit/inbredset-id/{data_.get('inbred-set-id')}") @app.route("/probeset/update", methods=["POST"]) -@admin_login_required +@edit_access_required def update_probeset(): conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"), user=current_app.config.get("DB_USER"), @@ -1018,10 +1014,10 @@ def loading_page(): if key in wanted: start_vars[key] = value + sample_vals_dict = json.loads(start_vars['sample_vals']) if 'n_samples' in start_vars: n_samples = int(start_vars['n_samples']) else: - sample_vals_dict = json.loads(start_vars['sample_vals']) if 'group' in start_vars: dataset = create_dataset( start_vars['dataset'], group_name=start_vars['group']) @@ -1043,6 +1039,10 @@ def loading_page(): n_samples += 1 start_vars['n_samples'] = n_samples + start_vars['vals_hash'] = generate_hash_of_string(str(sample_vals_dict)) + if start_vars['dataset'] != "Temp": # Currently can't get diff for temp traits + start_vars['vals_diff'] = get_diff_of_vals(sample_vals_dict, str(start_vars['trait_id'] + ":" + str(start_vars['dataset']))) + start_vars['wanted_inputs'] = initial_start_vars['wanted_inputs'] start_vars_container['start_vars'] = start_vars @@ -1067,6 +1067,7 @@ def mapping_results_page(): 'samples', 'vals', 'sample_vals', + 'vals_hash', 'first_run', 'output_files', 'geno_db_exists', @@ -1083,7 +1084,6 @@ def mapping_results_page(): 'num_perm', 'permCheck', 'perm_strata', - 'strat_var', 'categorical_vars', 'perm_output', 'num_bootstrap', @@ -1113,7 +1113,6 @@ def mapping_results_page(): 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', - 'reaper_version', 'n_samples', 'transform' ) @@ -1186,7 +1185,7 @@ def export_mapping_results(): results_csv = open(file_path, "r").read() response = Response(results_csv, mimetype='text/csv', - headers={"Content-Disposition": "attachment;filename=mapping_results.csv"}) + headers={"Content-Disposition": "attachment;filename=" + os.path.basename(file_path)}) return response @@ -1389,7 +1388,7 @@ def get_sample_data_as_csv(trait_name: int, phenotype_id: int): @app.route("/admin/data-sample/diffs/") -@admin_login_required +@edit_access_required def display_diffs_admin(): TMPDIR = current_app.config.get("TMPDIR") DIFF_DIR = f"{TMPDIR}/sample-data/diffs" |